https://launchpad.net/ubuntu/+source/ncbi-tools6/6.1.20170106+dfsg1-10.1/+build/27858619 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-047 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 1 Mar 17:40:45 ntpdate[1838]: adjust time server 10.211.37.1 offset 0.001942 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27858619 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27858619 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27858619 Starting target for build PACKAGEBUILD-27858619 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27858619 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27858619 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27858619 Updating target for build PACKAGEBUILD-27858619 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1435 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.5 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6036 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [376 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [116 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [1599 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [573 kB] Fetched 26.7 MB in 3s (8685 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libnpth0* libreadline8* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libnpth0t64 libperl5.38 libreadline8t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: optipng The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 158 upgraded, 15 newly installed, 6 to remove and 1 not upgraded. Need to get 117 MB of archives. After this operation, 77.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl-dev amd64 1.3.0-3build2 [70.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu5 [2125 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu5 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [193 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libnss-nisplus amd64 1.3-0ubuntu7 [22.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu4 [1909 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl2 amd64 1.3.0-3build2 [41.3 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6 amd64 2.39-0ubuntu5 [3262 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-bin amd64 2.39-0ubuntu5 [682 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-14-base amd64 14-20240221-2.1ubuntu1 [46.9 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 14-20240221-2.1ubuntu1 [78.1 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu7 [74.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.16 [93.9 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu2 [794 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.3-6ubuntu2 [94.6 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-3ubuntu2 [1412 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5ubuntu1 [34.6 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5ubuntu1 [34.4 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma5 amd64 5.6.0-0.2 [157 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 14-20240221-2.1ubuntu1 [795 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1 [16.7 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha4-0ubuntu1 [49.0 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit-common all 1:3.1.2-2.1 [5674 B] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.4-2 [15.0 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit1 amd64 1:3.1.2-2.1 [46.8 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.3-6ubuntu2 [122 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkmod2 amd64 31+20240202-2ubuntu1 [51.3 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libselinux1 amd64 3.5-2build2 [79.2 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.3-6ubuntu2 [134 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3ubuntu1 [3110 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [734 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38 amd64 5.38.2-3ubuntu1 [4871 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3ubuntu1 [231 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3ubuntu1 [1822 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 liblocale-gettext-perl amd64 1.07-6build1 [15.5 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-iconv-perl amd64 1.7-8build1 [13.4 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-charwidth-perl amd64 0.04-11build1 [9266 B] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.4-1ubuntu2 [2067 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.4-1ubuntu2 [103 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.4-1ubuntu2 [11.9 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.4-1ubuntu2 [3470 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.4-1ubuntu2 [432 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.3-5ubuntu2 [51.9 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.3-5ubuntu2 [279 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.45.1-1 [701 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg amd64 2.4.4-2ubuntu9 [565 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libreadline8t64 amd64 8.2-3.1 [153 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 readline-common all 8.2-3.1 [56.4 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg-agent amd64 2.4.4-2ubuntu9 [227 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgconf amd64 2.4.4-2ubuntu9 [103 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libnpth0t64 amd64 1.6-3.1 [8316 B] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu9 [157 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.3-1ubuntu1 [996 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libseccomp2 amd64 2.5.5-1ubuntu1 [50.3 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.13 [217 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0t64 amd64 2.7.13 [984 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.13 [1374 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.3-5ubuntu2 [67.5 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.4-1ubuntu2 [174 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu1 [139 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.3-6ubuntu2 [34.5 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu1 [266 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.3-6ubuntu2 [146 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.3-6ubuntu2 [118 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.5ubuntu2 [1284 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu4 [89.8 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.3-6ubuntu2 [1127 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.3-6ubuntu2 [64.1 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.3-6ubuntu2 [33.0 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.3-5ubuntu2 [40.8 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage-common all 3.5-1build3 [10.1 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage2 amd64 3.5-1build3 [93.0 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-16ubuntu1 [14.5 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-16ubuntu1 [475 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-16ubuntu1 [1032 B] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [11.2 MB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240221-2.1ubuntu1 [47.9 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-3ubuntu1 [851 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-3ubuntu1 [94.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-3ubuntu1 [97.1 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-3ubuntu1 [14.9 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-3ubuntu1 [2469 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-3ubuntu1 [573 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-3ubuntu1 [18.0 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-3ubuntu1 [239 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-16ubuntu1 [2339 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240221-2.1ubuntu1 [147 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240221-2.1ubuntu1 [29.1 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240221-2.1ubuntu1 [10.4 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240221-2.1ubuntu1 [3025 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240221-2.1ubuntu1 [1309 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-16ubuntu1 [2687 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240221-2.1ubuntu1 [2732 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240221-2.1ubuntu1 [1172 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240221-2.1ubuntu1 [1629 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240221-2.1ubuntu1 [155 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [21.8 MB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-16ubuntu1 [12.5 MB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-16ubuntu1 [47.2 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu1 [59.2 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 procps amd64 2:4.0.4-4ubuntu1 [708 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu4 [1002 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.3-6ubuntu2 [73.7 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.43-1 [186 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 psmisc amd64 23.6-2 [178 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 xz-utils amd64 5.6.0-0.2 [272 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:164 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:165 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.5ubuntu2 [1061 kB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.5ubuntu2 [269 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Preconfiguring packages ... 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Installing new version of config file /etc/gprofng.rc ... Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... Setting up libctf-nobfd0:amd64 (2.42-3ubuntu1) ... Setting up krb5-locales (1.20.1-5build1) ... Setting up libgomp1:amd64 (14-20240221-2.1ubuntu1) ... Setting up bzip2 (1.0.8-5ubuntu1) ... Setting up libsframe1:amd64 (2.42-3ubuntu1) ... Setting up libfakeroot:amd64 (1.33-1) ... Setting up libkrb5support0:amd64 (1.20.1-5build1) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 1 17:41:10 UTC 2024. Universal Time is now: Fri Mar 1 17:41:10 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:amd64 (13.2.0-16ubuntu1) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.0-0.2) ... Setting up perl-modules-5.38 (5.38.2-3ubuntu1) ... Setting up libquadmath0:amd64 (14-20240221-2.1ubuntu1) ... Setting up libproc2-0:amd64 (2:4.0.4-4ubuntu1) ... Setting up libpng16-16:amd64 (1.6.43-1) ... Setting up libatomic1:amd64 (14-20240221-2.1ubuntu1) ... Setting up libncursesw6:amd64 (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:amd64 (1.20.1-5build1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... Setting up libubsan1:amd64 (14-20240221-2.1ubuntu1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-6ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libhwasan0:amd64 (14-20240221-2.1ubuntu1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up libasan8:amd64 (14-20240221-2.1ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-5build1) ... Setting up libtsan2:amd64 (14-20240221-2.1ubuntu1) ... Setting up libbinutils:amd64 (2.42-3ubuntu1) ... Setting up libc-dev-bin (2.39-0ubuntu5) ... Setting up openssl (3.0.10-1ubuntu4) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3.1) ... Setting up libcc1-0:amd64 (14-20240221-2.1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6build1) ... Setting up liblsan0:amd64 (14-20240221-2.1ubuntu1) ... Setting up libitm1:amd64 (14-20240221-2.1ubuntu1) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libctf0:amd64 (2.42-3ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu1) ... Setting up apt-utils (2.7.13) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-16ubuntu1) ... Setting up debconf-i18n (1.5.86) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up libgprofng0:amd64 (2.42-3ubuntu1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5build1) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libreadline8t64:amd64 (8.2-3.1) ... Setting up libgcc-13-dev:amd64 (13.2.0-16ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu9) ... Setting up libc6-dev:amd64 (2.39-0ubuntu5) ... Setting up gpg (2.4.4-2ubuntu9) ... Setting up libstdc++-13-dev:amd64 (13.2.0-16ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.42-3ubuntu1) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu9) ... Setting up cpp-13 (13.2.0-16ubuntu1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-16ubuntu1) ... Setting up libperl5.38:amd64 (5.38.2-3ubuntu1) ... Setting up binutils (2.42-3ubuntu1) ... Setting up perl (5.38.2-3ubuntu1) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Setting up gcc-13 (13.2.0-16ubuntu1) ... Setting up libdpkg-perl (1.22.5ubuntu2) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build2) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-16ubuntu1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-0ubuntu7) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up dpkg-dev (1.22.5ubuntu2) ... Setting up libnsl-dev:amd64 (1.3.0-3build2) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-16ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu5) ... Processing triggers for debianutils (5.16) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27858619 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27858619 --arch=amd64 --dist=noble-proposed --nolog -A ncbi-tools6_6.1.20170106+dfsg1-10.1.dsc Initiating build PACKAGEBUILD-27858619 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-047.buildd +==============================================================================+ | ncbi-tools6 6.1.20170106+dfsg1-10.1 (amd64) Fri, 01 Mar 2024 17:41:13 +0000 | +==============================================================================+ Package: ncbi-tools6 Version: 6.1.20170106+dfsg1-10.1 Source Version: 6.1.20170106+dfsg1-10.1 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27858619/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/ncbi-tools6-IZqHzI/resolver-k9AQFo' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ncbi-tools6_6.1.20170106+dfsg1-10.1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/ncbi-tools6-IZqHzI/ncbi-tools6-6.1.20170106+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/ncbi-tools6-IZqHzI' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), build-essential, fakeroot, dpkg-dev (>= 1.22.5), csh | c-shell, libglu1-mesa-dev | libglu-dev, libgnutls28-dev | gnutls-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev, icoutils, imagemagick Filtered Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), build-essential, fakeroot, dpkg-dev (>= 1.22.5), csh | c-shell, libglu1-mesa-dev | libglu-dev, libgnutls28-dev | gnutls-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev, icoutils, imagemagick dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [469 B] Get:5 copy:/<>/apt_archive ./ Packages [539 B] Fetched 1965 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev csh debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base hicolor-icon-theme icoutils imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libbsd0 libbz2-dev libclone-perl libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libelf1t64 libencode-locale-perl libevent-2.1-7 libexpat1 libexpat1-dev libfftw3-double3 libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libgl-dev libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl libgnutls-dane0 libgnutls-openssl27 libgnutls28-dev libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhogweed6t64 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice-dev libice6 libicu74 libidn2-dev libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblerc4 libllvm17 liblqr-1-0 libltdl7 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmagickcore-6.q16-7 libmagickwand-6.q16-7 libmotif-common libmotif-dev libmrm4 libnet-http-perl libnet-ssleay-perl libnettle8t64 libopengl-dev libopengl0 libopenjp2-7 libp11-kit-dev libpciaccess0 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpkgconf3 libpng-dev libpng16-16t64 libpthread-stubs0-dev libraw23t64 libsensors-config libsensors5 libsharpyuv0 libsm-dev libsm6 libsub-override-perl libtasn1-6-dev libtiff6 libtimedate-perl libtool libtry-tiny-perl libuchardet0 libuil4 libunbound8 liburi-perl libvulkan1 libwebp7 libwebpdemux2 libwebpmux3 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxft-dev libxft2 libxm4 libxml2 libxmu-dev libxmu-headers libxmu6 libxrender-dev libxrender1 libxshmfence1 libxt-dev libxt6t64 libxxf86vm1 m4 man-db netbase nettle-dev perl-openssl-defaults pkgconf pkgconf-bin po-debconf uil uuid-dev x11-common x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libterm-readline-gnu-perl | libterm-readline-perl-perl imagemagick-6-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils texlive-base-bin transfig libraw-bin xdg-utils libfftw3-bin libfftw3-dev freetype2-doc low-memory-monitor gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc libdata-dump-perl libio-compress-brotli-perl libice-doc liblcms2-utils libcrypt-ssleay-perl libmagickcore-6.q16-7-extra p11-kit-doc pciutils lm-sensors libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libmagickcore-6.q16-7-extra ghostscript netpbm bzip2-doc libarchive-cpio-perl libgl1-amber-dri libglib2.0-data shared-mime-info xdg-user-dirs libheif-plugin-aomenc libheif-plugin-x265 libhtml-format-perl fonts-urw-base35 libpng-tools libtasn1-doc libltdl-dev mesa-vulkan-drivers | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libmail-sendmail-perl The following packages will be REMOVED: libhogweed6* libnettle8* libpng16-16* The following NEW packages will be installed: autoconf automake autopoint autotools-dev csh debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base hicolor-icon-theme icoutils imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libbsd0 libbz2-dev libclone-perl libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libelf1t64 libencode-locale-perl libevent-2.1-7 libexpat1 libexpat1-dev libfftw3-double3 libfile-listing-perl libfile-stripnondeterminism-perl libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libgl-dev libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl libgnutls-dane0 libgnutls-openssl27 libgnutls28-dev libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhogweed6t64 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice-dev libice6 libicu74 libidn2-dev libio-html-perl libio-socket-ssl-perl libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblerc4 libllvm17 liblqr-1-0 libltdl7 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmagickcore-6.q16-7 libmagickwand-6.q16-7 libmotif-common libmotif-dev libmrm4 libnet-http-perl libnet-ssleay-perl libnettle8t64 libopengl-dev libopengl0 libopenjp2-7 libp11-kit-dev libpciaccess0 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpkgconf3 libpng-dev libpng16-16t64 libpthread-stubs0-dev libraw23t64 libsensors-config libsensors5 libsharpyuv0 libsm-dev libsm6 libsub-override-perl libtasn1-6-dev libtiff6 libtimedate-perl libtool libtry-tiny-perl libuchardet0 libuil4 libunbound8 liburi-perl libvulkan1 libwebp7 libwebpdemux2 libwebpmux3 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxft-dev libxft2 libxm4 libxml2 libxmu-dev libxmu-headers libxmu6 libxrender-dev libxrender1 libxshmfence1 libxt-dev libxt6t64 libxxf86vm1 m4 man-db netbase nettle-dev perl-openssl-defaults pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy uil uuid-dev x11-common x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 194 newly installed, 3 to remove and 1 not upgraded. Need to get 82.3 MB of archives. After this operation, 320 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [760 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnettle8t64 amd64 3.9.1-2.1 [181 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhogweed6t64 amd64 3.9.1-2.1 [198 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpng16-16t64 amd64 1.6.43-2 [186 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu1 [835 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libexpat1 amd64 2.6.0-1 [86.0 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libbrotli1 amd64 1.1.0-2 [332 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfreetype6 amd64 2.13.2+dfsg-1build1 [402 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsharpyuv0 amd64 1.3.2-0.4build1 [15.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble/universe amd64 libdav1d7 amd64 1.4.0-1 [605 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libheif-plugin-dav1d amd64 1.17.6-1ubuntu2 [10.0 kB] Get:16 http://ftpmaster.internal/ubuntu noble/universe amd64 libde265-0 amd64 1.0.15-1 [192 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libheif-plugin-libde265 amd64 1.17.6-1ubuntu2 [8172 B] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libheif1 amd64 1.17.6-1ubuntu2 [276 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 liblcms2-2 amd64 2.14-2 [161 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libglib2.0-0 amd64 2.79.2-1~ubuntu1 [1537 kB] Get:24 http://ftpmaster.internal/ubuntu noble/universe amd64 liblqr-1-0 amd64 0.4.2-2.1 [27.7 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libltdl7 amd64 2.4.7-7 [40.5 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libopenjp2-7 amd64 2.5.0-2build1 [173 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libraw23t64 amd64 0.21.2-2.1 [378 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libwebp7 amd64 1.3.2-0.4build1 [230 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu1 [199 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libwebpdemux2 amd64 1.3.2-0.4build1 [12.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libwebpmux3 amd64 1.3.2-0.4build1 [25.7 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbsd0 amd64 0.12.1-1 [41.2 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-data all 2:1.8.7-1 [115 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-6 amd64 2:1.8.7-1 [642 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libicu74 amd64 74.2-1ubuntu1 [10.9 MB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu1 [762 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 imagemagick-6-common all 8:6.9.12.98+dfsg1-5build1 [69.3 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libmagickcore-6.q16-7 amd64 8:6.9.12.98+dfsg1-5build1 [1811 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libmagickwand-6.q16-7 amd64 8:6.9.12.98+dfsg1-5build1 [318 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libmotif-common all 2.3.8-3build1 [10.1 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [171 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libxmu6 amd64 2:1.1.3-3 [49.6 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libxm4 amd64 2.3.8-3build1 [1091 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libmrm4 amd64 2.3.8-3build1 [61.2 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libuil4 amd64 2.3.8-3build1 [148 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 netbase all 6.4 [13.1 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic-mgc amd64 1:5.45-2 [307 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic1 amd64 1:5.45-2 [86.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 file amd64 1:5.45-2 [21.9 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14ubuntu1 [38.3 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1 [75.3 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 groff-base amd64 1.23.0-3 [1023 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-common all 2.4.120-2 [7998 B] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm2 amd64 2.4.120-2 [40.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libedit2 amd64 3.1-20230828-1 [95.8 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 man-db amd64 2.12.0-3 [1230 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14ubuntu1 [422 kB] Get:74 http://ftpmaster.internal/ubuntu noble/universe amd64 csh amd64 20230828-1 [244 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libelf1t64 amd64 0.190-1.1 [57.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdw1t64 amd64 0.190-1.1 [261 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dwz amd64 0.15-1build5 [115 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14ubuntu1 [864 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 hicolor-icon-theme all 0.17-2 [9976 B] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-tagset-perl all 3.20-6 [11.3 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 liburi-perl all 5.27-1 [88.0 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-parser-perl amd64 3.81-1build1 [85.7 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-tree-perl all 5.07-3 [200 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libclone-perl amd64 0.46-1build1 [10.6 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libio-html-perl all 1.004-3 [15.9 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-message-perl all 6.45-1ubuntu1 [78.2 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 perl-openssl-defaults amd64 7 [7536 B] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libnet-ssleay-perl amd64 1.94-1 [316 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libio-socket-ssl-perl all 2.085-1 [195 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libnet-http-perl all 6.23-1 [22.3 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 liblwp-protocol-https-perl all 6.13-1 [9006 B] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libtry-tiny-perl all 0.31-2 [20.8 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libwww-perl all 6.76-1 [138 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 icoutils amd64 0.32.3-4build1 [55.8 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 imagemagick-6.q16 amd64 8:6.9.12.98+dfsg1-5build1 [254 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 imagemagick amd64 8:6.9.12.98+dfsg1-5build1 [14.2 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 libbrotli-dev amd64 1.1.0-2 [355 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [20.4 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 libpciaccess0 amd64 0.17-3 [18.9 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-intel1 amd64 2.4.120-2 [63.8 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [17.6 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 libdrm-radeon1 amd64 2.4.120-2 [20.7 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 libevent-2.1-7 amd64 2.1.12-stable-9 [144 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libexpat1-dev amd64 2.6.0-1 [139 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpng-dev amd64 1.6.43-2 [264 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfreetype-dev amd64 2.13.2+dfsg-1build1 [575 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-dev amd64 2.39.3-6ubuntu2 [33.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig-dev amd64 2.15.0-1ubuntu1 [161 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1-dev amd64 2.15.0-1ubuntu1 [1826 B] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 libglvnd0 amd64 1.7.0-1 [69.5 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libglapi-mesa amd64 24.0.2-1ubuntu1 [40.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [7798 B] Get:137 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-dri2-0 amd64 1.15-1 [7276 B] Get:138 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-dri3-0 amd64 1.15-1 [7174 B] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-glx0 amd64 1.15-1 [24.6 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-present0 amd64 1.15-1 [5708 B] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-randr0 amd64 1.15-1 [18.1 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-sync1 amd64 1.15-1 [9358 B] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-xfixes0 amd64 1.15-1 [10.2 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 libxfixes3 amd64 1:6.0.0-2 [10.9 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 libxshmfence1 amd64 1.3-1build4 [5394 B] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 libxxf86vm1 amd64 1:1.1.4-1build3 [10.4 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 libvulkan1 amd64 1.3.275.0-1 [142 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 libllvm17 amd64 1:17.0.6-5build1 [26.2 MB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 libsensors-config all 1:3.6.0-9 [5458 B] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 libsensors5 amd64 1:3.6.0-9 [26.5 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgl1-mesa-dri amd64 24.0.2-1ubuntu1 [8937 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libglx-mesa0 amd64 24.0.2-1ubuntu1 [154 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 libglx0 amd64 1.7.0-1 [38.7 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 libgl1 amd64 1.7.0-1 [103 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 x11proto-dev all 2023.2-1 [602 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 libxau-dev amd64 1:1.0.9-1build5 [9724 B] Get:159 http://ftpmaster.internal/ubuntu noble/main amd64 libxdmcp-dev amd64 1:1.1.3-0ubuntu5 [26.5 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 libpthread-stubs0-dev amd64 0.4-1build2 [5516 B] Get:162 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb1-dev amd64 1.15-1 [85.8 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-dev amd64 2:1.8.7-1 [731 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main amd64 libglx-dev amd64 1.7.0-1 [14.2 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main amd64 libgl-dev amd64 1.7.0-1 [102 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 libopengl0 amd64 1.7.0-1 [33.0 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 libglu1-mesa amd64 9.0.2-1.1 [151 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 libopengl-dev amd64 1.7.0-1 [3440 B] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1 [237 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu4 [9956 B] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu4 [342 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls-openssl27 amd64 3.8.3-1ubuntu1 [23.6 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main amd64 libunbound8 amd64 1.19.1-1ubuntu1 [440 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls-dane0 amd64 3.8.3-1ubuntu1 [23.3 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-dev amd64 2.3.7-2 [121 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit-dev amd64 0.25.3-4ubuntu1 [22.6 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main amd64 libtasn1-6-dev amd64 4.19.0-3 [90.6 kB] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 nettle-dev amd64 3.9.1-2.1 [1154 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls28-dev amd64 3.8.3-1ubuntu1 [1054 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main amd64 libice-dev amd64 2:1.0.10-1build2 [51.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble/universe amd64 libpcre16-3 amd64 2:8.39-15 [166 kB] Get:182 http://ftpmaster.internal/ubuntu noble/universe amd64 libpcre3 amd64 2:8.39-15 [250 kB] Get:183 http://ftpmaster.internal/ubuntu noble/universe amd64 libpcre32-3 amd64 2:8.39-15 [156 kB] Get:184 http://ftpmaster.internal/ubuntu noble/universe amd64 libpcrecpp0v5 amd64 2:8.39-15 [16.3 kB] Get:185 http://ftpmaster.internal/ubuntu noble/universe amd64 libpcre3-dev amd64 2:8.39-15 [583 kB] Get:186 http://ftpmaster.internal/ubuntu noble/main amd64 libsm-dev amd64 2:1.2.3-1build2 [18.1 kB] Get:187 http://ftpmaster.internal/ubuntu noble/main amd64 libxext-dev amd64 2:1.3.4-1build1 [84.7 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender-dev amd64 1:0.9.10-1.1 [26.5 kB] Get:189 http://ftpmaster.internal/ubuntu noble/main amd64 libxft-dev amd64 2.3.6-1 [64.5 kB] Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxt-dev amd64 1:1.2.1-1.2 [394 kB] Get:191 http://ftpmaster.internal/ubuntu noble/main amd64 libxmu-headers all 2:1.1.3-3 [54.1 kB] Get:192 http://ftpmaster.internal/ubuntu noble/main amd64 libxmu-dev amd64 2:1.1.3-3 [54.6 kB] Get:193 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 uil amd64 2.3.8-3build1 [7504 B] Get:194 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libmotif-dev amd64 2.3.8-3build1 [2596 kB] Preconfiguring packages ... Fetched 82.3 MB in 4s (18.9 MB/s) dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.9~). (Reading database ... 15750 files and directories currently installed.) Removing libnettle8:amd64 (3.9.1-2) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... 15743 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.1) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (Reading database ... 15751 files and directories currently installed.) Removing libhogweed6:amd64 (3.9.1-2) ... Selecting previously unselected package libhogweed6t64:amd64. (Reading database ... 15746 files and directories currently installed.) 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Setting up libpthread-stubs0-dev:amd64 (0.4-1build2) ... Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... Setting up libopengl0:amd64 (1.7.0-1) ... Setting up libelf1t64:amd64 (0.190-1.1) ... Setting up libdw1t64:amd64 (0.190-1.1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-2) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu4) ... Setting up libexpat1-dev:amd64 (2.6.0-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up uuid-dev:amd64 (2.39.3-6ubuntu2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-2) ... Setting up libpcre32-3:amd64 (2:8.39-15) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-9) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Setting up libltdl7:amd64 (2.4.7-7) ... Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu1) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up libglapi-mesa:amd64 (24.0.2-1ubuntu1) ... Setting up libvulkan1:amd64 (1.3.275.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4build1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libicu74:amd64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... Setting up dwz (0.15-1build5) ... Setting up libdav1d7:amd64 (1.4.0-1) ... Setting up liblqr-1-0:amd64 (0.4.2-2.1) ... Setting up libxshmfence1:amd64 (1.3-1build4) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up debugedit (1:5.0-5) ... Setting up libopenjp2-7:amd64 (2.5.0-2build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1) ... Setting up libopengl-dev:amd64 (1.7.0-1) ... Setting up libde265-0:amd64 (1.0.15-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3) ... Setting up libwebpmux3:amd64 (1.3.2-0.4build1) ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu1) ... Setting up liburi-perl (5.27-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2) ... Setting up libp11-kit-dev:amd64 (0.25.3-4ubuntu1) ... Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2023.2-1) ... Setting up libpcrecpp0v5:amd64 (2:8.39-15) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1build2) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu4) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libxau-dev:amd64 (1:1.0.9-1build5) ... Setting up csh (20230828-1) ... update-alternatives: using /bin/bsd-csh to provide /bin/csh (csh) in auto mode Setting up nettle-dev:amd64 (3.9.1-2.1) ... Setting up libice-dev:amd64 (2:1.0.10-1build2) ... Setting up libtool (2.4.7-7) ... Setting up libpcre3-dev:amd64 (2:8.39-15) ... Setting up fontconfig-config (2.15.0-1ubuntu1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.4build1) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libpng-dev:amd64 (1.6.43-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up pkgconf:amd64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.3-0ubuntu5) ... Setting up libunbound8:amd64 (1.19.1-1ubuntu1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1build1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libraw23t64:amd64 (0.21.2-2.1) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up groff-base (1.23.0-3) ... Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu1) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1build1) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... Setting up libllvm17:amd64 (1:17.0.6-5build1) ... Setting up libsm6:amd64 (2:1.2.3-1build2) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhttp-message-perl (6.45-1ubuntu1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libgnutls-dane0:amd64 (3.8.3-1ubuntu1) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libsm-dev:amd64 (2:1.2.3-1build2) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.2-1ubuntu1) ... Setting up libx11-dev:amd64 (2:1.8.7-1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libxxf86vm1:amd64 (1:1.1.4-1build3) ... Setting up libfreetype-dev:amd64 (2.13.2+dfsg-1build1) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxext-dev:amd64 (2:1.3.4-1build1) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1) ... Setting up libgnutls28-dev:amd64 (3.8.3-1ubuntu1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up libglx-mesa0:amd64 (24.0.2-1ubuntu1) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up libfontconfig-dev:amd64 (2.15.0-1ubuntu1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2) ... Setting up libglx-dev:amd64 (1.7.0-1) ... Setting up libgl-dev:amd64 (1.7.0-1) ... Setting up libxm4:amd64 (2.3.8-3build1) ... Setting up libxft-dev:amd64 (2.3.6-1) ... Setting up libfontconfig1-dev:amd64 (2.15.0-1ubuntu1) ... Setting up libxmu-dev:amd64 (2:1.1.3-3) ... Setting up libmrm4:amd64 (2.3.8-3build1) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1) ... Setting up libuil4:amd64 (2.3.8-3build1) ... Setting up uil (2.3.8-3build1) ... Setting up libmotif-dev:amd64 (2.3.8-3build1) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1ubuntu2) ... Setting up liblwp-protocol-https-perl (6.13-1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1ubuntu2) ... Setting up libwww-perl (6.76-1) ... Setting up libheif1:amd64 (1.17.6-1ubuntu2) ... Setting up libmagickcore-6.q16-7:amd64 (8:6.9.12.98+dfsg1-5build1) ... Setting up icoutils (0.32.3-4build1) ... Setting up libmagickwand-6.q16-7:amd64 (8:6.9.12.98+dfsg1-5build1) ... Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5build1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up imagemagick (8:6.9.12.98+dfsg1-5build1) ... Processing triggers for libc-bin (2.39-0ubuntu5) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-3ubuntu1 dpkg-dev_1.22.5ubuntu2 g++-13_13.2.0-16ubuntu1 gcc-13_13.2.0-16ubuntu1 libc6-dev_2.39-0ubuntu5 libstdc++-13-dev_13.2.0-16ubuntu1 libstdc++6_14-20240221-2.1ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.13 apt-utils_2.7.13 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu7 base-passwd_3.6.3 bash_5.2.21-2ubuntu2 bash-completion_1:2.11-8 binutils_2.42-3ubuntu1 binutils-common_2.42-3ubuntu1 binutils-x86-64-linux-gnu_2.42-3ubuntu1 bsdextrautils_2.39.3-6ubuntu2 bsdutils_1:2.39.3-6ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5ubuntu1 ca-certificates_20240203 coreutils_9.4-3ubuntu2 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-16ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-16ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 csh_20230828-1 dash_0.5.12-6ubuntu4 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.5ubuntu2 dpkg-dev_1.22.5ubuntu2 dwz_0.15-1build5 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 fontconfig-config_2.15.0-1ubuntu1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-16ubuntu1 g++-13-x86-64-linux-gnu_13.2.0-16ubuntu1 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-16ubuntu1 gcc-13-base_13.2.0-16ubuntu1 gcc-13-x86-64-linux-gnu_13.2.0-16ubuntu1 gcc-14-base_14-20240221-2.1ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu9 gpg-agent_2.4.4-2ubuntu9 gpgconf_2.4.4-2ubuntu9 gpgv_2.4.4-2ubuntu9 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu2 hicolor-icon-theme_0.17-2 hostname_3.23+nmu2ubuntu1 icoutils_0.32.3-4build1 imagemagick_8:6.9.12.98+dfsg1-5build1 imagemagick-6-common_8:6.9.12.98+dfsg1-5build1 imagemagick-6.q16_8:6.9.12.98+dfsg1-5build1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.2-1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0t64_2.7.13 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240221-2.1ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240221-2.1ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-3ubuntu1 libblkid1_2.39.3-6ubuntu2 libbrotli-dev_1.1.0-2 libbrotli1_1.1.0-2 libbsd0_0.12.1-1 libbz2-1.0_1.0.8-5ubuntu1 libbz2-dev_1.0.8-5ubuntu1 libc-bin_2.39-0ubuntu5 libc-dev-bin_2.39-0ubuntu5 libc6_2.39-0ubuntu5 libc6-dev_2.39-0ubuntu5 libcap-ng0_0.8.4-2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240221-2.1ubuntu1 libclone-perl_0.46-1build1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu1 libctf-nobfd0_2.42-3ubuntu1 libctf0_2.42-3ubuntu1 libdav1d7_1.4.0-1 libdb5.3t64_5.3.28+dfsg2-5 libde265-0_1.0.15-1 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-3ubuntu1 libdpkg-perl_1.22.5ubuntu2 libdrm-amdgpu1_2.4.120-2 libdrm-common_2.4.120-2 libdrm-intel1_2.4.120-2 libdrm-nouveau2_2.4.120-2 libdrm-radeon1_2.4.120-2 libdrm2_2.4.120-2 libdw1t64_0.190-1.1 libedit2_3.1-20230828-1 libelf1t64_0.190-1.1 libencode-locale-perl_1.05-3 libevent-2.1-7_2.1.12-stable-9 libexpat1_2.6.0-1 libexpat1-dev_2.6.0-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.3-6ubuntu2 libffi8_3.4.6-1 libfftw3-double3_3.3.10-1ubuntu1 libfile-listing-perl_6.16-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig-dev_2.15.0-1ubuntu1 libfontconfig1_2.15.0-1ubuntu1 libfontconfig1-dev_2.15.0-1ubuntu1 libfreetype-dev_2.13.2+dfsg-1build1 libfreetype6_2.13.2+dfsg-1build1 libgcc-13-dev_13.2.0-16ubuntu1 libgcc-s1_14-20240221-2.1ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgl-dev_1.7.0-1 libgl1_1.7.0-1 libgl1-mesa-dri_24.0.2-1ubuntu1 libglapi-mesa_24.0.2-1ubuntu1 libglib2.0-0_2.79.2-1~ubuntu1 libglu1-mesa_9.0.2-1.1 libglu1-mesa-dev_9.0.2-1.1 libglvnd0_1.7.0-1 libglx-dev_1.7.0-1 libglx-mesa0_24.0.2-1ubuntu1 libglx0_1.7.0-1 libgmp-dev_2:6.3.0+dfsg-2ubuntu4 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgmpxx4ldbl_2:6.3.0+dfsg-2ubuntu4 libgnutls-dane0_3.8.3-1ubuntu1 libgnutls-openssl27_3.8.3-1ubuntu1 libgnutls28-dev_3.8.3-1ubuntu1 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240221-2.1ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgprofng0_2.42-3ubuntu1 libgssapi-krb5-2_1.20.1-5build1 libheif-plugin-dav1d_1.17.6-1ubuntu2 libheif-plugin-libde265_1.17.6-1ubuntu2 libheif1_1.17.6-1ubuntu2 libhogweed6t64_3.9.1-2.1 libhtml-parser-perl_3.81-1build1 libhtml-tagset-perl_3.20-6 libhtml-tree-perl_5.07-3 libhttp-cookies-perl_6.11-1 libhttp-date-perl_6.06-1 libhttp-message-perl_6.45-1ubuntu1 libhttp-negotiate-perl_6.01-2 libhwasan0_14-20240221-2.1ubuntu1 libice-dev_2:1.0.10-1build2 libice6_2:1.0.10-1build2 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libio-html-perl_1.004-3 libio-socket-ssl-perl_2.085-1 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libitm1_14-20240221-2.1ubuntu1 libjansson4_2.14-2 libjbig0_2.1-6.1ubuntu1 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjson-c5_0.17-1 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-3 libkmod2_31+20240202-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 liblcms2-2_2.14-2 liblerc4_4.0.0+ds-4ubuntu1 libllvm17_1:17.0.6-5build1 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblqr-1-0_0.4.2-2.1 liblsan0_14-20240221-2.1ubuntu1 libltdl7_2.4.7-7 liblwp-mediatypes-perl_6.04-2 liblwp-protocol-https-perl_6.13-1 liblz4-1_1.9.4-1 liblzma5_5.6.0-0.2 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmagickcore-6.q16-7_8:6.9.12.98+dfsg1-5build1 libmagickwand-6.q16-7_8:6.9.12.98+dfsg1-5build1 libmd0_1.1.0-2 libmotif-common_2.3.8-3build1 libmotif-dev_2.3.8-3build1 libmount1_2.39.3-6ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmrm4_2.3.8-3build1 libncursesw6_6.4+20240113-1ubuntu1 libnet-http-perl_6.23-1 libnet-ssleay-perl_1.94-1 libnettle8t64_3.9.1-2.1 libnpth0t64_1.6-3.1 libnsl-dev_1.3.0-3build2 libnsl2_1.3.0-3build2 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu7 libopengl-dev_1.7.0-1 libopengl0_1.7.0-1 libopenjp2-7_2.5.0-2build1 libp11-kit-dev_0.25.3-4ubuntu1 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.3-5ubuntu2 libpam-modules-bin_1.5.3-5ubuntu2 libpam-runtime_1.5.3-5ubuntu2 libpam0g_1.5.3-5ubuntu2 libpciaccess0_0.17-3 libpcre16-3_2:8.39-15 libpcre2-8-0_10.42-4ubuntu1 libpcre3_2:8.39-15 libpcre3-dev_2:8.39-15 libpcre32-3_2:8.39-15 libpcrecpp0v5_2:8.39-15 libperl5.36_5.36.0-9ubuntu1 libperl5.38_5.38.2-3ubuntu1 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng-dev_1.6.43-2 libpng16-16t64_1.6.43-2 libproc2-0_2:4.0.4-4ubuntu1 libpthread-stubs0-dev_0.4-1build2 libquadmath0_14-20240221-2.1ubuntu1 libraw23t64_0.21.2-2.1 libreadline8t64_8.2-3.1 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build2 libsemanage-common_3.5-1build3 libsemanage2_3.5-1build3 libsensors-config_1:3.6.0-9 libsensors5_1:3.6.0-9 libsepol2_3.5-2 libsframe1_2.42-3ubuntu1 libsharpyuv0_1.3.2-0.4build1 libsm-dev_2:1.2.3-1build2 libsm6_2:1.2.3-1build2 libsmartcols1_2.39.3-6ubuntu2 libsqlite3-0_3.45.1-1 libss2_1.47.0-2ubuntu1 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-16ubuntu1 libstdc++6_14-20240221-2.1ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu2 libsystemd0_255.4-1ubuntu2 libtasn1-6_4.19.0-3 libtasn1-6-dev_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtiff6_4.5.1+git230720-4ubuntu1 libtimedate-perl_2.3300-2 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1.1 libtirpc-dev_1.3.4+ds-1.1 libtirpc3t64_1.3.4+ds-1.1 libtool_2.4.7-7 libtry-tiny-perl_0.31-2 libtsan2_14-20240221-2.1ubuntu1 libubsan1_14-20240221-2.1ubuntu1 libuchardet0_0.0.8-1 libudev1_255.4-1ubuntu2 libuil4_2.3.8-3build1 libunbound8_1.19.1-1ubuntu1 libunistring2_1.0-2 libunistring5_1.1-2 liburi-perl_5.27-1 libuuid1_2.39.3-6ubuntu2 libvulkan1_1.3.275.0-1 libwebp7_1.3.2-0.4build1 libwebpdemux2_1.3.2-0.4build1 libwebpmux3_1.3.2-0.4build1 libwww-perl_6.76-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libx11-dev_2:1.8.7-1 libx11-xcb1_2:1.8.7-1 libxau-dev_1:1.0.9-1build5 libxau6_1:1.0.9-1build5 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-randr0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 libxdmcp-dev_1:1.1.3-0ubuntu5 libxdmcp6_1:1.1.3-0ubuntu5 libxext-dev_2:1.3.4-1build1 libxext6_2:1.3.4-1build1 libxfixes3_1:6.0.0-2 libxft-dev_2.3.6-1 libxft2_2.3.6-1 libxm4_2.3.8-3build1 libxml2_2.9.14+dfsg-1.3ubuntu1 libxmu-dev_2:1.1.3-3 libxmu-headers_2:1.1.3-3 libxmu6_2:1.1.3-3 libxrender-dev_1:0.9.10-1.1 libxrender1_1:0.9.10-1.1 libxshmfence1_1.3-1build4 libxt-dev_1:1.2.1-1.2 libxt6t64_1:1.2.1-1.2 libxxf86vm1_1:1.1.4-1build3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-11.11 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 mount_2.39.3-6ubuntu2 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 netbase_6.4 nettle-dev_3.9.1-2.1 openssl_3.0.10-1ubuntu4 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3ubuntu1 perl-base_5.38.2-3ubuntu1 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3ubuntu1 perl-openssl-defaults_7 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu1 psmisc_23.6-2 readline-common_8.2-3.1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.4-1ubuntu2 systemd-dev_255.4-1ubuntu2 systemd-sysv_255.4-1ubuntu2 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 uil_2.3.8-3build1 util-linux_2.39.3-6ubuntu2 uuid-dev_2.39.3-6ubuntu2 uuid-runtime_2.39.3-6ubuntu2 x11-common_1:7.7+23ubuntu2 x11proto-dev_2023.2-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.6.0-0.2 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ncbi-tools6 Binary: libncbi6t64, libncbi6-dev, ncbi-data, ncbi-rrna-data, ncbi-tools-bin, ncbi-tools-x11, ncbi-cn3d, libvibrant6t64, libvibrant6-dev Architecture: any all Version: 6.1.20170106+dfsg1-10.1 Maintainer: Debian Med Packaging Team Uploaders: Aaron M. Ucko Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6 Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git Testsuite: autopkgtest Testsuite-Triggers: netcat Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13) Build-Depends-Arch: dpkg-dev (>= 1.22.5), csh | c-shell, libglu1-mesa-dev | libglu-dev, libgnutls28-dev | gnutls-dev, libmotif-dev, libpcre3-dev, libpng-dev, libxmu-dev Build-Depends-Indep: icoutils, imagemagick Package-List: libncbi6-dev deb libdevel optional arch=any libncbi6t64 deb libs optional arch=any libvibrant6-dev deb libdevel optional arch=any libvibrant6t64 deb libs optional arch=any ncbi-cn3d deb science optional arch=any ncbi-data deb libs optional arch=all ncbi-rrna-data deb science optional arch=all ncbi-tools-bin deb science optional arch=any ncbi-tools-x11 deb science optional arch=any Checksums-Sha1: cb0fbd5bab413805b9661f36b5d275c94e51560e 58331860 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ncbi-tools6_6.1.20170106+dfsg1-10.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-changes Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27858619 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27858619 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27858619 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package ncbi-tools6 dpkg-buildpackage: info: source version 6.1.20170106+dfsg1-10.1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from ncbi-tools6-6.1.20170106+dfsg1/debian/source/options: --single-debian-patch debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf build/* bin/* include/* lib/* shlib mkdir -p build bin include lib rm -f debian/*.menu debian/asntool.xpm debian/ncbilogo.xpm chmod -x debian/makemenu debian/installman make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary debian/rules build make[1]: Entering directory '/<>' dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build-arch make[2]: Entering directory '/<>' cd build && ln -s ../make/*.unx . ln -s ../make/ln-if-absent build mv build/makeall.unx build/makefile /usr/bin/make -C build all LCL=lnx CC="x86_64-linux-gnu-gcc" LDFLAGS1="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS NCBI_LINKINGLIBDIR="../shlib" \ CFLAGS1="-c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG" \ LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ LIB30=libncbicn3d.a LIB45=libddvlib.a LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a make[3]: Entering directory '/<>/build' chmod -R ug+rw,o+r . ../include ./ln-if-absent ../corelib/tsprintf.h ../include ./ln-if-absent ../corelib/gifgen.h ../include ./ln-if-absent ../corelib/ncbi*.h ../include ./ln-if-absent ../corelib/tree*.h ../include ./ln-if-absent ../corelib/regex.h ../include ./ln-if-absent ../corelib/matrix.h ../include ./ln-if-absent ../corelib/binary.h ../include ./ln-if-absent ../corelib/morefile/*.h ../include ./ln-if-absent ../corelib/morefile/*.c . ./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include ./ln-if-absent ../corelib/ncbilcl.lnx ../include/ncbilcl.h ./ln-if-absent ../corelib/*.c . ./ln-if-absent ../corelib/core*.h . ./ln-if-absent ../asnlib/*.h . rm -f ../include/asn.h mv asn.h ../include ./ln-if-absent ../asnlib/*.c . ./ln-if-absent ../connect/*.c . ./ln-if-absent ../connect/ncbi_ansi_ext.h . ./ln-if-absent ../connect/ncbi_assert.h . ./ln-if-absent ../connect/ncbi_priv.h . ./ln-if-absent ../connect/ncbi_comm.h . ./ln-if-absent ../connect/ncbi_config.h . ./ln-if-absent ../connect/ncbi_connssl.h . ./ln-if-absent ../connect/ncbi_lbos.h . ./ln-if-absent ../connect/ncbi_lbosp.h . ./ln-if-absent ../connect/parson.h . ./ln-if-absent ../connect/ncbi_lbsm.h . make[3]: [makefile:714: copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_lbsm_ipc.h . make[3]: [makefile:715: copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_host_infop.h . ./ln-if-absent ../connect/ncbi_server_infop.h . ./ln-if-absent ../connect/ncbi_servicep.h . ./ln-if-absent ../connect/ncbi_socketp.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/ncbi_local.h . ./ln-if-absent ../connect/ncbi_lb.h . ./ln-if-absent ../connect/ncbi_version.h . ./ln-if-absent ../connect/ncbi_base64.h . ./ln-if-absent ../connect/urlquery.h ../include mkdir ../include/connect chmod ug+rw,o+r ../include/connect cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect ./ln-if-absent ../util/tables/*.c . mkdir -p ../include/util/tables cp -fp ../util/tables/*.h ../include/util/tables ./ln-if-absent ../util/creaders/*.c . mkdir -p ../include/util/creaders cp -fp ../util/creaders/*.h ../include/util/creaders ./ln-if-absent ../ctools/*.c . ./ln-if-absent ../ctools/*.h . mkdir ../include/ctools chmod ug+rw,o+r ../include/ctools cp -fp ../ctools/*.h ../include/ctools ./ln-if-absent ../object/*.c . ./ln-if-absent ../object/*.h ../include ./ln-if-absent ../access/*.c . ./ln-if-absent ../access/*.h ../include ./ln-if-absent ../asnstat/*.h ../include ./ln-if-absent ../api/*.h ../include ./ln-if-absent ../api/*.c . ./ln-if-absent ../api/*.inc . ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../cdromlib/*.c . ./ln-if-absent ../vibrant/*.h ../include ./ln-if-absent ../vibrant/*.c . ./ln-if-absent ../desktop/*.h ../include ./ln-if-absent ../desktop/*.c . ./ln-if-absent ../biostruc/*.h ../include ./ln-if-absent ../biostruc/*.c . ./ln-if-absent ../biostruc/cdd/*.h ../include ./ln-if-absent ../biostruc/cdd/*.c . ./ln-if-absent ../biostruc/cn3d/*.h ../include ./ln-if-absent ../biostruc/cn3d/*.c . ./ln-if-absent ../tools/*.h ../include ./ln-if-absent ../tools/*.c . ./ln-if-absent ../cn3d/*.h ../include ./ln-if-absent ../cn3d/*.c . ./ln-if-absent ../gif/*.c . ./ln-if-absent ../gif/*.h ../include ./ln-if-absent ../ddv/*.h ../include ./ln-if-absent ../ddv/*.c . ./ln-if-absent ../regexp/*.c . ./ln-if-absent ../regexp/*.h ../include ./ln-if-absent ../internal/compr/*.c . set: No match. make[3]: [makefile:771: copy] Error 1 (ignored) ./ln-if-absent ../internal/compr/*.h ../include set: No match. make[3]: [makefile:772: copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.c . set: No match. make[3]: [makefile:773: copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.h ../include set: No match. make[3]: [makefile:774: copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.c . set: No match. make[3]: [makefile:775: copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.h ../include set: No match. make[3]: [makefile:776: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.c . set: No match. make[3]: [makefile:777: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.dat . set: No match. make[3]: [makefile:778: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideochr*.h ../include set: No match. make[3]: [makefile:779: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideoorgs.h . make[3]: [makefile:780: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.c . set: No match. make[3]: [makefile:781: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.dat . set: No match. make[3]: [makefile:782: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.h ../include set: No match. make[3]: [makefile:783: copy] Error 1 (ignored) ./ln-if-absent ncbidraw.c ncbidrwg.c ./ln-if-absent ncbithr.c ncbithrs.c ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id2arch/*.h ../include mkdir -p ../include/algo/blast/core ./ln-if-absent ../algo/blast/core/*.c . ./ln-if-absent ../algo/blast/core/*.h . ./ln-if-absent ../algo/blast/core/*.inl . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/composition_adjustment ./ln-if-absent ../algo/blast/composition_adjustment/*.c . cp -fp ../algo/blast/composition_adjustment/*.h \ ../include/algo/blast/composition_adjustment mkdir -p ../include/algo/blast/api ./ln-if-absent ../algo/blast/api/*.c . cp -fp ../algo/blast/api/*.h ../include/algo/blast/api chmod -R ug+rw,o+r . echo Waiting...go Waiting...go x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ncbithr.c:289: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbithr.c: In function ‘s_TlsDestroyAll’: ncbithr.c:2529:11: warning: variable ‘err_code’ set but not used [-Wunused-but-set-variable] 2529 | int err_code = 0; | ^~~~~~~~ cp -p ncbithr.o ../lib x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimain.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimain.c:82:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 82 | main(int argc, char *argv[]) | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbibs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbibs.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbibs.c: In function ‘Nlm_BSSeek’: ncbibs.c:448:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 448 | if (sp == bsp->seekptr) /* already in right position */ | ^~ ncbibs.c:451:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 451 | bsp->seekptr = sp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF wwwutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbiwww.h:106, from wwwutils.c:150: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbierr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbierr.c:235: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbierr.c: In function ‘Nlm_ErrGetLogfile’: ncbierr.c:1380:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘logfile’ will never be NULL [-Waddress] 1380 | if (info->logfile != NULL && *info->logfile == '\0') | ^~ ncbierr.c:253:15: note: ‘logfile’ declared here 253 | char logfile[PATH_MAX]; | ^~~~~~~ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘ErrMsgRoot_fopen’ at ncbierr.c:955:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 4096 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbienv.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbienv.c:310: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:62: ncbienv.c: In function ‘Nlm_WorkGetAppParam’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen ncbienv.c: In function ‘Nlm_TransientLookup.constprop.0’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbifile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbifile.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbiprop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbiprop.c:104: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimath.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbimath.h:69, from ncbimath.c:90: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimath.c: In function ‘general_lngamma’: ncbimath.c:230:12: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 230 | ++y[0]; | ~^~~ ncbimath.c:207:25: note: ‘y’ declared here 207 | Nlm_FloatHi y[POLYGAMMA_ORDER_MAX+1]; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimem.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimem.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimisc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimisc.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimisc.c: In function ‘Nlm_MD5Final’: ncbimisc.c:2250:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] 2250 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ | ^ ncbimisc.c: In function ‘XmlPathSuffixIs’: ncbimisc.c:2966:58: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2966 | if (StringHasNoText (parentFilter) || parent != NULL && StringICmp (parent->name, parentFilter) == 0) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbimsg.c:167: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbistr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbistr.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisgml.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbisgml.c:83: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisgml.c: In function ‘Nlm_Sgml2Ascii’: ncbisgml.c:292:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 292 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ ncbisgml.c:273:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 273 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ncbisgml.c:273:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ncbisgml.c:292:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ ncbisgml.c: In function ‘Nlm_Sgml2AsciiLen’: ncbisgml.c:362:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 362 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ ncbisgml.c:348:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 348 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ncbisgml.c:348:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ncbisgml.c:362:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbitime.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbitime.c:77: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbilang.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbilang.c:57: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnbufo.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asnbufo.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asndebin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asndebin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asndebin.c: In function ‘AsnBinReadVal’: asndebin.c:565:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 565 | else | ^~~~ asndebin.c:568:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 568 | if (atp == NULL) | ^~ asndebin.c:634:41: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 634 | else /* empty sequence written */ | ^~~~ asndebin.c:636:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 636 | while (atp2 != NULL) | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnenbin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnenbin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asngen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asngen.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asngen.c: In function ‘AsnFindNthPieceOfObject’: asngen.c:540:16: warning: variable ‘aeop’ set but not used [-Wunused-but-set-variable] 540 | AsnExpOptPtr aeop; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnio.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnio.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnio.c: In function ‘AsnIoWriteBlock’: asnio.c:698:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 698 | else /* use alternative write function */ | ^~~~ asnio.c:701:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 701 | if (retval != bytes_to_write) | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnlex.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnlex.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnlex.c: In function ‘AsnTxtReadId’: asnlex.c:198:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 198 | if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE))) | ^~ asnlex.c:201:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 201 | if (token != IDENT) | ^~ asnlex.c: In function ‘AsnTxtReadVal’: asnlex.c:345:41: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 345 | else /* empty sequence written */ | ^~~~ asnlex.c:347:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 347 | while (atp2 != NULL) | ^~~~~ asnlex.c: At top level: asnlex.c:1290:13: warning: ‘AsnLexWordUTF8’ defined but not used [-Wunused-function] 1290 | static Int2 AsnLexWordUTF8 (AsnIoPtr aip) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnlext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnlext.c:57: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnout.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnout.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnout.c: In function ‘AsnOutput’: asnout.c:159:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 159 | else | ^~~~ asnout.c:162:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 162 | for (i = 0; i < 12; i++) | ^~~ asnout.c:213:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 213 | if (! loader) | ^~ asnout.c:216:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 216 | attvp = p.root_tmpvalue.next; | ^~~~~ asnout.c:270:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 270 | if (! loader) | ^~ asnout.c:273:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 273 | attp = p.root_tmptype.next; | ^~~~ asnout.c:450:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 450 | if (! loader) | ^~ asnout.c:453:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 453 | i = 1; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asnprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnprint.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnprint.c: In function ‘GetXMLModuleName’: asnprint.c:102:9: warning: statement with no effect [-Wunused-value] 102 | for (currmod; currmod != NULL; currmod = currmod->next) | ^~~ asnprint.c: In function ‘AsnPrintCloseStruct’: asnprint.c:1774:14: warning: variable ‘isa’ set but not used [-Wunused-but-set-variable] 1774 | Int2 isa; | ^~~ asnprint.c: In function ‘AsnPrintModuleXMLInc’: asnprint.c:2095:17: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 2095 | CharPtr ptr; | ^~~ asnprint.c: In function ‘AsnPrintTreeType’: asnprint.c:2575:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2575 | ptr = (Uint4)(atp); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asntypes.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asntypes.c:111: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asntypes.c: In function ‘AsnEnumTypeStr’: asntypes.c:1383:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1383 | if ((atp->type->isa != ENUM_TYPE) && (atp->type->isa != INTEGER_TYPE)) | ^~ asntypes.c:1386:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1386 | avnp = (AsnValxNodePtr) atp->branch; | ^~~~ asntypes.c: In function ‘AsnTreeLoad’: asntypes.c:1274:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1274 | fscanf(fp, "%d %d %d", &numval, &numtype, &nummod); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1288:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1288 | fscanf(fp, "%d %s %ld %lf %d", &isa, name, &intvalue, &realvalue, &next); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1301:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1301 | fscanf(fp, "%d %s %d %d %d %d %d %d %d %d %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1302 | &isa, name, &tagclass, &tagnumber, bools, bools+1, bools+2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1303 | bools+3, bools+4, &defaultvalue, &type, &branch, &next); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1333:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1333 | fscanf(fp, "%s %s %d %d", name, fname, &type, &next); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asngenob.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asngenob.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gifgen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from gifgen.c:137: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gifgen.c: In function ‘gdImageSetPixel’: gifgen.c:1027:34: warning: ‘<<’ in boolean context, did you mean ‘<’? [-Wint-in-bool-context] 1027 | (!im->use_pattern || (char)(im->pattern[7-y%8] >> x%8 << 7))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF togif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from togif.c:111: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ togif.c: In function ‘gdImageCreateFromGif’: togif.c:961:12: warning: variable ‘AspectRatio’ set but not used [-Wunused-but-set-variable] 961 | int AspectRatio; | ^~~~~~~~~~~ togif.c:960:12: warning: variable ‘Background’ set but not used [-Wunused-but-set-variable] 960 | int Background; | ^~~~~~~~~~ togif.c:959:12: warning: variable ‘ColorResolution’ set but not used [-Wunused-but-set-variable] 959 | int ColorResolution; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -DNCBI_NOTHREADS_AVAIL -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithrs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ncbithrs.c:289: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbithrs.c: In function ‘s_TlsDestroyAll’: ncbithrs.c:2529:11: warning: unused variable ‘err_code’ [-Wunused-variable] 2529 | int err_code = 0; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -DHAVE_STRING_H -DREGEX_MALLOC regex.c regex.c: In function ‘re_match_2’: regex.c:3762:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3762 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ regex.c:3762:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3762 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2509:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2509 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4074:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4074 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ regex.c:2512:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2512 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4074:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4074 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ regex.c:4071:25: warning: variable ‘sdummy’ set but not used [-Wunused-but-set-variable] 4071 | const char *sdummy; | ^~~~~~ regex.c:4070:28: warning: variable ‘pdummy’ set but not used [-Wunused-but-set-variable] 4070 | unsigned char *pdummy; | ^~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2509:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2509 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4288:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4288 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ regex.c:2512:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2512 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4288:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4288 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ regex.c: In function ‘regex_compile’: regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tsprintf.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbiargs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbiargs.c:82: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from tree.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF matrix.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/matrix.h:44, from matrix.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_socket.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_socket.c:75: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_socket.c: In function ‘s_GetLocalPort’: ncbi_socket.c:440:50: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 440 | if (getsockname(fd, (struct sockaddr*) &sin, &sinlen) == 0 | ^~~~~~~ | | | TSOCK_socklen_t * {aka int *} In file included from ncbi_socketp.h:54, from ncbi_connssl.h:37, from ncbi_socket.c:76: /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_IsConnected_’: ncbi_socket.c:2572:73: warning: pointer targets in passing argument 5 of ‘getsockopt’ differ in signedness [-Wpointer-sign] 2572 | if (getsockopt(sock->sock, SOL_SOCKET, SO_ERROR, (void*) error, &len) | ^~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:257:46: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 257 | socklen_t *__restrict __optlen) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ ncbi_socket.c: In function ‘s_CreateOnTop’: ncbi_socket.c:4435:35: warning: pointer targets in passing argument 3 of ‘getpeername’ differ in signedness [-Wpointer-sign] 4435 | if (getpeername(fd, &peer.sa, &peerlen) != 0) { | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:131:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 131 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c:4471:43: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 4471 | if (getsockname(fd, &peer.sa, &peerlen) != 0) | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_CreateListening’: ncbi_socket.c:4865:48: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 4865 | error = getsockname(x_lsock, &addr.sa, &addrlen) != 0 | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_Accept’: ncbi_socket.c:5105:49: warning: pointer targets in passing argument 3 of ‘accept’ differ in signedness [-Wpointer-sign] 5105 | if ((x_sock = accept(lsock->sock, &addr.sa, &addrlen)) == SOCK_INVALID) { | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:307:42: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 307 | socklen_t *__restrict __addr_len); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ncbi_socket.c: In function ‘s_RecvMsg’: ncbi_socket.c:5409:52: warning: pointer targets in passing argument 6 of ‘recvfrom’ differ in signedness [-Wpointer-sign] 5409 | (struct sockaddr*) &sin, &sinlen); | ^~~~~~~ | | | TSOCK_socklen_t * {aka int *} In file included from /usr/include/x86_64-linux-gnu/sys/socket.h:343: /usr/include/x86_64-linux-gnu/bits/socket2.h:62:56: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 62 | __SOCKADDR_ARG __addr, socklen_t *__restrict __addr_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ncbi_socket.c: In function ‘TRIGGER_Create’: ncbi_socket.c:5661:18: warning: unused variable ‘x_id’ [-Wunused-variable] 5661 | unsigned int x_id = ++s_ID_Counter; | ^~~~ ncbi_socket.c: In function ‘DSOCK_Bind’: ncbi_socket.c:7390:51: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 7390 | error = getsockname(sock->sock, &addr.sa, &addrlen) != 0 | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_buffer.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_types.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_core.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_core.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_core_c.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_core_c.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_util.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_util.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_priv.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_priv.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ansi_ext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ansi_ext.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connection.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_connection.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_connector.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_connutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_connutil.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_file_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_file_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_heapmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_heapmgr.c:115: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_heapmgr.c: In function ‘s_HEAP_Take’: ncbi_heapmgr.c:617:12: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 617 | return &b->head; | ^~~~~~~~ ncbi_heapmgr.c: In function ‘s_HEAP_Walk’: ncbi_heapmgr.c:1169:12: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1169 | return &b->head; | ^~~~~~~~ ncbi_heapmgr.c: In function ‘HEAP_Walk’: ncbi_heapmgr.c:1184:20: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1184 | return &heap->base->head; | ^~~~~~~~~~~~~~~~~ ncbi_heapmgr.c:1187:15: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1187 | ? &b->head : 0; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_http_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_http_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_memory_connector.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lbsmd_stub.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_host_info.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_server_info.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_server_info.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strcpy’, inlined from ‘SERV_CreateNcbidInfoEx’ at ncbi_server_info.c:716:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strcpy’, inlined from ‘SERV_CreateHttpInfoEx’ at ncbi_server_info.c:902:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_service.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_service.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_version.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_version.h:37, from ncbi_version.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_service_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_service_connector.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ftp_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ftp_connector.c:49: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_dispd.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_dispd.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lb.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_local.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_local.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_socket_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_socket_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urlquery.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from urlquery.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF binary.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/binary.h:60, from binary.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_sendmail.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_sendmail.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_base64.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn_connection.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_lbos.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_lbos.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_lbos.c: In function ‘s_LBOS_ReadLbosresolver’: ncbi_lbos.c:756:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 756 | if (s_LBOS_Lbosresolver == NULL) | ^~ ncbi_lbos.c:759:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 759 | s_LBOS_Lbosresolver = strdup(str + 7); | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF parson.c parson.c: In function ‘remove_comments’: parson.c:281:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 281 | for (i = 0; i < (ptr - string) + end_token_len; i++) | ^~~ parson.c:283:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 283 | string = ptr + end_token_len - 1; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_ipv6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ipv6.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF raw_scoremat.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF drwnflpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnflpt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF drwnfspc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnfspc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF drwnmfls.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnmfls.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rm -f libncbi.a ar cru libncbi.a ncbimain.o ncbibs.o wwwutils.o ncbierr.o ncbienv.o ncbifile.o ncbiprop.o ncbimath.o ncbimem.o ncbimisc.o ncbimsg.o ncbistr.o ncbisgml.o ncbitime.o ncbilang.o asnbufo.o asndebin.o asnenbin.o asngen.o asnio.o asnlex.o asnlext.o asnout.o asnprint.o asntypes.o asngenob.o gifgen.o togif.o ncbithrs.o regex.o tsprintf.o ncbiargs.o tree.o matrix.o ncbi_socket.o ncbi_buffer.o ncbi_types.o ncbi_core.o ncbi_core_c.o ncbi_util.o ncbi_priv.o ncbi_ansi_ext.o ncbi_connection.o ncbi_connector.o ncbi_connutil.o ncbi_file_connector.o ncbi_heapmgr.o ncbi_http_connector.o ncbi_memory_connector.o ncbi_lbsmd_stub.o ncbi_host_info.o ncbi_server_info.o ncbi_service.o ncbi_version.o ncbi_service_connector.o ncbi_ftp_connector.o ncbi_dispd.o ncbi_lb.o ncbi_local.o ncbi_socket_connector.o urlquery.o binary.o ncbi_sendmail.o ncbi_base64.o asn_connection.o ncbi_lbos.o parson.o ncbi_ipv6.o raw_scoremat.o drwnflpt.o drwnfspc.o drwnmfls.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbi.a ../lib ranlib ../lib/libncbi.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -DHAVE_LIBGNUTLS ncbi_gnutls.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_gnutls.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_gnutls.c: In function ‘s_GnuTlsCreate’: ncbi_gnutls.c:293:5: warning: ‘gnutls_connection_end_t’ is deprecated [-Wdeprecated-declarations] 293 | gnutls_connection_end_t end = (side == eSOCK_Client | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ncbi_gnutls.c:35: ncbi_gnutls.c: In function ‘s_GnuTlsInit’: ncbi_priv.h:217:33: warning: ‘version’ may be used uninitialized [-Wmaybe-uninitialized] 217 | _mess.message = NcbiMessagePlusError(&_mess.dynamic, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | (_message), \ | ~~~~~~~~~~~~~~~~~~~~ 219 | (_error), \ | ~~~~~~~~~~~~~~~~~~~~ 220 | (_descr)); \ | ~~~~~~~~~ ncbi_gnutls.c:582:17: note: ‘version’ was declared here 582 | const char* version; | ^~~~~~~ rm -f libconnssl.a ar cru libconnssl.a ncbi_gnutls.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libconnssl.a ../lib ranlib ../lib/libconnssl.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objacces.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnacces.h:9, from objacces.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objacces.c: In function ‘LinkSetAsnWrite’: objacces.c:140:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 140 | if (atp == NULL) | ^~ objacces.c:143:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 143 | if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objacces.c: In function ‘LinkSetAsnRead’: objacces.c:216:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 216 | if (atp == NULL) | ^~ objacces.c:219:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 219 | lsp = LinkSetNew(); | ^~~ objacces.c:220:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 220 | if (lsp == NULL) | ^~ objacces.c:223:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 223 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objacces.c:226:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 226 | if (atp == NULL) | ^~ objacces.c:228:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 228 | if (AsnReadVal(aip, atp, &av) <= 0) /* get the num */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objalign.h:103, from objalign.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objalign.c: In function ‘CommonSeqAlignLabelFunc’: objalign.c:135:34: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 135 | CharPtr curr, typelabel, tmp; | ^~~ objalign.c: In function ‘SeqAlignAsnRead’: objalign.c:597:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 597 | if (atp == NULL) | ^~ objalign.c:600:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 600 | sap = SeqAlignNew(); | ^~~ objalign.c:601:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 601 | if (sap == NULL) | ^~ objalign.c:604:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 604 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘DenseDiagAsnWrite’: objalign.c:1020:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1020 | if (atp == NULL) | ^~ objalign.c:1023:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1023 | if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c: In function ‘DenseDiagAsnRead’: objalign.c:1112:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1112 | if (atp == NULL) | ^~ objalign.c:1115:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1115 | ddp = DenseDiagNew(); | ^~~ objalign.c:1116:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1116 | if (ddp == NULL) | ^~ objalign.c:1119:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1119 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘DenseSegAsnWrite’: objalign.c:1268:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1268 | if (atp == NULL) | ^~ objalign.c:1271:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1271 | if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c: In function ‘DenseSegAsnRead’: objalign.c:1374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1374 | if (atp == NULL) | ^~ objalign.c:1377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1377 | dsp = DenseSegNew(); | ^~~ objalign.c:1378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1378 | if (dsp == NULL) | ^~ objalign.c:1381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1381 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘StdSegAsnWrite’: objalign.c:1559:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1559 | if (atp == NULL) | ^~ objalign.c:1562:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1562 | if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c:1581:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1581 | if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E)) | ^~ objalign.c:1584:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1584 | if (ssp->scores != NULL) | ^~ objalign.c: In function ‘StdSegAsnRead’: objalign.c:1626:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1626 | if (atp == NULL) | ^~ objalign.c:1629:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1629 | ssp = StdSegNew(); | ^~~ objalign.c:1630:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1630 | if (ssp == NULL) | ^~ objalign.c:1633:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1633 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘SeqAlignSetAsnWrite’: objalign.c:1704:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1704 | if (atp == NULL) | ^~ objalign.c:1708:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1708 | oldsap = sap; | ^~~~~~ objalign.c: In function ‘PackSegAsnWrite’: objalign.c:1892:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1892 | if (atp == NULL) | ^~ objalign.c:1895:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1895 | if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c:1926:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1926 | if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts)) | ^~ objalign.c:1929:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1929 | av.ptrvalue = psp->present; | ^~ objalign.c: In function ‘PackSegAsnRead’: objalign.c:1999:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1999 | if (atp == NULL) | ^~ objalign.c:2002:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2002 | psp = PackSegNew(); | ^~~ objalign.c:2003:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2003 | if (psp == NULL) | ^~ objalign.c:2006:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2006 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘SplicedSegAsnRead’: objalign.c:2179:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2179 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseSegAsnRead’: objalign.c:2422:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2422 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedExonAsnRead’: objalign.c:2614:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2614 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedSegModifierFree’: objalign.c:2875:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2875 | Pointer pnt; | ^~~ objalign.c: In function ‘ProductPosFree’: objalign.c:3050:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3050 | Pointer pnt; | ^~~ objalign.c: In function ‘SplicedExonChunkFree’: objalign.c:3225:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3225 | Pointer pnt; | ^~~ objalign.c: In function ‘SpliceSiteAsnRead’: objalign.c:3469:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3469 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘ProtPosAsnRead’: objalign.c:3626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3626 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseAlignAsnRead’: objalign.c:3798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3798 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseSegExtAsnRead’: objalign.c:4020:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4020 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedSegModifierAsnRead’: objalign.c:2955:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2955 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:2903:10: note: ‘choice’ was declared here 2903 | Uint1 choice; | ^~~~~~ objalign.c: In function ‘SplicedExonChunkAsnRead’: objalign.c:3326:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3326 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:3253:10: note: ‘choice’ was declared here 3253 | Uint1 choice; | ^~~~~~ objalign.c: In function ‘ProductPosAsnRead’: objalign.c:3130:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3130 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:3081:10: note: ‘choice’ was declared here 3081 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objall.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objall.h:64, from objall.c:63: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objbibli.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnbibli.h:9, from objbibli.c:113: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objbibli.c: In function ‘AffilAsnRead’: objbibli.c:208:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 208 | if (atp == NULL) | ^~ objbibli.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 211 | afp = AffilNew(); | ^~~ objbibli.c: In function ‘AffilAsnWrite’: objbibli.c:296:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 296 | if (atp == NULL) | ^~ objbibli.c:299:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 299 | if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘AuthListFree’: objbibli.c:458:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 458 | if (alp->affil != NULL) | ^~ objbibli.c:460:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 460 | return (AuthListPtr)MemFree(alp); | ^~~~~~ objbibli.c: In function ‘AuthListAsnRead’: objbibli.c:489:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 489 | if (atp == NULL) | ^~ objbibli.c:492:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 492 | alp = AuthListNew(); | ^~~ objbibli.c: In function ‘AuthListAsnWrite’: objbibli.c:583:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 583 | if (atp == NULL) | ^~ objbibli.c:586:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 586 | if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:590:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 590 | if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */ | ^~ objbibli.c:593:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 593 | av.ptrvalue = alp->names; | ^~ objbibli.c: In function ‘AuthorFree’: objbibli.c:677:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 677 | if (ap->affil != NULL) | ^~ objbibli.c:679:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 679 | return (AuthorPtr)MemFree(ap); | ^~~~~~ objbibli.c: In function ‘AuthorAsnRead’: objbibli.c:707:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 707 | if (atp == NULL) | ^~ objbibli.c:710:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 710 | ap = AuthorNew(); | ^~ objbibli.c: In function ‘AuthorAsnWrite’: objbibli.c:779:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 779 | if (atp == NULL) | ^~ objbibli.c:782:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 782 | if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitArtAsnRead’: objbibli.c:925:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 925 | if (atp == NULL) | ^~ objbibli.c:928:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 928 | cap = CitArtNew(); | ^~~ objbibli.c: In function ‘CitArtAsnWrite’: objbibli.c:1027:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1027 | if (atp == NULL) | ^~ objbibli.c:1030:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1030 | if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1034:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1034 | if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */ | ^~ objbibli.c:1037:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1037 | if (cap->title != NULL) | ^~ objbibli.c: In function ‘ImprintAsnRead’: objbibli.c:1152:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1152 | if (atp == NULL) | ^~ objbibli.c:1155:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1155 | ip = ImprintNew(); | ^~ objbibli.c: In function ‘ImprintAsnWrite’: objbibli.c:1251:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1251 | if (atp == NULL) | ^~ objbibli.c:1254:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1254 | if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitRetractFree’: objbibli.c:1360:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1360 | if (crp == NULL) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objbibli.c:1363:9: note: in expansion of macro ‘MemFree’ 1363 | MemFree(crp->exp); | ^~~~~~~ objbibli.c: In function ‘CitRetractAsnRead’: objbibli.c:1391:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1391 | if (atp == NULL) | ^~ objbibli.c:1394:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1394 | crp = CitRetractNew(); | ^~~ objbibli.c: In function ‘CitRetractAsnWrite’: objbibli.c:1445:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1445 | if (atp == NULL) | ^~ objbibli.c:1448:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1448 | if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitJourAsnRead’: objbibli.c:1524:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1524 | if (atp == NULL) | ^~ objbibli.c:1527:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1527 | cjp = CitJourNew(); | ^~~ objbibli.c: In function ‘CitJourAsnWrite’: objbibli.c:1576:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1576 | if (atp == NULL) | ^~ objbibli.c:1579:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1579 | if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1585:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1585 | if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp)) | ^~ objbibli.c:1587:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1587 | if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitBookAsnRead’: objbibli.c:1676:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1676 | if (atp == NULL) | ^~ objbibli.c:1679:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1679 | cbp = CitBookNew(); | ^~~ objbibli.c: In function ‘CitBookAsnWrite’: objbibli.c:1744:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1744 | if (atp == NULL) | ^~ objbibli.c:1747:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1747 | if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1760:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1760 | if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp)) | ^~ objbibli.c:1762:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1762 | if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitProcAsnWrite’: objbibli.c:1879:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1879 | if (atp == NULL) | ^~ objbibli.c:1882:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1882 | if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1901:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1901 | if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata)) | ^~ objbibli.c:1903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1903 | if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitLetAsnWrite’: objbibli.c:1995:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1995 | if (atp == NULL) | ^~ objbibli.c:1998:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1998 | if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitPatAsnRead’: objbibli.c:2091:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2091 | if (atp == NULL) | ^~ objbibli.c:2094:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2094 | cpp = CitPatNew(); | ^~~ objbibli.c: In function ‘CitPatAsnWrite’: objbibli.c:2213:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2213 | if (atp == NULL) | ^~ objbibli.c:2216:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2216 | if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘IdPatAsnRead’: objbibli.c:2346:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2346 | if (atp == NULL) | ^~ objbibli.c:2349:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2349 | idp = IdPatNew(); | ^~~ objbibli.c: In function ‘IdPatAsnWrite’: objbibli.c:2412:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2412 | if (atp == NULL) | ^~ objbibli.c:2415:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2415 | if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitGenAsnRead’: objbibli.c:2546:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2546 | if (atp == NULL) | ^~ objbibli.c:2549:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2549 | cgp = CitGenNew(); | ^~~ objbibli.c: In function ‘CitGenAsnWrite’: objbibli.c:2627:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2627 | if (atp == NULL) | ^~ objbibli.c:2630:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2630 | if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘TitleAsnWrite’: objbibli.c:2825:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2825 | if (atp == NULL) | ^~ objbibli.c:2828:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2828 | if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitSubFree’: objbibli.c:2909:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2909 | if (csp == NULL) | ^~ objbibli.c:2912:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2912 | AuthListFree(csp->authors); | ^~~~~~~~~~~~ objbibli.c: In function ‘CitSubAsnRead’: objbibli.c:2943:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2943 | if (atp == NULL) | ^~ objbibli.c:2946:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2946 | csp = CitSubNew(); | ^~~ objbibli.c:2958:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2958 | if (atp == NULL) | ^~ objbibli.c:2961:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2961 | if (atp == CIT_SUB_imp) | ^~ objbibli.c: In function ‘CitSubAsnWrite’: objbibli.c:3029:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3029 | if (atp == NULL) | ^~ objbibli.c:3032:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3032 | if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:3038:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3038 | if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors)) | ^~ objbibli.c:3041:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3041 | if (csp->imp != NULL) | ^~ objbibli.c: In function ‘PatPrioritySetAsnRead’: objbibli.c:3694:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3694 | if (ppp == NULL) | ^~ objbibli.c:3697:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3697 | if (head == NULL) | ^~ objbibli.c:3715:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3715 | if (atp == NULL) | ^~ objbibli.c:3717:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3717 | ppp->date = DateAsnRead(aip, atp); | ^~~ objbibli.c: In function ‘PatPrioritySetAsnWrite’: objbibli.c:3755:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3755 | if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */ | ^~ objbibli.c:3758:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3758 | for (tmp = ppp; tmp != NULL; tmp = tmp->next) | ^~~ objbibli.c: In function ‘ArticleIdAsnRead’: objbibli.c:3849:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3849 | if (atp == NULL) | ^~ objbibli.c:3852:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3852 | aidp = ArticleIdNew(); | ^~~~ objbibli.c: In function ‘ArticleIdAsnWrite’: objbibli.c:3925:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3925 | if (atp == NULL) | ^~ objbibli.c:3928:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3928 | if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘PubStatusDateAsnRead’: objbibli.c:4039:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4039 | if (atp == NULL) | ^~ objbibli.c:4042:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4042 | psdp = PubStatusDateNew(); | ^~~~ objbibli.c: In function ‘PubStatusDateAsnWrite’: objbibli.c:4091:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4091 | if (atp == NULL) | ^~ objbibli.c:4094:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4094 | if (psdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objfeat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objfeat.h:48, from objfeat.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objfeat.c: In function ‘ModelEvidenceSupportAsnRead’: objfeat.c:1500:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1500 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ExperimentSupportAsnRead’: objfeat.c:1748:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1748 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ProgramIdAsnRead’: objfeat.c:1933:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1933 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘EvidenceBasisAsnRead’: objfeat.c:2103:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2103 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘InferenceSupportAsnRead’: objfeat.c:2267:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2267 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ModelEvidenceItemAsnRead’: objfeat.c:2483:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2483 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SeqFeatSupportAsnRead’: objfeat.c:2688:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2688 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAQualAsnRead’: objfeat.c:4244:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4244 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAQualSetAsnRead’: objfeat.c:4396:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4396 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAGenAsnRead’: objfeat.c:4524:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4524 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘GeneNomenclatureAsnRead’: objfeat.c:4707:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4707 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘OrgNameMatch’: objfeat.c:5957:28: warning: self-comparison always evaluates to false [-Wtautological-compare] 5957 | || onp2->mgcode != onp2->mgcode | ^~ objfeat.c: In function ‘TaxElementAsnWrite’: objfeat.c:7399:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 7399 | if (! AsnOpenStruct(aip, atp, (Pointer)tep)) | ^~ objfeat.c:7402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 7402 | av.intvalue = (Int4)(tep->fixed_level); | ^~ objfeat.c: In function ‘PCRPrimerAsnRead’: objfeat.c:8276:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8276 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRPrimerSetAsnRead’: objfeat.c:8421:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8421 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRReactionAsnRead’: objfeat.c:8542:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8542 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRReactionSetAsnRead’: objfeat.c:8685:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8685 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneRefAsnRead’: objfeat.c:8812:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8812 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneSeqSetAsnRead’: objfeat.c:9005:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9005 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneSeqAsnRead’: objfeat.c:9135:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9135 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SomaticOriginAsnRead’: objfeat.c:9487:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9487 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SomaticOriginConditionAsnRead’: objfeat.c:9566:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9566 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘VariationRefAsnRead’: objfeat.c:9645:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9645 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_loss_of_heterozygosityAsnRead’: objfeat.c:10687:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10687 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_frameshiftAsnRead’: objfeat.c:10765:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10765 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘VarRefDataFree’: objfeat.c:10865:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 10865 | Pointer pnt; | ^~~ objfeat.c: In function ‘VarRefDataSetAsnRead’: objfeat.c:10918:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10918 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_elementFree’: objfeat.c:11112:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 11112 | Pointer pnt; | ^~~ objfeat.c: In function ‘VariationInstAsnRead’: objfeat.c:11241:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11241 | AsnReadFunc func; | ^~~~ objfeat.c: At top level: objfeat.c:11393:1: warning: "/*" within comment [-Wcomment] 11393 | /************************************************** | objfeat.c: In function ‘VariantPropertiesAsnRead’: objfeat.c:11422:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11422 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PhenotypeAsnRead’: objfeat.c:11746:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11746 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PopulationDataAsnRead’: objfeat.c:11945:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11945 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ExtLocAsnRead’: objfeat.c:12161:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12161 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Seq_seqFree’: objfeat.c:12327:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12327 | Pointer pnt; | ^~~ objfeat.c: In function ‘DeltaItemAsnRead’: objfeat.c:12360:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12360 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objgen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asngen.h:9, from objgen.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objgen.c: In function ‘DateFree’: objgen.c:147:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 147 | if (dp == NULL) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objgen.c:150:9: note: in expansion of macro ‘MemFree’ 150 | MemFree(dp->str); | ^~~~~~~ objgen.c: In function ‘DateClean’: objgen.c:161:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 161 | if (dp == NULL) | ^~ objgen.c:164:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 164 | memset(dp, 0, sizeof(NCBI_Date)); | ^~~~~~ objgen.c: In function ‘DateAsnWrite’: objgen.c:399:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 399 | if (atp == NULL) | ^~ objgen.c:402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 402 | if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘DateAsnRead’: objgen.c:494:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 494 | if (atp == NULL) | ^~ objgen.c:497:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 497 | dp = DateNew(); | ^~ objgen.c:498:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 498 | if (dp == NULL) | ^~ objgen.c:501:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 501 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */ | ^~ objgen.c: In function ‘DbtagFree’: objgen.c:752:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | if (dbt == NULL) | ^~ objgen.c:755:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 755 | dbt->tag = ObjectIdFree(dbt->tag); | ^~~ objgen.c: In function ‘DbtagAsnRead’: objgen.c:784:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 784 | if (atp == NULL) | ^~ objgen.c:787:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 787 | dbt = DbtagNew(); | ^~~ objgen.c:788:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 788 | if (dbt == NULL) | ^~ objgen.c:791:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 791 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */ | ^~ objgen.c:799:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 799 | if (dbt->tag == NULL) | ^~ objgen.c:802:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 802 | atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */ | ^~~ objgen.c: In function ‘DbtagAsnWrite’: objgen.c:833:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 833 | if (atp == NULL) | ^~ objgen.c:836:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 836 | if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘ObjectIdFree’: objgen.c:949:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 949 | if (oid == NULL) | ^~ ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objgen.c:952:9: note: in expansion of macro ‘MemFree’ 952 | MemFree(oid->str); | ^~~~~~~ objgen.c: In function ‘ObjectIdAsnRead’: objgen.c:980:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 980 | if (atp == NULL) | ^~ objgen.c:983:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 983 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */ | ^~ objgen.c:989:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 989 | if (oid == NULL) | ^~ objgen.c:991:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 991 | if (atp == OBJECT_ID_id) | ^~ objgen.c: In function ‘ObjectIdAsnWrite’: objgen.c:1024:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1024 | if (atp == NULL) | ^~ objgen.c:1027:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1027 | if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘NameStdFree’: objgen.c:1174:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1174 | if (nsp == NULL) | ^~ objgen.c:1177:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1177 | for (i = 0; i < 7; i++) | ^~~ objgen.c: In function ‘NameStdAsnRead’: objgen.c:1208:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1208 | if (atp == NULL) | ^~ objgen.c:1211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1211 | nsp = NameStdNew(); | ^~~ objgen.c:1212:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1212 | if (nsp == NULL) | ^~ objgen.c:1215:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1215 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */ | ^~ objgen.c: In function ‘NameStdAsnWrite’: objgen.c:1271:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1271 | if (atp == NULL) | ^~ objgen.c:1274:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1274 | if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘PersonIdFree’: objgen.c:1368:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1368 | if (pid == NULL) | ^~ objgen.c:1371:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1371 | if (pid->choice == 1) /* Dbtag */ | ^~ objgen.c: In function ‘PersonIdAsnWrite’: objgen.c:1464:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1464 | if (atp == NULL) | ^~ objgen.c:1467:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1467 | if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘IntFuzzAsnRead’: objgen.c:1682:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1682 | if (atp == NULL) | ^~ objgen.c:1685:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1685 | ifp = IntFuzzNew(); | ^~~ objgen.c:1686:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1686 | if (ifp == NULL) | ^~ objgen.c:1689:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1689 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */ | ^~ objgen.c: In function ‘UserFieldAsnRead’: objgen.c:1944:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1944 | if (atp == NULL) | ^~ objgen.c:1947:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1947 | ufp = UserFieldNew(); | ^~~ objgen.c: In function ‘UserObjectAsnRead’: objgen.c:2434:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2434 | if (atp == NULL) | ^~ objgen.c:2437:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2437 | uop = UserObjectNew(); | ^~~ objgen.c:2438:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2438 | if (uop == NULL) | ^~ objgen.c:2441:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2441 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objloc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from objloc.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objloc.c: In function ‘SeqIdAsnWrite’: objloc.c:313:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 313 | if (atp == NULL) | ^~ objloc.c:316:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 316 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqIdAsnRead’: objloc.c:443:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 443 | if (atp == NULL) | ^~ objloc.c:446:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 446 | anp = ValNodeNew(NULL); | ^~~ objloc.c: In function ‘SeqIdDup’: objloc.c:587:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 587 | if (oldid == NULL) | ^~ objloc.c:590:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 590 | newid = ValNodeNew(NULL); | ^~~~~ objloc.c: In function ‘SeqIdSetAsnRead’: objloc.c:752:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */ | ^~ objloc.c:754:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 754 | if (first == NULL) | ^~ objloc.c: In function ‘SeqIdSetAsnWrite’: objloc.c:786:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 786 | if (atp2 == NULL) | ^~ objloc.c:789:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 789 | if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; } | ^~ objloc.c: In function ‘TextSeqIdAsnWrite’: objloc.c:864:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 864 | if (atp == NULL) | ^~ objloc.c:867:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 867 | if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘TextSeqIdAsnRead’: objloc.c:934:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 934 | if (atp == NULL) | ^~ objloc.c:937:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 937 | tsip = TextSeqIdNew(); | ^~~~ objloc.c:938:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 938 | if (tsip == NULL) | ^~ objloc.c:941:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 941 | if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PatentSeqIdAsnWrite’: objloc.c:1018:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1018 | if (atp == NULL) | ^~ objloc.c:1021:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1021 | if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PatentSeqIdAsnRead’: objloc.c:1068:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1068 | if (atp == NULL) | ^~ objloc.c:1071:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1071 | psip = PatentSeqIdNew(); | ^~~~ objloc.c:1072:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1072 | if (psip == NULL) | ^~ objloc.c:1075:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1075 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘GiimAsnWrite’: objloc.c:1151:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1151 | if (atp == NULL) | ^~ objloc.c:1154:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1154 | if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘GiimAsnRead’: objloc.c:1216:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1216 | if (gip == NULL) | ^~ objloc.c:1219:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1219 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PDBSeqIdAsnWrite’: objloc.c:1305:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1305 | if (atp == NULL) | ^~ objloc.c:1308:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1308 | if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PDBSeqIdAsnRead’: objloc.c:1374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1374 | if (atp == NULL) | ^~ objloc.c:1377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1377 | pdbsip = PDBSeqIdNew(); | ^~~~~~ objloc.c:1378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1378 | if (pdbsip == NULL) | ^~ objloc.c:1381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1381 | if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘SeqLocAsnWrite’: objloc.c:1528:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1528 | if (atp == NULL) | ^~ objloc.c:1531:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1531 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocAsnRead’: objloc.c:1624:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1624 | if (atp == NULL) | ^~ objloc.c:1627:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1627 | anp = ValNodeNew(NULL); | ^~~ objloc.c:1628:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1628 | if (anp == NULL) | ^~ objloc.c:1631:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1631 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */ | ^~ objloc.c: In function ‘SeqLocMixAsnWrite’: objloc.c:1738:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1738 | if (atp == NULL) | ^~ objloc.c:1741:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1741 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocEquivAsnWrite’: objloc.c:1805:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1805 | if (atp == NULL) | ^~ objloc.c:1808:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1808 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocSetAsnWrite’: objloc.c:1873:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1873 | if (atp2 == NULL) | ^~ objloc.c:1876:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1876 | if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; } | ^~ objloc.c: In function ‘SeqLocSetAsnRead’: objloc.c:1940:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1940 | if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */ | ^~ objloc.c:1942:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1942 | if (first == NULL) | ^~ objloc.c: In function ‘SeqIntAsnWrite’: objloc.c:2022:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022 | if (atp == NULL) | ^~ objloc.c:2025:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025 | if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqIntAsnRead’: objloc.c:2095:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2095 | if (atp == NULL) | ^~ objloc.c:2098:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2098 | sip = SeqIntNew(); | ^~~ objloc.c:2099:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if (sip == NULL) | ^~ objloc.c:2102:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2102 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PackSeqIntAsnWrite’: objloc.c:2179:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2179 | if (atp == NULL) | ^~ objloc.c:2181:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2181 | oldsip = sip; | ^~~~~~ objloc.c:2185:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2185 | if (! AsnOpenStruct(aip, atp, (Pointer)oldsip)) | ^~ objloc.c:2187:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2187 | for ( ;sip != NULL; sip = sip->next) | ^~~ objloc.c: In function ‘SeqPntAsnWrite’: objloc.c:2309:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2309 | if (atp == NULL) | ^~ objloc.c:2312:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2312 | if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqPntAsnRead’: objloc.c:2374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2374 | if (atp == NULL) | ^~ objloc.c:2377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2377 | spp = SeqPntNew(); | ^~~ objloc.c:2378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2378 | if (spp == NULL) | ^~ objloc.c:2381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2381 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PackSeqPntAsnWrite’: objloc.c:2479:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2479 | if (atp == NULL) | ^~ objloc.c:2482:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2482 | if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PackSeqPntAsnRead’: objloc.c:2553:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2553 | if (atp == NULL) | ^~ objloc.c:2556:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2556 | pspp = PackSeqPntNew(); | ^~~~ objloc.c:2557:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2557 | if (pspp == NULL) | ^~ objloc.c:2560:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2560 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘SeqBondAsnWrite’: objloc.c:2724:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2724 | if (atp == NULL) | ^~ objloc.c:2727:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2727 | if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqBondAsnRead’: objloc.c:2776:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2776 | if (atp == NULL) | ^~ objloc.c:2779:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2779 | sbp = SeqBondNew(); | ^~~ objloc.c:2780:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2780 | if (sbp == NULL) | ^~ objloc.c:2783:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2783 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmedli.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmedli.h:80, from objmedli.c:104: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmedli.c: In function ‘MedlineMeshAsnRead’: objmedli.c:248:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 248 | if (atp == NULL) | ^~ objmedli.c:251:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 251 | mmp = MedlineMeshNew(); | ^~~ objmedli.c: In function ‘DocRefFree’: objmedli.c:1190:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1190 | if (drp == NULL) | ^~ objmedli.c:1193:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1193 | return (DocRefPtr)MemFree(drp); | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objpub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objpub.h:70, from objpub.c:125: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objpub.c: In function ‘PubSetAsnRead’: objpub.c:831:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 831 | if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */ | ^~ objpub.c:834:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 834 | if (settype == PUB_SET_pub) | ^~ objpub.c:901:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 901 | if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */ | ^~ objpub.c:903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 903 | if (anp == NULL) | ^~ objpub.c: In function ‘PubLabelUnique’: objpub.c:1360:24: warning: unused variable ‘pmid’ [-Wunused-variable] 1360 | Int4 muid = 0, pmid = 0; | ^~~~ objpub.c:1360:14: warning: unused variable ‘muid’ [-Wunused-variable] 1360 | Int4 muid = 0, pmid = 0; | ^~~~ objpub.c: In function ‘PubSetAsnRead’: objpub.c:870:17: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 870 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objpub.c:805:11: note: ‘choice’ was declared here 805 | Uint1 choice; | ^~~~~~ objpub.c:876:16: warning: ‘func’ may be used uninitialized [-Wmaybe-uninitialized] 876 | pnt = (* func)(aip, atp); | ~^~~~~~~~~~~~~~~~~ objpub.c:806:17: note: ‘func’ was declared here 806 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objres.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from objres.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objres.c: In function ‘SeqGraphFree’: objres.c:208:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 208 | else /* byte */ | ^~~~ objres.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 211 | ObjMgrDelete(OBJ_SEQGRAPH, (Pointer)sgp); | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objscoremat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objscoremat.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objscoremat.c: In function ‘PssmAsnRead’: objscoremat.c:93:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 93 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmIntermediateDataAsnRead’: objscoremat.c:339:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 339 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmFinalDataAsnRead’: objscoremat.c:548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 548 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmParametersAsnRead’: objscoremat.c:766:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 766 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmWithParametersAsnRead’: objscoremat.c:946:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 946 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘BlockPropertyAsnRead’: objscoremat.c:1113:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1113 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘CoreBlockAsnRead’: objscoremat.c:1289:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1289 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘LoopConstraintAsnRead’: objscoremat.c:1480:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1480 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘CoreDefAsnRead’: objscoremat.c:1646:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1646 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘FormatRpsDbParametersAsnRead’: objscoremat.c:1817:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1817 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from objseq.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objseq.c: In function ‘LinkageEvidenceAsnRead’: objseq.c:1609:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1609 | AsnReadFunc func; | ^~~~ objseq.c: In function ‘SeqGapAsnRead’: objseq.c:1764:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1764 | AsnReadFunc func; | ^~~~ objseq.c: In function ‘SeqDescrAsnWriteExtra’: objseq.c:2035:48: warning: variable ‘had_anp’ set but not used [-Wunused-but-set-variable] 2035 | Boolean retval = FALSE, had_extra = FALSE, had_anp = FALSE; | ^~~~~~~ objseq.c: In function ‘AnnotIdAsnWrite’: objseq.c:4841:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 4841 | else | ^~~~ objseq.c:4843:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 4843 | break; | ^~~~~ objseq.c:4849:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 4849 | else | ^~~~ objseq.c:4851:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 4851 | break; | ^~~~~ objseq.c: In function ‘AnnotDescAsnWrite’: objseq.c:5226:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 5226 | else | ^~~~ objseq.c:5228:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 5228 | break; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objblock.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objblock.h:70, from objblock.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objblock.c: In function ‘EMBLBlockFree’: objblock.c:900:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 900 | if (ebp == NULL) | ^~ objblock.c:903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 903 | DateFree(ebp->creation_date); | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objcode.c objcode.c:48:51: warning: "/*" within comment [-Wcomment] 48 | * environment variables to allow reading from data/*.val, replaced tabs in source code with spaces | In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objcode.h:64, from objcode.c:105: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objsset.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from objsset.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objsset.c: In function ‘BioseqSetFree’: objsset.c:363:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 363 | if (bsp == NULL) | ^~ objsset.c:366:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 366 | if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) { | ^~ objsset.c: In function ‘SeqEntryFree’: objsset.c:878:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | else if (sep->choice == 2) | ^~ objsset.c:881:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 881 | return (SeqEntryPtr)MemFree(sep); | ^~~~~~ objsset.c: In function ‘SeqEntryFreeComponents’: objsset.c:898:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 898 | else if (sep->choice == 2) | ^~ objsset.c:901:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 901 | return sep; | ^~~~~~ objsset.c: In function ‘SeqEntryAsnGet’: objsset.c:1075:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1075 | if (retcode == 1) /* just after a Bioseq */ | ^~ objsset.c:1077:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1077 | av.ptrvalue = (Pointer) osp; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objsub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnsubmt.h:9, from objsub.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objsub.c: In function ‘SubmitAsnLoad’: objsub.c:341:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 341 | if (loaded) | ^~ objsub.c:344:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 344 | if (! SeqSetAsnLoad ()) | ^~ objsub.c:347:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 347 | if (AsnLoad()) | ^~ objsub.c:350:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 350 | ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission", | ^~~~~~~~~~~~~~ objsub.c: In function ‘SeqSubmitAsnWrite’: objsub.c:455:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 455 | if (atp == NULL) | ^~ objsub.c:458:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 458 | if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:462:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 462 | if (! AsnOpenStruct(aip, atp, (Pointer)ssp)) | ^~ objsub.c:465:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 465 | if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret; | ^~ objsub.c: In function ‘SeqSubmitAsnRead’: objsub.c:539:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 539 | if (atp == NULL) | ^~ objsub.c:542:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 542 | ssp = SeqSubmitNew(); | ^~~ objsub.c:543:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 543 | if (ssp == NULL) | ^~ objsub.c:546:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 546 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objsub.c: In function ‘SubmitBlockAsnWrite’: objsub.c:682:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 682 | if (atp == NULL) | ^~ objsub.c:685:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 685 | if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:689:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 689 | if (! AsnOpenStruct(aip, atp, (Pointer)sbp)) | ^~ objsub.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 692 | if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact)) | ^~ objsub.c: In function ‘SubmitBlockAsnRead’: objsub.c:770:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 770 | if (atp == NULL) | ^~ objsub.c:773:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 773 | oldatp = atp; | ^~~~~~ objsub.c:775:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 775 | if (sbp == NULL) | ^~ objsub.c:778:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 778 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objsub.c: In function ‘ContactInfoAsnWrite’: objsub.c:942:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 942 | if (atp == NULL) | ^~ objsub.c:945:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 945 | if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:949:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 949 | if (! AsnOpenStruct(aip, atp, (Pointer)cip)) | ^~ objsub.c:952:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 952 | if (cip->name != NULL) | ^~ objsub.c: In function ‘ContactInfoAsnRead’: objsub.c:1068:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1068 | if (atp == NULL) | ^~ objsub.c:1070:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1070 | oldatp = atp; | ^~~~~~ objsub.c:1073:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1073 | if (cip == NULL) | ^~ objsub.c:1076:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1076 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objprt.h:67, from objprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objprt.c: In function ‘PrintFormBooleanAsnRead’: objprt.c:892:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 892 | ptr=PrintFormBooleanFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~~~~ objprt.c:853:29: note: ‘ptr’ was declared here 853 | PrintFormBooleanPtr ptr; | ^~~ objprt.c: In function ‘PrintFormEnumAsnRead’: objprt.c:1010:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1010 | ptr=PrintFormEnumFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~ objprt.c:969:26: note: ‘ptr’ was declared here 969 | PrintFormEnumPtr ptr; | ^~~ objprt.c: In function ‘PrintFormTextAsnRead’: objprt.c:1119:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1119 | ptr=PrintFormTextFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~ objprt.c:1086:26: note: ‘ptr’ was declared here 1086 | PrintFormTextPtr ptr; | ^~~ objprt.c: In function ‘PrintFormAsnRead’: objprt.c:600:15: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 600 | vnp = PrintFormFree(vnp); | ^~~~~~~~~~~~~~~~~~ objprt.c:533:20: note: ‘vnp’ was declared here 533 | ValNodePtr vnp; | ^~~ objprt.c: In function ‘PrintFormatAsnRead’: objprt.c:435:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 435 | ptr=PrintFormatFree(ptr); | ^~~~~~~~~~~~~~~~~~~~ objprt.c:379:24: note: ‘ptr’ was declared here 379 | PrintFormatPtr ptr; | ^~~ objprt.c: In function ‘PrintTemplateAsnRead’: objprt.c:250:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 250 | ptr=PrintTemplateFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~ objprt.c:206:26: note: ‘ptr’ was declared here 206 | PrintTemplatePtr ptr; | ^~~ objprt.c: In function ‘PrintFormBlockAsnRead’: objprt.c:767:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 767 | ptr=PrintFormBlockFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~~ objprt.c:707:27: note: ‘ptr’ was declared here 707 | PrintFormBlockPtr ptr; | ^~~ objprt.c: In function ‘UserFormatAsnRead’: objprt.c:1231:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1231 | ptr=UserFormatFree(ptr); | ^~~~~~~~~~~~~~~~~~~ objprt.c:1192:23: note: ‘ptr’ was declared here 1192 | UserFormatPtr ptr; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objfdef.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objfeat.h:48, from ../include/objfdef.h:48, from objfdef.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objalignloc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objalignloc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objalignloc.c: In function ‘AlignLocSetAsnRead’: objalignloc.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objalignloc.c: In function ‘Loc_locFree’: objalignloc.c:196:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 196 | Pointer pnt; | ^~~ objalignloc.c: In function ‘AlignLocAsnRead’: objalignloc.c:233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 233 | AsnReadFunc func; | ^~~~ objalignloc.c:232:12: warning: unused variable ‘isError’ [-Wunused-variable] 232 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘Loc_locAsnRead’: objalignloc.c:313:12: warning: unused variable ‘isError’ [-Wunused-variable] 313 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignIdFree’: objalignloc.c:527:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 527 | Pointer pnt; | ^~~ objalignloc.c: In function ‘AlignIdAsnRead’: objalignloc.c:559:12: warning: unused variable ‘isError’ [-Wunused-variable] 559 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignBoxAsnRead’: objalignloc.c:750:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 750 | AsnReadFunc func; | ^~~~ objalignloc.c:749:12: warning: unused variable ‘isError’ [-Wunused-variable] 749 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignRowsAsnRead’: objalignloc.c:932:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 932 | AsnReadFunc func; | ^~~~ objalignloc.c:931:12: warning: unused variable ‘isError’ [-Wunused-variable] 931 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignColumnsAsnRead’: objalignloc.c:1096:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1096 | AsnReadFunc func; | ^~~~ objalignloc.c:1095:12: warning: unused variable ‘isError’ [-Wunused-variable] 1095 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignIdAsnRead’: objalignloc.c:615:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 615 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalignloc.c:558:10: note: ‘choice’ was declared here 558 | Uint1 choice; | ^~~~~~ In function ‘Loc_locAsnRead’, inlined from ‘AlignLocAsnRead’ at objalignloc.c:276:24: objalignloc.c:370:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 370 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalignloc.c: In function ‘AlignLocAsnRead’: objalignloc.c:312:10: note: ‘choice’ was declared here 312 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objtable.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtable.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtable.c: In function ‘SeqTableColumnInfoAsnRead’: objtable.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objtable.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableColumnAsnRead’: objtable.c:269:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 269 | AsnReadFunc func; | ^~~~ objtable.c:268:12: warning: unused variable ‘isError’ [-Wunused-variable] 268 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableAsnRead’: objtable.c:474:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 474 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘CommonStringTableAsnRead’: objtable.c:657:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 657 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘CommonBytesTableAsnRead’: objtable.c:819:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 819 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘SeqTableSingleDataFree’: objtable.c:1225:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1225 | Pointer pnt; | ^~~ objtable.c: In function ‘SeqTableSingleDataAsnRead’: objtable.c:1269:12: warning: unused variable ‘isError’ [-Wunused-variable] 1269 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableMultiDataAsnRead’: objtable.c:1111:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1111 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1001:10: note: ‘choice’ was declared here 1001 | Uint1 choice; | ^~~~~~ objtable.c: In function ‘SeqTableSingleDataAsnRead’: objtable.c:1354:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1354 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1268:10: note: ‘choice’ was declared here 1268 | Uint1 choice; | ^~~~~~ objtable.c: In function ‘SeqTableSparseIndexAsnRead’: objtable.c:1559:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1559 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1505:10: note: ‘choice’ was declared here 1505 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objpubme.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objpubme.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objpubme.c: In function ‘PubmedEntryAsnRead’: objpubme.c:89:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 89 | AsnReadFunc func; | ^~~~ objpubme.c: In function ‘PubmedUrlAsnRead’: objpubme.c:288:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 288 | AsnReadFunc func; | ^~~~ objpubme.c:287:12: warning: unused variable ‘isError’ [-Wunused-variable] 287 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmdrs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmdrs.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmdrs.c: In function ‘MedlarsEntryAsnRead’: objmdrs.c:85:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 85 | AsnReadFunc func; | ^~~~ objmdrs.c: In function ‘MedlarsRecordAsnRead’: objmdrs.c:259:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 259 | AsnReadFunc func; | ^~~~ objmdrs.c:258:12: warning: unused variable ‘isError’ [-Wunused-variable] 258 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objproj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objproj.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objproj.c: In function ‘ProjectAsnRead’: objproj.c:116:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 116 | AsnReadFunc func; | ^~~~ objproj.c:115:12: warning: unused variable ‘isError’ [-Wunused-variable] 115 | Boolean isError = FALSE; | ^~~~~~~ objproj.c: In function ‘ProjectDescrAsnRead’: objproj.c:720:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 720 | AsnReadFunc func; | ^~~~ objproj.c: In function ‘ProjdescFree’: objproj.c:857:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 857 | Pointer pnt; | ^~~ objproj.c: In function ‘ProjdescAsnRead’: objproj.c:898:12: warning: unused variable ‘isError’ [-Wunused-variable] 898 | Boolean isError = FALSE; | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/mmdbapi.h:92, from ../include/mapproj.h:45, from objproj.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objproj.c: In function ‘ProjdescAsnRead’: objproj.c:958:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 958 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objproj.c:897:10: note: ‘choice’ was declared here 897 | Uint1 choice; | ^~~~~~ objproj.c: In function ‘ProjectItemAsnRead’: objproj.c:536:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 536 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objproj.c:331:10: note: ‘choice’ was declared here 331 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objgbseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objgbseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objgbseq.c: In function ‘GBSetAsnRead’: objgbseq.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objgbseq.c:66:12: warning: unused variable ‘av’ [-Wunused-variable] 66 | DataVal av; | ^~ objgbseq.c: In function ‘GBSeqAsnRead’: objgbseq.c:235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 235 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBReferenceAsnRead’: objgbseq.c:742:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 742 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBCommentAsnRead’: objgbseq.c:983:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 983 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBStrucCommentAsnRead’: objgbseq.c:1150:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1150 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBFeatureAsnRead’: objgbseq.c:1321:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1321 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBFeatureSetAsnRead’: objgbseq.c:1548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1548 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBAltSeqDataAsnRead’: objgbseq.c:1715:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1715 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBXrefAsnRead’: objgbseq.c:1882:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1882 | AsnReadFunc func; | ^~~~ objgbseq.c:1881:12: warning: unused variable ‘isError’ [-Wunused-variable] 1881 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBStrucCommentItemAsnRead’: objgbseq.c:2053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2053 | AsnReadFunc func; | ^~~~ objgbseq.c:2052:12: warning: unused variable ‘isError’ [-Wunused-variable] 2052 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBIntervalAsnRead’: objgbseq.c:2233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2233 | AsnReadFunc func; | ^~~~ objgbseq.c:2232:12: warning: unused variable ‘isError’ [-Wunused-variable] 2232 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBQualifierAsnRead’: objgbseq.c:2447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2447 | AsnReadFunc func; | ^~~~ objgbseq.c:2446:12: warning: unused variable ‘isError’ [-Wunused-variable] 2446 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBAltSeqItemAsnRead’: objgbseq.c:2622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2622 | AsnReadFunc func; | ^~~~ objgbseq.c:2621:12: warning: unused variable ‘isError’ [-Wunused-variable] 2621 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objtseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtseq.c: In function ‘TSeqAsnRead’: objtseq.c:89:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 89 | AsnReadFunc func; | ^~~~ objtseq.c: In function ‘TSeqSetAsnRead’: objtseq.c:325:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 325 | AsnReadFunc func; | ^~~~ objtseq.c: In function ‘BioseqToTSeq’: objtseq.c:452:15: warning: variable ‘seqcode’ set but not used [-Wunused-but-set-variable] 452 | Uint1 seqcode; | ^~~~~~~ objtseq.c: In function ‘BioseqToMiniTSeq’: objtseq.c:564:15: warning: variable ‘seqcode’ set but not used [-Wunused-but-set-variable] 564 | Uint1 seqcode; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objinsdseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objinsdseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objinsdseq.c: In function ‘INSDSetAsnRead’: objinsdseq.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objinsdseq.c:66:12: warning: unused variable ‘av’ [-Wunused-variable] 66 | DataVal av; | ^~ objinsdseq.c: In function ‘INSDSeqAsnRead’: objinsdseq.c:235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 235 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDReferenceAsnRead’: objinsdseq.c:742:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 742 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDCommentAsnRead’: objinsdseq.c:983:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 983 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDStrucCommentAsnRead’: objinsdseq.c:1150:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1150 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDFeatureAsnRead’: objinsdseq.c:1321:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1321 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDFeatureSetAsnRead’: objinsdseq.c:1548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1548 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDAltSeqDataAsnRead’: objinsdseq.c:1715:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1715 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDXrefAsnRead’: objinsdseq.c:1882:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1882 | AsnReadFunc func; | ^~~~ objinsdseq.c:1881:12: warning: unused variable ‘isError’ [-Wunused-variable] 1881 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDStrucCommentItemAsnRead’: objinsdseq.c:2053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2053 | AsnReadFunc func; | ^~~~ objinsdseq.c:2052:12: warning: unused variable ‘isError’ [-Wunused-variable] 2052 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDIntervalAsnRead’: objinsdseq.c:2233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2233 | AsnReadFunc func; | ^~~~ objinsdseq.c:2232:12: warning: unused variable ‘isError’ [-Wunused-variable] 2232 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDQualifierAsnRead’: objinsdseq.c:2447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2447 | AsnReadFunc func; | ^~~~ objinsdseq.c:2446:12: warning: unused variable ‘isError’ [-Wunused-variable] 2446 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDAltSeqItemAsnRead’: objinsdseq.c:2622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2622 | AsnReadFunc func; | ^~~~ objinsdseq.c:2621:12: warning: unused variable ‘isError’ [-Wunused-variable] 2621 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmacro.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmacro.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmacro.c: In function ‘AECRActionAsnRead’: objmacro.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objmacro.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseActionAsnRead’: objmacro.c:272:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 272 | AsnReadFunc func; | ^~~~ objmacro.c:271:12: warning: unused variable ‘isError’ [-Wunused-variable] 271 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MacroActionListAsnRead’: objmacro.c:478:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 478 | AsnReadFunc func; | ^~~~ objmacro.c:475:12: warning: unused variable ‘av’ [-Wunused-variable] 475 | DataVal av; | ^~ objmacro.c: In function ‘SuspectRuleSetAsnRead’: objmacro.c:595:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 595 | AsnReadFunc func; | ^~~~ objmacro.c:592:12: warning: unused variable ‘av’ [-Wunused-variable] 592 | DataVal av; | ^~ objmacro.c: In function ‘WordSubstitutionAsnRead’: objmacro.c:731:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 731 | AsnReadFunc func; | ^~~~ objmacro.c: In function ‘WordSubstitutionSetAsnRead’: objmacro.c:899:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 899 | AsnReadFunc func; | ^~~~ objmacro.c:896:12: warning: unused variable ‘av’ [-Wunused-variable] 896 | DataVal av; | ^~ objmacro.c: In function ‘StringConstraintAsnRead’: objmacro.c:1045:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1045 | AsnReadFunc func; | ^~~~ objmacro.c:1044:12: warning: unused variable ‘isError’ [-Wunused-variable] 1044 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StringConstraintSetAsnRead’: objmacro.c:1307:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1307 | AsnReadFunc func; | ^~~~ objmacro.c:1304:12: warning: unused variable ‘av’ [-Wunused-variable] 1304 | DataVal av; | ^~ objmacro.c: In function ‘LocationPosConstraintFree’: objmacro.c:1403:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1403 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationPosConstraintAsnRead’: objmacro.c:1432:12: warning: unused variable ‘isError’ [-Wunused-variable] 1432 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationConstraintAsnRead’: objmacro.c:1633:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1633 | AsnReadFunc func; | ^~~~ objmacro.c:1632:12: warning: unused variable ‘isError’ [-Wunused-variable] 1632 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalValAsnRead’: objmacro.c:1849:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1849 | AsnReadFunc func; | ^~~~ objmacro.c:1848:12: warning: unused variable ‘isError’ [-Wunused-variable] 1848 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalValChoiceFree’: objmacro.c:1979:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1979 | Pointer pnt; | ^~~ objmacro.c: In function ‘FeatQualLegalValChoiceAsnRead’: objmacro.c:2011:12: warning: unused variable ‘isError’ [-Wunused-variable] 2011 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalSetAsnRead’: objmacro.c:2165:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2165 | AsnReadFunc func; | ^~~~ objmacro.c:2162:12: warning: unused variable ‘av’ [-Wunused-variable] 2162 | DataVal av; | ^~ objmacro.c: In function ‘FeatQualChoiceFree’: objmacro.c:2261:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2261 | Pointer pnt; | ^~~ objmacro.c: In function ‘FeatQualChoiceAsnRead’: objmacro.c:2293:12: warning: unused variable ‘isError’ [-Wunused-variable] 2293 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldAsnRead’: objmacro.c:2474:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2474 | AsnReadFunc func; | ^~~~ objmacro.c:2473:12: warning: unused variable ‘isError’ [-Wunused-variable] 2473 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldLegalAsnRead’: objmacro.c:2641:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2641 | AsnReadFunc func; | ^~~~ objmacro.c:2640:12: warning: unused variable ‘isError’ [-Wunused-variable] 2640 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldPairAsnRead’: objmacro.c:2807:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2807 | AsnReadFunc func; | ^~~~ objmacro.c:2806:12: warning: unused variable ‘isError’ [-Wunused-variable] 2806 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaFeatTypeFree’: objmacro.c:2950:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2950 | Pointer pnt; | ^~~ objmacro.c: In function ‘RnaFeatTypeAsnRead’: objmacro.c:2982:12: warning: unused variable ‘isError’ [-Wunused-variable] 2982 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaQualAsnRead’: objmacro.c:3232:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3232 | AsnReadFunc func; | ^~~~ objmacro.c:3231:12: warning: unused variable ‘isError’ [-Wunused-variable] 3231 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaQualPairAsnRead’: objmacro.c:3400:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3400 | AsnReadFunc func; | ^~~~ objmacro.c:3399:12: warning: unused variable ‘isError’ [-Wunused-variable] 3399 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualPairAsnRead’: objmacro.c:3576:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3576 | AsnReadFunc func; | ^~~~ objmacro.c:3575:12: warning: unused variable ‘isError’ [-Wunused-variable] 3575 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualChoiceFree’: objmacro.c:3704:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3704 | Pointer pnt; | ^~~ objmacro.c: In function ‘SourceQualChoiceAsnRead’: objmacro.c:3733:12: warning: unused variable ‘isError’ [-Wunused-variable] 3733 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualTextValAsnRead’: objmacro.c:3950:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3950 | AsnReadFunc func; | ^~~~ objmacro.c:3949:12: warning: unused variable ‘isError’ [-Wunused-variable] 3949 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualValChoiceFree’: objmacro.c:4080:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4080 | Pointer pnt; | ^~~ objmacro.c: In function ‘SourceQualValChoiceAsnRead’: objmacro.c:4112:12: warning: unused variable ‘isError’ [-Wunused-variable] 4112 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualValSetAsnRead’: objmacro.c:4310:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4310 | AsnReadFunc func; | ^~~~ objmacro.c:4307:12: warning: unused variable ‘av’ [-Wunused-variable] 4307 | DataVal av; | ^~ objmacro.c: In function ‘CDSGeneProtFieldPairAsnRead’: objmacro.c:4442:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4442 | AsnReadFunc func; | ^~~~ objmacro.c:4441:12: warning: unused variable ‘isError’ [-Wunused-variable] 4441 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldFree’: objmacro.c:4570:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4570 | Pointer pnt; | ^~~ objmacro.c: In function ‘MolinfoFieldAsnRead’: objmacro.c:4599:12: warning: unused variable ‘isError’ [-Wunused-variable] 4599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoMoleculePairAsnRead’: objmacro.c:4826:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4826 | AsnReadFunc func; | ^~~~ objmacro.c:4825:12: warning: unused variable ‘isError’ [-Wunused-variable] 4825 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoTechniquePairAsnRead’: objmacro.c:4990:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4990 | AsnReadFunc func; | ^~~~ objmacro.c:4989:12: warning: unused variable ‘isError’ [-Wunused-variable] 4989 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoCompletednessPairAsnRead’: objmacro.c:5154:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5154 | AsnReadFunc func; | ^~~~ objmacro.c:5153:12: warning: unused variable ‘isError’ [-Wunused-variable] 5153 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoMolClassPairAsnRead’: objmacro.c:5318:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5318 | AsnReadFunc func; | ^~~~ objmacro.c:5317:12: warning: unused variable ‘isError’ [-Wunused-variable] 5317 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoTopologyPairAsnRead’: objmacro.c:5482:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5482 | AsnReadFunc func; | ^~~~ objmacro.c:5481:12: warning: unused variable ‘isError’ [-Wunused-variable] 5481 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoStrandPairAsnRead’: objmacro.c:5646:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5646 | AsnReadFunc func; | ^~~~ objmacro.c:5645:12: warning: unused variable ‘isError’ [-Wunused-variable] 5645 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldPairFree’: objmacro.c:5774:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 5774 | Pointer pnt; | ^~~ objmacro.c: In function ‘MolinfoFieldPairAsnRead’: objmacro.c:5821:12: warning: unused variable ‘isError’ [-Wunused-variable] 5821 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldListAsnRead’: objmacro.c:6015:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6015 | AsnReadFunc func; | ^~~~ objmacro.c:6012:12: warning: unused variable ‘av’ [-Wunused-variable] 6012 | DataVal av; | ^~ objmacro.c: In function ‘MolinfoFieldConstraintAsnRead’: objmacro.c:6149:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6149 | AsnReadFunc func; | ^~~~ objmacro.c:6148:12: warning: unused variable ‘isError’ [-Wunused-variable] 6148 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StructuredCommentFieldFree’: objmacro.c:6280:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 6280 | Pointer pnt; | ^~~ objmacro.c: In function ‘StructuredCommentFieldAsnRead’: objmacro.c:6312:12: warning: unused variable ‘isError’ [-Wunused-variable] 6312 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StructuredCommentFieldPairAsnRead’: objmacro.c:6508:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6508 | AsnReadFunc func; | ^~~~ objmacro.c:6507:12: warning: unused variable ‘isError’ [-Wunused-variable] 6507 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘DBLinkFieldPairAsnRead’: objmacro.c:6678:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6678 | AsnReadFunc func; | ^~~~ objmacro.c:6677:12: warning: unused variable ‘isError’ [-Wunused-variable] 6677 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldConstraintAsnRead’: objmacro.c:6843:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6843 | AsnReadFunc func; | ^~~~ objmacro.c:6842:12: warning: unused variable ‘isError’ [-Wunused-variable] 6842 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeFree’: objmacro.c:6974:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 6974 | Pointer pnt; | ^~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeAsnRead’: objmacro.c:7003:12: warning: unused variable ‘isError’ [-Wunused-variable] 7003 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintAsnRead’: objmacro.c:7220:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7220 | AsnReadFunc func; | ^~~~ objmacro.c:7219:12: warning: unused variable ‘isError’ [-Wunused-variable] 7219 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PublicationConstraintAsnRead’: objmacro.c:7389:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7389 | AsnReadFunc func; | ^~~~ objmacro.c:7388:12: warning: unused variable ‘isError’ [-Wunused-variable] 7388 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceConstraintAsnRead’: objmacro.c:7571:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7571 | AsnReadFunc func; | ^~~~ objmacro.c:7570:12: warning: unused variable ‘isError’ [-Wunused-variable] 7570 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtPseudoConstraintAsnRead’: objmacro.c:7763:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7763 | AsnReadFunc func; | ^~~~ objmacro.c:7762:12: warning: unused variable ‘isError’ [-Wunused-variable] 7762 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtConstraintFieldFree’: objmacro.c:7891:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 7891 | Pointer pnt; | ^~~ objmacro.c: In function ‘CDSGeneProtConstraintFieldAsnRead’: objmacro.c:7920:12: warning: unused variable ‘isError’ [-Wunused-variable] 7920 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtQualConstraintAsnRead’: objmacro.c:8095:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8095 | AsnReadFunc func; | ^~~~ objmacro.c:8094:12: warning: unused variable ‘isError’ [-Wunused-variable] 8094 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldConstraintAsnRead’: objmacro.c:8279:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8279 | AsnReadFunc func; | ^~~~ objmacro.c:8278:12: warning: unused variable ‘isError’ [-Wunused-variable] 8278 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldTypeFree’: objmacro.c:8413:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8413 | Pointer pnt; | ^~~ objmacro.c: In function ‘FieldTypeAsnRead’: objmacro.c:8457:12: warning: unused variable ‘isError’ [-Wunused-variable] 8457 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintFree’: objmacro.c:8666:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8666 | Pointer pnt; | ^~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintAsnRead’: objmacro.c:8695:12: warning: unused variable ‘isError’ [-Wunused-variable] 8695 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘QuantityConstraintFree’: objmacro.c:8875:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8875 | Pointer pnt; | ^~~ objmacro.c: In function ‘QuantityConstraintAsnRead’: objmacro.c:8904:12: warning: unused variable ‘isError’ [-Wunused-variable] 8904 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceConstraintAsnRead’: objmacro.c:9104:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9104 | AsnReadFunc func; | ^~~~ objmacro.c:9103:12: warning: unused variable ‘isError’ [-Wunused-variable] 9103 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TranslationConstraintAsnRead’: objmacro.c:9332:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9332 | AsnReadFunc func; | ^~~~ objmacro.c:9331:12: warning: unused variable ‘isError’ [-Wunused-variable] 9331 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConstraintChoiceFree’: objmacro.c:9487:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 9487 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConstraintChoiceAsnRead’: objmacro.c:9549:12: warning: unused variable ‘isError’ [-Wunused-variable] 9549 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConstraintChoiceSetAsnRead’: objmacro.c:9783:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9783 | AsnReadFunc func; | ^~~~ objmacro.c:9780:12: warning: unused variable ‘av’ [-Wunused-variable] 9780 | DataVal av; | ^~ objmacro.c: In function ‘TextMarkerFree’: objmacro.c:9879:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 9879 | Pointer pnt; | ^~~ objmacro.c: In function ‘TextMarkerAsnRead’: objmacro.c:9911:12: warning: unused variable ‘isError’ [-Wunused-variable] 9911 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextPortionAsnRead’: objmacro.c:10109:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10109 | AsnReadFunc func; | ^~~~ objmacro.c:10108:12: warning: unused variable ‘isError’ [-Wunused-variable] 10108 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldEditAsnRead’: objmacro.c:10328:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10328 | AsnReadFunc func; | ^~~~ objmacro.c:10327:12: warning: unused variable ‘isError’ [-Wunused-variable] 10327 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldPairTypeFree’: objmacro.c:10478:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 10478 | Pointer pnt; | ^~~ objmacro.c: In function ‘FieldPairTypeAsnRead’: objmacro.c:10528:12: warning: unused variable ‘isError’ [-Wunused-variable] 10528 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyActionAsnRead’: objmacro.c:10747:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10747 | AsnReadFunc func; | ^~~~ objmacro.c:10746:12: warning: unused variable ‘isError’ [-Wunused-variable] 10746 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditActionAsnRead’: objmacro.c:10927:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10927 | AsnReadFunc func; | ^~~~ objmacro.c:10926:12: warning: unused variable ‘isError’ [-Wunused-variable] 10926 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextTransformFree’: objmacro.c:11061:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 11061 | Pointer pnt; | ^~~ objmacro.c: In function ‘TextTransformAsnRead’: objmacro.c:11096:12: warning: unused variable ‘isError’ [-Wunused-variable] 11096 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextTransformSetAsnRead’: objmacro.c:11269:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11269 | AsnReadFunc func; | ^~~~ objmacro.c:11266:12: warning: unused variable ‘av’ [-Wunused-variable] 11266 | DataVal av; | ^~ objmacro.c: In function ‘ConvertActionAsnRead’: objmacro.c:11405:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11405 | AsnReadFunc func; | ^~~~ objmacro.c:11404:12: warning: unused variable ‘isError’ [-Wunused-variable] 11404 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CopyActionAsnRead’: objmacro.c:11600:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11600 | AsnReadFunc func; | ^~~~ objmacro.c:11599:12: warning: unused variable ‘isError’ [-Wunused-variable] 11599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SwapActionAsnRead’: objmacro.c:11768:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11768 | AsnReadFunc func; | ^~~~ objmacro.c:11767:12: warning: unused variable ‘isError’ [-Wunused-variable] 11767 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AECRParseActionAsnRead’: objmacro.c:11932:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11932 | AsnReadFunc func; | ^~~~ objmacro.c:11931:12: warning: unused variable ‘isError’ [-Wunused-variable] 11931 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveActionAsnRead’: objmacro.c:12151:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12151 | AsnReadFunc func; | ^~~~ objmacro.c:12150:12: warning: unused variable ‘isError’ [-Wunused-variable] 12150 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveOutsideActionAsnRead’: objmacro.c:12312:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12312 | AsnReadFunc func; | ^~~~ objmacro.c:12311:12: warning: unused variable ‘isError’ [-Wunused-variable] 12311 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ActionChoiceFree’: objmacro.c:12455:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12455 | Pointer pnt; | ^~~ objmacro.c: In function ‘ActionChoiceAsnRead’: objmacro.c:12508:12: warning: unused variable ‘isError’ [-Wunused-variable] 12508 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcOrgChoiceFree’: objmacro.c:12697:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12697 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcOrgChoiceAsnRead’: objmacro.c:12726:12: warning: unused variable ‘isError’ [-Wunused-variable] 12726 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcOrgAsnRead’: objmacro.c:12911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12911 | AsnReadFunc func; | ^~~~ objmacro.c:12910:12: warning: unused variable ‘isError’ [-Wunused-variable] 12910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcGeneralIdFree’: objmacro.c:13042:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13042 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcGeneralIdAsnRead’: objmacro.c:13074:12: warning: unused variable ‘isError’ [-Wunused-variable] 13074 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcFree’: objmacro.c:13232:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13232 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcAsnRead’: objmacro.c:13270:12: warning: unused variable ‘isError’ [-Wunused-variable] 13270 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseDstOrgAsnRead’: objmacro.c:13526:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 13526 | AsnReadFunc func; | ^~~~ objmacro.c:13525:12: warning: unused variable ‘isError’ [-Wunused-variable] 13525 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseDestFree’: objmacro.c:13657:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13657 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseDestAsnRead’: objmacro.c:13695:12: warning: unused variable ‘isError’ [-Wunused-variable] 13695 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationIntervalAsnRead’: objmacro.c:13905:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 13905 | AsnReadFunc func; | ^~~~ objmacro.c:13904:12: warning: unused variable ‘isError’ [-Wunused-variable] 13904 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationChoiceFree’: objmacro.c:14033:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 14033 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationChoiceAsnRead’: objmacro.c:14065:12: warning: unused variable ‘isError’ [-Wunused-variable] 14065 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceListAsnRead’: objmacro.c:14241:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14241 | AsnReadFunc func; | ^~~~ objmacro.c:14238:12: warning: unused variable ‘av’ [-Wunused-variable] 14238 | DataVal av; | ^~ objmacro.c: In function ‘SequenceListChoiceFree’: objmacro.c:14337:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 14337 | Pointer pnt; | ^~~ objmacro.c: In function ‘SequenceListChoiceAsnRead’: objmacro.c:14369:12: warning: unused variable ‘isError’ [-Wunused-variable] 14369 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyFeatureActionAsnRead’: objmacro.c:14560:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14560 | AsnReadFunc func; | ^~~~ objmacro.c:14559:12: warning: unused variable ‘isError’ [-Wunused-variable] 14559 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveFeatureActionAsnRead’: objmacro.c:14827:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14827 | AsnReadFunc func; | ^~~~ objmacro.c:14826:12: warning: unused variable ‘isError’ [-Wunused-variable] 14826 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFromCDSOptionsAsnRead’: objmacro.c:14994:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14994 | AsnReadFunc func; | ^~~~ objmacro.c:14993:12: warning: unused variable ‘isError’ [-Wunused-variable] 14993 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureSrcOptionsFree’: objmacro.c:15131:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 15131 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConvertFeatureSrcOptionsAsnRead’: objmacro.c:15163:12: warning: unused variable ‘isError’ [-Wunused-variable] 15163 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RegionTypeAsnRead’: objmacro.c:15332:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15332 | AsnReadFunc func; | ^~~~ objmacro.c:15331:12: warning: unused variable ‘isError’ [-Wunused-variable] 15331 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureDstOptionsFree’: objmacro.c:15451:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 15451 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConvertFeatureDstOptionsAsnRead’: objmacro.c:15486:12: warning: unused variable ‘isError’ [-Wunused-variable] 15486 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureActionAsnRead’: objmacro.c:15702:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15702 | AsnReadFunc func; | ^~~~ objmacro.c:15701:12: warning: unused variable ‘isError’ [-Wunused-variable] 15701 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditLocationStrandAsnRead’: objmacro.c:15911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15911 | AsnReadFunc func; | ^~~~ objmacro.c:15910:12: warning: unused variable ‘isError’ [-Wunused-variable] 15910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘Partial5SetActionAsnRead’: objmacro.c:16075:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16075 | AsnReadFunc func; | ^~~~ objmacro.c:16074:12: warning: unused variable ‘isError’ [-Wunused-variable] 16074 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘Partial3SetActionAsnRead’: objmacro.c:16239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16239 | AsnReadFunc func; | ^~~~ objmacro.c:16238:12: warning: unused variable ‘isError’ [-Wunused-variable] 16238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PartialBothSetActionAsnRead’: objmacro.c:16403:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16403 | AsnReadFunc func; | ^~~~ objmacro.c:16402:12: warning: unused variable ‘isError’ [-Wunused-variable] 16402 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ExtendToFeatureAsnRead’: objmacro.c:16568:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16568 | AsnReadFunc func; | ^~~~ objmacro.c:16567:12: warning: unused variable ‘isError’ [-Wunused-variable] 16567 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationEditTypeFree’: objmacro.c:16708:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 16708 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationEditTypeAsnRead’: objmacro.c:16755:12: warning: unused variable ‘isError’ [-Wunused-variable] 16755 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditFeatureLocationActionAsnRead’: objmacro.c:17032:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17032 | AsnReadFunc func; | ^~~~ objmacro.c:17031:12: warning: unused variable ‘isError’ [-Wunused-variable] 17031 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoBlockAsnRead’: objmacro.c:17232:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17232 | AsnReadFunc func; | ^~~~ objmacro.c:17231:12: warning: unused variable ‘isError’ [-Wunused-variable] 17231 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveDescriptorActionAsnRead’: objmacro.c:17415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17415 | AsnReadFunc func; | ^~~~ objmacro.c:17414:12: warning: unused variable ‘isError’ [-Wunused-variable] 17414 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AutodefActionAsnRead’: objmacro.c:17584:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17584 | AsnReadFunc func; | ^~~~ objmacro.c: In function ‘FixPubCapsActionAsnRead’: objmacro.c:17758:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17758 | AsnReadFunc func; | ^~~~ objmacro.c:17757:12: warning: unused variable ‘isError’ [-Wunused-variable] 17757 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SortFieldsActionAsnRead’: objmacro.c:17963:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17963 | AsnReadFunc func; | ^~~~ objmacro.c:17962:12: warning: unused variable ‘isError’ [-Wunused-variable] 17962 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixAuthorCapsAsnRead’: objmacro.c:18142:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18142 | AsnReadFunc func; | ^~~~ objmacro.c:18141:12: warning: unused variable ‘isError’ [-Wunused-variable] 18141 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixCapsActionFree’: objmacro.c:18261:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 18261 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixCapsActionAsnRead’: objmacro.c:18296:12: warning: unused variable ‘isError’ [-Wunused-variable] 18296 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixFormatActionFree’: objmacro.c:18470:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 18470 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixFormatActionAsnRead’: objmacro.c:18499:12: warning: unused variable ‘isError’ [-Wunused-variable] 18499 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveDuplicateFeatureActionAsnRead’: objmacro.c:18705:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18705 | AsnReadFunc func; | ^~~~ objmacro.c:18704:12: warning: unused variable ‘isError’ [-Wunused-variable] 18704 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘GeneXrefTypeAsnRead’: objmacro.c:18899:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18899 | AsnReadFunc func; | ^~~~ objmacro.c:18898:12: warning: unused variable ‘isError’ [-Wunused-variable] 18898 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘XrefTypeFree’: objmacro.c:19036:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 19036 | Pointer pnt; | ^~~ objmacro.c: In function ‘XrefTypeAsnRead’: objmacro.c:19068:12: warning: unused variable ‘isError’ [-Wunused-variable] 19068 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveXrefsActionAsnRead’: objmacro.c:19239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19239 | AsnReadFunc func; | ^~~~ objmacro.c:19238:12: warning: unused variable ‘isError’ [-Wunused-variable] 19238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MakeGeneXrefActionAsnRead’: objmacro.c:19410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19410 | AsnReadFunc func; | ^~~~ objmacro.c:19409:12: warning: unused variable ‘isError’ [-Wunused-variable] 19409 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AuthorFixActionAsnRead’: objmacro.c:19578:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19578 | AsnReadFunc func; | ^~~~ objmacro.c:19577:12: warning: unused variable ‘isError’ [-Wunused-variable] 19577 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘UpdateSequencesActionAsnRead’: objmacro.c:19747:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19747 | AsnReadFunc func; | ^~~~ objmacro.c:19746:12: warning: unused variable ‘isError’ [-Wunused-variable] 19746 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CreateTSAIdsSrcFree’: objmacro.c:19877:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 19877 | Pointer pnt; | ^~~ objmacro.c: In function ‘CreateTSAIdsSrcAsnRead’: objmacro.c:19909:12: warning: unused variable ‘isError’ [-Wunused-variable] 19909 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CreateTSAIdsActionAsnRead’: objmacro.c:20092:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20092 | AsnReadFunc func; | ^~~~ objmacro.c:20091:12: warning: unused variable ‘isError’ [-Wunused-variable] 20091 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AutofixActionAsnRead’: objmacro.c:20274:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20274 | AsnReadFunc func; | ^~~~ objmacro.c:20273:12: warning: unused variable ‘isError’ [-Wunused-variable] 20273 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixSetsActionFree’: objmacro.c:20395:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 20395 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixSetsActionAsnRead’: objmacro.c:20424:12: warning: unused variable ‘isError’ [-Wunused-variable] 20424 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TableMatchTypeFree’: objmacro.c:20582:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 20582 | Pointer pnt; | ^~~ objmacro.c: In function ‘TableMatchTypeAsnRead’: objmacro.c:20614:12: warning: unused variable ‘isError’ [-Wunused-variable] 20614 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TableMatchAsnRead’: objmacro.c:20873:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20873 | AsnReadFunc func; | ^~~~ objmacro.c:20872:12: warning: unused variable ‘isError’ [-Wunused-variable] 20872 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyTableExtraDataFree’: objmacro.c:21004:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 21004 | Pointer pnt; | ^~~ objmacro.c: In function ‘ApplyTableExtraDataAsnRead’: objmacro.c:21033:12: warning: unused variable ‘isError’ [-Wunused-variable] 21033 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyTableActionAsnRead’: objmacro.c:21210:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21210 | AsnReadFunc func; | ^~~~ objmacro.c:21209:12: warning: unused variable ‘isError’ [-Wunused-variable] 21209 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AddFileActionAsnRead’: objmacro.c:21411:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21411 | AsnReadFunc func; | ^~~~ objmacro.c:21410:12: warning: unused variable ‘isError’ [-Wunused-variable] 21410 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AddDescriptorListActionAsnRead’: objmacro.c:21582:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21582 | AsnReadFunc func; | ^~~~ objmacro.c:21581:12: warning: unused variable ‘isError’ [-Wunused-variable] 21581 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveSequencesActionAsnRead’: objmacro.c:21753:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21753 | AsnReadFunc func; | ^~~~ objmacro.c:21752:12: warning: unused variable ‘isError’ [-Wunused-variable] 21752 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘UpdateReplacedEcNumbersActionAsnRead’: objmacro.c:21911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21911 | AsnReadFunc func; | ^~~~ objmacro.c:21910:12: warning: unused variable ‘isError’ [-Wunused-variable] 21910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RetranslateCdsActionAsnRead’: objmacro.c:22084:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 22084 | AsnReadFunc func; | ^~~~ objmacro.c:22083:12: warning: unused variable ‘isError’ [-Wunused-variable] 22083 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AdjustFeaturesForGapsActionAsnRead’: objmacro.c:22239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 22239 | AsnReadFunc func; | ^~~~ objmacro.c:22238:12: warning: unused variable ‘isError’ [-Wunused-variable] 22238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MacroActionChoiceFree’: objmacro.c:22412:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 22412 | Pointer pnt; | ^~~ objmacro.c: In function ‘MacroActionChoiceAsnRead’: objmacro.c:22522:12: warning: unused variable ‘isError’ [-Wunused-variable] 22522 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SearchFuncFree’: objmacro.c:23116:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 23116 | Pointer pnt; | ^~~ objmacro.c: In function ‘SearchFuncAsnRead’: objmacro.c:23154:12: warning: unused variable ‘isError’ [-Wunused-variable] 23154 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SimpleReplaceAsnRead’: objmacro.c:23425:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23425 | AsnReadFunc func; | ^~~~ objmacro.c:23424:12: warning: unused variable ‘isError’ [-Wunused-variable] 23424 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ReplaceFuncFree’: objmacro.c:23564:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 23564 | Pointer pnt; | ^~~ objmacro.c: In function ‘ReplaceFuncAsnRead’: objmacro.c:23599:12: warning: unused variable ‘isError’ [-Wunused-variable] 23599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ReplaceRuleAsnRead’: objmacro.c:23781:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23781 | AsnReadFunc func; | ^~~~ objmacro.c:23780:12: warning: unused variable ‘isError’ [-Wunused-variable] 23780 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SuspectRuleAsnRead’: objmacro.c:23955:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23955 | AsnReadFunc func; | ^~~~ objmacro.c:23954:12: warning: unused variable ‘isError’ [-Wunused-variable] 23954 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualChoiceAsnRead’: objmacro.c:3806:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3806 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:3732:10: note: ‘choice’ was declared here 3732 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SourceQualValChoiceAsnRead’: objmacro.c:4182:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4182 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:4111:10: note: ‘choice’ was declared here 4111 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘MolinfoFieldAsnRead’: objmacro.c:4679:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4679 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:4598:10: note: ‘choice’ was declared here 4598 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘MolinfoFieldPairAsnRead’: objmacro.c:5883:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5883 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:5820:10: note: ‘choice’ was declared here 5820 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘StructuredCommentFieldAsnRead’: objmacro.c:6371:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 6371 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:6311:10: note: ‘choice’ was declared here 6311 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FieldTypeAsnRead’: objmacro.c:8543:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8543 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8456:10: note: ‘choice’ was declared here 8456 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ConstraintChoiceAsnRead’: objmacro.c:9631:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 9631 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:9548:10: note: ‘choice’ was declared here 9548 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TextTransformAsnRead’: objmacro.c:11149:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 11149 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:11095:10: note: ‘choice’ was declared here 11095 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcGeneralIdAsnRead’: objmacro.c:13133:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13133 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13073:10: note: ‘choice’ was declared here 13073 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixCapsActionAsnRead’: objmacro.c:18363:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 18363 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:18295:10: note: ‘choice’ was declared here 18295 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixFormatActionAsnRead’: objmacro.c:18565:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 18565 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:18498:10: note: ‘choice’ was declared here 18498 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixSetsActionAsnRead’: objmacro.c:20483:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 20483 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:20423:10: note: ‘choice’ was declared here 20423 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘MacroActionChoiceAsnRead’: objmacro.c:22829:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 22829 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:22521:10: note: ‘choice’ was declared here 22521 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationPosConstraintAsnRead’: objmacro.c:1491:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1491 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:1431:10: note: ‘choice’ was declared here 1431 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FeatQualChoiceAsnRead’: objmacro.c:2342:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2342 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:2292:10: note: ‘choice’ was declared here 2292 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘RnaFeatTypeAsnRead’: objmacro.c:3076:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3076 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:2981:10: note: ‘choice’ was declared here 2981 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeAsnRead’: objmacro.c:7076:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 7076 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:7002:10: note: ‘choice’ was declared here 7002 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintAsnRead’: objmacro.c:8768:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8768 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8694:10: note: ‘choice’ was declared here 8694 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘QuantityConstraintAsnRead’: objmacro.c:8963:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8963 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8903:10: note: ‘choice’ was declared here 8903 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TextMarkerAsnRead’: objmacro.c:9970:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 9970 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:9910:10: note: ‘choice’ was declared here 9910 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FieldPairTypeAsnRead’: objmacro.c:10594:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 10594 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:10527:10: note: ‘choice’ was declared here 10527 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ActionChoiceAsnRead’: objmacro.c:12578:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 12578 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:12507:10: note: ‘choice’ was declared here 12507 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcOrgChoiceAsnRead’: objmacro.c:12778:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 12778 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:12725:10: note: ‘choice’ was declared here 12725 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcAsnRead’: objmacro.c:13365:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13365 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13269:10: note: ‘choice’ was declared here 13269 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseDestAsnRead’: objmacro.c:13762:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13762 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13694:10: note: ‘choice’ was declared here 13694 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationChoiceAsnRead’: objmacro.c:14121:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 14121 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:14064:10: note: ‘choice’ was declared here 14064 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SequenceListChoiceAsnRead’: objmacro.c:14418:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 14418 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:14368:10: note: ‘choice’ was declared here 14368 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ConvertFeatureDstOptionsAsnRead’: objmacro.c:15556:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 15556 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:15485:10: note: ‘choice’ was declared here 15485 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationEditTypeAsnRead’: objmacro.c:16859:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 16859 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:16754:10: note: ‘choice’ was declared here 16754 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘CreateTSAIdsSrcAsnRead’: objmacro.c:19958:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 19958 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:19908:10: note: ‘choice’ was declared here 19908 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TableMatchTypeAsnRead’: objmacro.c:20712:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 20712 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:20613:10: note: ‘choice’ was declared here 20613 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SearchFuncAsnRead’: objmacro.c:23259:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 23259 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:23153:10: note: ‘choice’ was declared here 23153 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ReplaceFuncAsnRead’: objmacro.c:23648:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 23648 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:23598:10: note: ‘choice’ was declared here 23598 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objent2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objent2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objent2.c: In function ‘Entrez2IdListAsnRead’: objent2.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objent2.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanExpAsnRead’: objent2.c:277:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 277 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2BooleanElementFree’: objent2.c:416:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 416 | Pointer pnt; | ^~~ objent2.c: In function ‘Entrez2BooleanElementAsnRead’: objent2.c:457:12: warning: unused variable ‘isError’ [-Wunused-variable] 457 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LimitsAsnRead’: objent2.c:666:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 666 | AsnReadFunc func; | ^~~~ objent2.c:665:12: warning: unused variable ‘isError’ [-Wunused-variable] 665 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanTermAsnRead’: objent2.c:844:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 844 | AsnReadFunc func; | ^~~~ objent2.c:843:12: warning: unused variable ‘isError’ [-Wunused-variable] 843 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2RequestAsnRead’: objent2.c:1041:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1041 | AsnReadFunc func; | ^~~~ objent2.c:1040:12: warning: unused variable ‘isError’ [-Wunused-variable] 1040 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘E2RequestFree’: objent2.c:1203:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1203 | Pointer pnt; | ^~~ objent2.c: In function ‘E2RequestAsnRead’: objent2.c:1256:12: warning: unused variable ‘isError’ [-Wunused-variable] 1256 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2EvalBooleanAsnRead’: objent2.c:1493:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1493 | AsnReadFunc func; | ^~~~ objent2.c:1492:12: warning: unused variable ‘isError’ [-Wunused-variable] 1492 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermQueryAsnRead’: objent2.c:1670:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1670 | AsnReadFunc func; | ^~~~ objent2.c:1669:12: warning: unused variable ‘isError’ [-Wunused-variable] 1669 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermPosAsnRead’: objent2.c:1849:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1849 | AsnReadFunc func; | ^~~~ objent2.c:1848:12: warning: unused variable ‘isError’ [-Wunused-variable] 1848 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2HierQueryAsnRead’: objent2.c:2036:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2036 | AsnReadFunc func; | ^~~~ objent2.c:2035:12: warning: unused variable ‘isError’ [-Wunused-variable] 2035 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2GetLinksAsnRead’: objent2.c:2224:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2224 | AsnReadFunc func; | ^~~~ objent2.c:2223:12: warning: unused variable ‘isError’ [-Wunused-variable] 2223 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2IdAsnRead’: objent2.c:2419:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2419 | AsnReadFunc func; | ^~~~ objent2.c:2418:12: warning: unused variable ‘isError’ [-Wunused-variable] 2418 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DtFilterAsnRead’: objent2.c:2584:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2584 | AsnReadFunc func; | ^~~~ objent2.c:2583:12: warning: unused variable ‘isError’ [-Wunused-variable] 2583 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2ReplyAsnRead’: objent2.c:2762:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2762 | AsnReadFunc func; | ^~~~ objent2.c:2761:12: warning: unused variable ‘isError’ [-Wunused-variable] 2761 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘E2ReplyFree’: objent2.c:2935:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2935 | Pointer pnt; | ^~~ objent2.c: In function ‘E2ReplyAsnRead’: objent2.c:2991:12: warning: unused variable ‘isError’ [-Wunused-variable] 2991 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2InfoAsnRead’: objent2.c:3237:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3237 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2BooleanReplyAsnRead’: objent2.c:3409:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3409 | AsnReadFunc func; | ^~~~ objent2.c:3408:12: warning: unused variable ‘isError’ [-Wunused-variable] 3408 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumListAsnRead’: objent2.c:3587:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3587 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2TermListAsnRead’: objent2.c:3749:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3749 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2HierNodeAsnRead’: objent2.c:3922:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3922 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2LinkSetAsnRead’: objent2.c:4122:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4122 | AsnReadFunc func; | ^~~~ objent2.c:4121:12: warning: unused variable ‘isError’ [-Wunused-variable] 4121 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkCountListAsnRead’: objent2.c:4299:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4299 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2DbInfoAsnRead’: objent2.c:4466:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4466 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2FieldInfoAsnRead’: objent2.c:4706:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4706 | AsnReadFunc func; | ^~~~ objent2.c:4705:12: warning: unused variable ‘isError’ [-Wunused-variable] 4705 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkInfoAsnRead’: objent2.c:4950:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4950 | AsnReadFunc func; | ^~~~ objent2.c:4949:12: warning: unused variable ‘isError’ [-Wunused-variable] 4949 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumFieldInfoAsnRead’: objent2.c:5149:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5149 | AsnReadFunc func; | ^~~~ objent2.c:5148:12: warning: unused variable ‘isError’ [-Wunused-variable] 5148 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumAsnRead’: objent2.c:5325:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5325 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2DocsumDataAsnRead’: objent2.c:5488:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5488 | AsnReadFunc func; | ^~~~ objent2.c:5487:12: warning: unused variable ‘isError’ [-Wunused-variable] 5487 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermAsnRead’: objent2.c:5655:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5655 | AsnReadFunc func; | ^~~~ objent2.c:5654:12: warning: unused variable ‘isError’ [-Wunused-variable] 5654 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkCountAsnRead’: objent2.c:5838:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5838 | AsnReadFunc func; | ^~~~ objent2.c:5837:12: warning: unused variable ‘isError’ [-Wunused-variable] 5837 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanElementAsnRead’: objent2.c:524:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 524 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:456:10: note: ‘choice’ was declared here 456 | Uint1 choice; | ^~~~~~ objent2.c: In function ‘E2RequestAsnRead’: objent2.c:1333:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1333 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:1255:10: note: ‘choice’ was declared here 1255 | Uint1 choice; | ^~~~~~ objent2.c: In function ‘E2ReplyAsnRead’: objent2.c:3075:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3075 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:2990:10: note: ‘choice’ was declared here 2990 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ent2api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ent2api.h:45, from ent2api.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pmfapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pmfapi.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pmfapi.c:2813:24: warning: ‘SortByInt4’ defined but not used [-Wunused-function] 2813 | static int LIBCALLBACK SortByInt4 (VoidPtr vp1, VoidPtr vp2) | ^~~~~~~~~~ pmfapi.c: In function ‘ConfirmAccStrInSep’: pmfapi.c:1314:3: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1314 | SeqIdFree (tmp); | ^~~~~~~~~~~~~~~ pmfapi.c:1294:22: note: ‘tmp’ was declared here 1294 | SeqIdPtr sip, tmp; | ^~~ pmfapi.c: In function ‘PubMedSynchronousQuery’: pmfapi.c:1224:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1224 | printf ("PubMedWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1187:19: note: ‘starttime’ was declared here 1187 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQueryEx’: pmfapi.c:1479:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1479 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1434:16: note: ‘starttime’ was declared here 1434 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQueryTI’: pmfapi.c:1663:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1663 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1622:16: note: ‘starttime’ was declared here 1622 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQuerySRA’: pmfapi.c:1744:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1744 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1703:16: note: ‘starttime’ was declared here 1703 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiRevHistSynchronousQuery’: pmfapi.c:1817:61: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1817 | printf ("GiRevHistWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1783:15: note: ‘starttime’ was declared here 1783 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiAccVerSynchronousQuery’: pmfapi.c:1869:60: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1869 | printf ("GiAccVerWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1835:15: note: ‘starttime’ was declared here 1835 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘AccnRevHistSynchronousQuery’: pmfapi.c:1920:63: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1920 | printf ("AccnRevHistWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1885:15: note: ‘starttime’ was declared here 1885 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiSeqIdSetSynchronousQuery’: pmfapi.c:1971:62: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1971 | printf ("GiSeqIdSetWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1936:15: note: ‘starttime’ was declared here 1936 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘AccnListSynchronousQuery’: pmfapi.c:2021:60: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 2021 | printf ("AccnListWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1987:15: note: ‘starttime’ was declared here 1987 | clock_t starttime; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objtax3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtax3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtax3.c: In function ‘Taxon3RequestAsnRead’: objtax3.c:86:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 86 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3RequestFree’: objtax3.c:200:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 200 | Pointer pnt; | ^~~ objtax3.c: In function ‘SequenceOfIntAsnRead’: objtax3.c:418:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 418 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘Taxon3ReplyAsnRead’: objtax3.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3ReplyFree’: objtax3.c:661:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 661 | Pointer pnt; | ^~~ objtax3.c: In function ‘T3ErrorAsnRead’: objtax3.c:872:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 872 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3DataAsnRead’: objtax3.c:1072:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1072 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘Value_valueFree’: objtax3.c:1253:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1253 | Pointer pnt; | ^~~ objtax3.c: In function ‘T3StatusFlagsAsnRead’: objtax3.c:1283:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1283 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3RefreshFlagsAsnRead’: objtax3.c:1608:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1608 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objtax3.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objtax3.c: In function ‘T3RequestAsnRead’: objtax3.c:297:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 297 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c:237:10: note: ‘choice’ was declared here 237 | Uint1 choice; | ^~~~~~ objtax3.c: In function ‘T3ReplyAsnRead’: objtax3.c:741:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 741 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c:695:10: note: ‘choice’ was declared here 695 | Uint1 choice; | ^~~~~~ In function ‘Value_valueAsnRead’, inlined from ‘T3StatusFlagsAsnRead’ at objtax3.c:1326:28: objtax3.c:1421:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1421 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c: In function ‘T3StatusFlagsAsnRead’: objtax3.c:1362:10: note: ‘choice’ was declared here 1362 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tax3api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from tax3api.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tax3api.c: In function ‘Tax3SynchronousQuery’: tax3api.c:189:27: warning: variable ‘t3’ set but not used [-Wunused-but-set-variable] 189 | time_t t1, t2, t3; | ^~ tax3api.c: In function ‘CheckSuggestedFixes’: tax3api.c:1030:20: warning: variable ‘tep’ set but not used [-Wunused-but-set-variable] 1030 | T3ErrorPtr tep; | ^~~ tax3api.c: In function ‘TryNewSuggestedFixes’: tax3api.c:1142:20: warning: variable ‘tep’ set but not used [-Wunused-but-set-variable] 1142 | T3ErrorPtr tep; | ^~~ tax3api.c: In function ‘RemoveSpeciesSpecific’: tax3api.c:1398:13: warning: unused variable ‘cp’ [-Wunused-variable] 1398 | CharPtr cp; | ^~ tax3api.c: At top level: tax3api.c:3399:13: warning: ‘AddBioSourcesToChecklist’ defined but not used [-Wunused-function] 3399 | static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list) | ^~~~~~~~~~~~~~~~~~~~~~~~ tax3api.c:2699:16: warning: ‘MatchesGenBankSynonym’ defined but not used [-Wunused-function] 2699 | static Boolean MatchesGenBankSynonym (CharPtr txt, OrgRefPtr response_org) | ^~~~~~~~~~~~~~~~~~~~~ tax3api.c:2682:16: warning: ‘MatchesSynonym’ defined but not used [-Wunused-function] 2682 | static Boolean MatchesSynonym (CharPtr txt, OrgRefPtr response_org) | ^~~~~~~~~~~~~~ tax3api.c:2273:16: warning: ‘EndsWithSp’ defined but not used [-Wunused-function] 2273 | static Boolean EndsWithSp (CharPtr str) | ^~~~~~~~~~ tax3api.c:990:19: warning: ‘MakeTaxFixRequestList’ defined but not used [-Wunused-function] 990 | static ValNodePtr MakeTaxFixRequestList (ValNodePtr biop_list) | ^~~~~~~~~~~~~~~~~~~~~ tax3api.c:362:16: warning: ‘HasMisspellingFlag’ defined but not used [-Wunused-function] 362 | static Boolean HasMisspellingFlag (T3DataPtr t) | ^~~~~~~~~~~~~~~~~~ tax3api.c:298:13: warning: ‘SaveTaxon3Request’ defined but not used [-Wunused-function] 298 | static void SaveTaxon3Request (Taxon3RequestPtr t3rp, CharPtr path) | ^~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objegkludge.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objegkludge.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objentgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objentgene.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objentgene.c: In function ‘EntrezgeneAsnRead’: objentgene.c:103:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 103 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘EntrezgeneSetAsnRead’: objentgene.c:412:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 412 | AsnReadFunc func; | ^~~~ objentgene.c:409:12: warning: unused variable ‘av’ [-Wunused-variable] 409 | DataVal av; | ^~ objentgene.c: In function ‘GeneTrackAsnRead’: objentgene.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘GeneCommentaryAsnRead’: objentgene.c:768:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 768 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘Method_methodFree’: objentgene.c:1073:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1073 | Pointer pnt; | ^~~ objentgene.c: In function ‘MapsAsnRead’: objentgene.c:1104:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1104 | AsnReadFunc func; | ^~~~ objentgene.c:1103:12: warning: unused variable ‘isError’ [-Wunused-variable] 1103 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘Method_methodAsnRead’: objentgene.c:1184:12: warning: unused variable ‘isError’ [-Wunused-variable] 1184 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘GeneSourceAsnRead’: objentgene.c:1426:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1426 | AsnReadFunc func; | ^~~~ objentgene.c:1425:12: warning: unused variable ‘isError’ [-Wunused-variable] 1425 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘XtraTermsAsnRead’: objentgene.c:1641:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1641 | AsnReadFunc func; | ^~~~ objentgene.c:1640:12: warning: unused variable ‘isError’ [-Wunused-variable] 1640 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘OtherSourceAsnRead’: objentgene.c:1812:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1812 | AsnReadFunc func; | ^~~~ objentgene.c:1811:12: warning: unused variable ‘isError’ [-Wunused-variable] 1811 | Boolean isError = FALSE; | ^~~~~~~ In function ‘Method_methodAsnRead’, inlined from ‘MapsAsnRead’ at objentgene.c:1147:30: objentgene.c:1236:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1236 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objentgene.c: In function ‘MapsAsnRead’: objentgene.c:1183:10: note: ‘choice’ was declared here 1183 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmla2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmla2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmla2.c: In function ‘Mla2RequestFree’: objmla2.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objmla2.c: In function ‘Mla22RequestAsnRead’: objmla2.c:96:12: warning: unused variable ‘isError’ [-Wunused-variable] 96 | Boolean isError = FALSE; | ^~~~~~~ objmla2.c: In function ‘TitleMsg2AsnRead’: objmla2.c:447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 447 | AsnReadFunc func; | ^~~~ objmla2.c:446:12: warning: unused variable ‘isError’ [-Wunused-variable] 446 | Boolean isError = FALSE; | ^~~~~~~ objmla2.c: In function ‘TitleMsgList2AsnRead’: objmla2.c:613:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 613 | AsnReadFunc func; | ^~~~ objmla2.c: In function ‘Mla22RequestAsnRead’: objmla2.c:249:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 249 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla2.c:95:10: note: ‘choice’ was declared here 95 | Uint1 choice; | ^~~~~~ objmla2.c: In function ‘Mla2BackAsnRead’: objmla2.c:904:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 904 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla2.c:787:10: note: ‘choice’ was declared here 787 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mla2api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/mla2api.h:45, from mla2api.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF qblastapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from qblastapi.c:123: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ qblastapi.c: In function ‘SecondQBlastCallback’: qblastapi.c:262:15: warning: variable ‘waiting’ set but not used [-Wunused-but-set-variable] 262 | Boolean waiting = FALSE; | ^~~~~~~ qblastapi.c: In function ‘BLASTGetSeqAnnotByRIDEx’: qblastapi.c:826:18: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 826 | EIO_Status status; | ^~~~~~ qblastapi.c: In function ‘BLASTGetQueryBioseqByRIDEx’: qblastapi.c:871:18: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 871 | EIO_Status status; | ^~~~~~ qblastapi.c: In function ‘QBlastCheckQueue’: qblastapi.c:688:36: warning: ‘&FORMAT_OBJECT=Alignment&FOR...’ directive writing 43 bytes into a region of size between 5 and 68 [-Wformat-overflow=] 688 | sprintf (str, "CMD=Get&RID=%s&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1\n", curr->rid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘QBlastCheckQueue’ at qblastapi.c:688:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 56 and 119 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vecscnapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from vecscnapi.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmim.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmim.c: In function ‘MimSetAsnRead’: objmim.c:86:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 86 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimDateAsnRead’: objmim.c:248:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 248 | AsnReadFunc func; | ^~~~ objmim.c:247:12: warning: unused variable ‘isError’ [-Wunused-variable] 247 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimEntryAsnRead’: objmim.c:448:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 448 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimCitAsnRead’: objmim.c:909:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 909 | AsnReadFunc func; | ^~~~ objmim.c:908:12: warning: unused variable ‘isError’ [-Wunused-variable] 908 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimTextAsnRead’: objmim.c:1096:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1096 | AsnReadFunc func; | ^~~~ objmim.c:1095:12: warning: unused variable ‘isError’ [-Wunused-variable] 1095 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimEditItemAsnRead’: objmim.c:1276:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1276 | AsnReadFunc func; | ^~~~ objmim.c:1275:12: warning: unused variable ‘isError’ [-Wunused-variable] 1275 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimAllelicVariantAsnRead’: objmim.c:1448:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1448 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimIndexTermAsnRead’: objmim.c:1640:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1640 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimReferenceAsnRead’: objmim.c:1819:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1819 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimLinkAsnRead’: objmim.c:2195:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2195 | AsnReadFunc func; | ^~~~ objmim.c:2194:12: warning: unused variable ‘isError’ [-Wunused-variable] 2194 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimAuthorAsnRead’: objmim.c:2369:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2369 | AsnReadFunc func; | ^~~~ objmim.c:2368:12: warning: unused variable ‘isError’ [-Wunused-variable] 2368 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimPageAsnRead’: objmim.c:2535:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2535 | AsnReadFunc func; | ^~~~ objmim.c:2534:12: warning: unused variable ‘isError’ [-Wunused-variable] 2534 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objvalid.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objvalid.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objvalid.c: In function ‘FieldRuleAsnRead’: objvalid.c:88:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 88 | AsnReadFunc func; | ^~~~ objvalid.c:87:12: warning: unused variable ‘isError’ [-Wunused-variable] 87 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘FieldSetAsnRead’: objvalid.c:259:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 259 | AsnReadFunc func; | ^~~~ objvalid.c:256:12: warning: unused variable ‘av’ [-Wunused-variable] 256 | DataVal av; | ^~ objvalid.c: In function ‘DependentFieldRuleAsnRead’: objvalid.c:396:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 396 | AsnReadFunc func; | ^~~~ objvalid.c:395:12: warning: unused variable ‘isError’ [-Wunused-variable] 395 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘DependentFieldSetAsnRead’: objvalid.c:582:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 582 | AsnReadFunc func; | ^~~~ objvalid.c:579:12: warning: unused variable ‘av’ [-Wunused-variable] 579 | DataVal av; | ^~ objvalid.c: In function ‘CommentRuleAsnRead’: objvalid.c:721:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 721 | AsnReadFunc func; | ^~~~ objvalid.c:720:12: warning: unused variable ‘isError’ [-Wunused-variable] 720 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘CommentSetAsnRead’: objvalid.c:926:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 926 | AsnReadFunc func; | ^~~~ objvalid.c:923:12: warning: unused variable ‘av’ [-Wunused-variable] 923 | DataVal av; | ^~ objvalid.c: In function ‘PhraseListAsnRead’: objvalid.c:1043:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1043 | AsnReadFunc func; | ^~~~ objvalid.c:1040:12: warning: unused variable ‘av’ [-Wunused-variable] 1040 | DataVal av; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mimapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mimapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cddapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqport.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from seqport.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqport.c: In function ‘productLoc_to_locationLoc’: seqport.c:4260:13: warning: variable ‘is_cdregion’ set but not used [-Wunused-but-set-variable] 4260 | Boolean is_cdregion = FALSE; | ^~~~~~~~~~~ seqport.c: In function ‘NaLocFromNaInterval’: seqport.c:4590:8: warning: variable ‘p_end_pos’ set but not used [-Wunused-but-set-variable] 4590 | Int4 p_end_pos; /*the end of the product sequence in the current loc*/ | ^~~~~~~~~ seqport.c: In function ‘dnaLoc_to_aaLoc’: seqport.c:4706:18: warning: variable ‘cds_right’ set but not used [-Wunused-but-set-variable] 4706 | Int4 cds_left, cds_right; | ^~~~~~~~~ seqport.c:4706:8: warning: variable ‘cds_left’ set but not used [-Wunused-but-set-variable] 4706 | Int4 cds_left, cds_right; | ^~~~~~~~ seqport.c: In function ‘DeltaRevComp’: seqport.c:5388:21: warning: variable ‘dspnext’ set but not used [-Wunused-but-set-variable] 5388 | DeltaSeqPtr dsp, dspnext; | ^~~~~~~ seqport.c: In function ‘SeqSearchEnterNucWord’: seqport.c:6943:18: warning: variable ‘patLen’ set but not used [-Wunused-but-set-variable] 6943 | Int2 next, patLen, state; | ^~~~~~ seqport.c: In function ‘ProtSearchEnterProtWord’: seqport.c:7817:18: warning: variable ‘patLen’ set but not used [-Wunused-but-set-variable] 7817 | Int2 next, patLen, state; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from seqport.c:62: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sequtil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from sequtil.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequtil.c: In function ‘GetPointsForLeftAndRightOffsets’: sequtil.c:7994:11: warning: variable ‘first_strand’ set but not used [-Wunused-but-set-variable] 7994 | Uint1 first_strand, last_strand; | ^~~~~~~~~~~~ sequtil.c: In function ‘SeqPointWriteEx’: sequtil.c:8532:15: warning: variable ‘fuzzlen’ set but not used [-Wunused-but-set-variable] 8532 | Int4 fuzzlen, id_len; | ^~~~~~~ sequtil.c: In function ‘TaxNameFromCommon’: sequtil.c:8687:42: warning: missing braces around initializer [-Wmissing-braces] 8687 | static Nlm_TaxCommon taxcommon[40] = { | ^ 8688 | "Chinese hamsters", "Cricetulus sp." | { 8689 | ,"Syrian golden hamsters", "Mesocricetus auratus" | }{ 8690 | ,"Syrian hamsters", "Mesocricetus sp." | }{ 8691 | ,"barley", "Hordeum sp." | }{ 8692 | ,"carrots", "Daucus sp." | }{ 8693 | ,"cats", "Felis sp." | }{ 8694 | ,"cattles", "Bos sp." | }{ 8695 | ,"chickens", "Gallus sp." | }{ 8696 | ,"chimpanzees", "Pan sp." | }{ 8697 | ,"chimpanzes", "Pan sp." | }{ 8698 | ,"corn", "Zea sp." | }{ 8699 | ,"cucumber", "Cucumis sativus" | }{ 8700 | ,"dogs", "Canis sp." | }{ 8701 | ,"goats", "Capra sp." | }{ 8702 | ,"gorillas", "Gorilla sp." | }{ 8703 | ,"guinea pigs", "Cavia sp." | }{ 8704 | ,"hamsters", "Cricetidae gen. sp." | }{ 8705 | ,"horses", "Equus sp." | }{ 8706 | ,"humans", "Homo sapiens" | }{ 8707 | ,"maize", "Zea sp." | }{ 8708 | ,"mice", "Mus sp." | }{ 8709 | ,"mouse", "Mus sp." | }{ 8710 | ,"peas", "Pisum sp." | }{ 8711 | ,"potatoes", "Solanum sp." | }{ 8712 | ,"potato", "Solanum sp." | }{ 8713 | ,"quails", "Phasianidae gen. sp." | }{ 8714 | ,"rabbits", "Oryctolagus sp." | }{ 8715 | ,"rats", "Rattus sp." | }{ 8716 | ,"rices", "Oryza sp." | }{ 8717 | ,"sheeps", "Ovis sp." | }{ 8718 | ,"sorghums", "Sorghum sp." | }{ 8719 | ,"soybeans", "Glycine sp." | }{ 8720 | ,"spinach", "Spinacia sp." | }{ 8721 | ,"swine", "Sus sp." | }{ 8722 | ,"tobacco", "Nicotiania sp." | }{ 8723 | ,"tomatoes", "Lycopersicon sp." | }{ 8724 | ,"tomato", "Lycopersicon sp." | }{ 8725 | ,"turkeys", "Meleagris sp." | }{ 8726 | ,"wheat", "Triticum sp." | }{ 8727 | ,"zebrafish", "Brachydanio sp." | }{ 8728 | }; | } sequtil.c: In function ‘GetBestScoreAndEvalueFromScorePtr’: sequtil.c:9510:48: warning: variable ‘sum_set’ set but not used [-Wunused-but-set-variable] 9510 | Boolean score_set=FALSE, evalue_set=FALSE, sum_set=FALSE, bit_set=FALSE; | ^~~~~~~ sequtil.c: In function ‘SeqIdFromAccessionEx’: sequtil.c:10110:38: warning: variable ‘sip2’ set but not used [-Wunused-but-set-variable] 10110 | SeqIdPtr sip2; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prtutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objprt.h:67, from ../include/prtutil.h:69, from prtutil.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prtutil.c: In function ‘StdFormatPrint’: prtutil.c:1422:17: warning: unused variable ‘ptr’ [-Wunused-variable] 1422 | CharPtr ptr = NULL; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF simple.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/simple.h:63, from simple.c:68: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from simple.c:69: ../include/all.h:7293: warning: "RNA_QUAL" redefined 7293 | #define RNA_QUAL &at[2254] | ../include/all.h:5823: note: this is the location of the previous definition 5823 | #define RNA_QUAL &at[1025] | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tofasta.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/tofasta.h:47, from tofasta.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tofasta.c: In function ‘DoSpecialDefline’: tofasta.c:1461:22: warning: variable ‘gene’ set but not used [-Wunused-but-set-variable] 1461 | SeqFeatPtr gene = NULL; | ^~~~ tofasta.c: In function ‘FastaIdEx’: tofasta.c:3100:15: warning: variable ‘sip’ set but not used [-Wunused-but-set-variable] 3100 | SeqIdPtr sip; | ^~~ tofasta.c: In function ‘CreateDefLineExEx’: tofasta.c:4991:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4991 | if (vnp != NULL) | ^~ tofasta.c:4993:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4993 | if (title != NULL) { | ^~ tofasta.c: In function ‘x_SetSuffix’: tofasta.c:8313:24: warning: variable ‘buf2’ set but not used [-Wunused-but-set-variable] 8313 | Char buf1 [512], buf2 [256]; | ^~~~ tofasta.c: In function ‘FastaToSeqEntryInternalExEx’: tofasta.c:2838:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2838 | fgets(buffer+1, BuffSize, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c:2863:13: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2863 | fgets(buffer+i+1, FTSE_BUFF_CHUNK, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c: At top level: tofasta.c:8058:17: warning: ‘x_StringInList’ defined but not used [-Wunused-function] 8058 | static Boolean x_StringInList ( | ^~~~~~~~~~~~~~ tofasta.c:3661:19: warning: ‘GatherGenesForCDS’ defined but not used [-Wunused-function] 3661 | static ValNodePtr GatherGenesForCDS(SeqLocPtr slp) | ^~~~~~~~~~~~~~~~~ tofasta.c:3627:19: warning: ‘GatherSeqFeatProt’ defined but not used [-Wunused-function] 3627 | static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~ tofasta.c:3541:19: warning: ‘GetCDSProtUnindexed’ defined but not used [-Wunused-function] 3541 | static SeqFeatPtr GetCDSProtUnindexed ( | ^~~~~~~~~~~~~~~~~~~ tofasta.c:3378:19: warning: ‘IndexedGatherDescrOnBioseq’ defined but not used [-Wunused-function] 3378 | static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c:3283:16: warning: ‘get_descr’ defined but not used [-Wunused-function] 3283 | static Boolean get_descr (GatherContextPtr gcp) | ^~~~~~~~~ tofasta.c:3254:16: warning: ‘get_descr_on_top’ defined but not used [-Wunused-function] 3254 | static Boolean get_descr_on_top (GatherContextPtr gcp) | ^~~~~~~~~~~~~~~~ tofasta.c: In function ‘FastaReadSequenceInternalEx’: tofasta.c:2578:43: warning: ‘mask_to’ may be used uninitialized [-Wmaybe-uninitialized] 2578 | mask_sint->to = mask_to; | ~~~~~~~~~~~~~~^~~~~~~~~ tofasta.c:2512:20: note: ‘mask_to’ was declared here 2512 | Int4 mask_to; | ^~~~~~~ tofasta.c: In function ‘FastaToSeqEntryInternalExEx’: tofasta.c:2866:29: warning: ‘firstchar’ may be used uninitialized [-Wmaybe-uninitialized] 2866 | for(i =0; (ch = *firstchar) != NULLB; firstchar++, i++) { | ^~~~~~~~~~ tofasta.c:2774:25: note: ‘firstchar’ was declared here 2774 | const Char PNTR firstchar; | ^~~~~~~~~ tofasta.c:2954:13: warning: ‘fd’ may be used uninitialized [-Wmaybe-uninitialized] 2954 | ungetc(ch, fd); | ^~~~~~~~~~~~~~ tofasta.c:2773:21: note: ‘fd’ was declared here 2773 | FILE *fd; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tofile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from tofile.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tomedlin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmedli.h:80, from tomedlin.c:153: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF valid.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from valid.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valid.c: In function ‘GetUserFieldValueString’: valid.c:2212:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 2212 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld valid.c: In function ‘ValidateSeqIdCase’: valid.c:3574:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 3574 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘ValidateGenProdSet’: valid.c:6046:19: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 6046 | GeneRefPtr grp; | ^~~ valid.c: In function ‘CountAdjacentProc’: valid.c:6730:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 6730 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘CheckBioseqEndsForNAndGap’: valid.c:7040:44: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 7040 | if (str [0] == 'n' || str [0] == 'N' && begin_n != NULL) { | ^ valid.c:7061:56: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 7061 | if (str [len - 1] == 'n' || str [len - 1] == 'N' && end_n != NULL) { | ^ valid.c: In function ‘ValidateBioseqInst’: valid.c:7341:19: warning: variable ‘tech’ set but not used [-Wunused-but-set-variable] 7341 | Uint1 tech; | ^~~~ valid.c:7278:19: warning: variable ‘prot’ set but not used [-Wunused-but-set-variable] 7278 | SeqFeatPtr prot; | ^~~~ valid.c: In function ‘FixOrgModVoucher’: valid.c:13882:22: warning: unused variable ‘allowed_type’ [-Wunused-variable] 13882 | Uint1 type = 0, allowed_type = 0; | ^~~~~~~~~~~~ valid.c: In function ‘ValidateBioSource’: valid.c:15514:19: warning: variable ‘isMicrosporidia’ set but not used [-Wunused-but-set-variable] 15514 | Boolean isMicrosporidia = FALSE; | ^~~~~~~~~~~~~~~ valid.c:15512:19: warning: variable ‘isEukaryote’ set but not used [-Wunused-but-set-variable] 15512 | Boolean isEukaryote = FALSE; | ^~~~~~~~~~~ valid.c:15503:19: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 15503 | Int4 id; | ^~ valid.c: In function ‘ValidateDblink’: valid.c:16786:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 16786 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘ValidateSeqDescrCommon’: valid.c:16883:19: warning: variable ‘pdp’ set but not used [-Wunused-but-set-variable] 16883 | PubdescPtr pdp; | ^~~ valid.c: In function ‘GetFeatsInGaps’: valid.c:18858:21: warning: variable ‘realBases’ set but not used [-Wunused-but-set-variable] 18858 | Int4 realBases; | ^~~~~~~~~ valid.c:18857:21: warning: variable ‘plusses’ set but not used [-Wunused-but-set-variable] 18857 | Int4 plusses; | ^~~~~~~ valid.c:18854:21: warning: variable ‘Ns’ set but not used [-Wunused-but-set-variable] 18854 | Int4 Ns; | ^~ valid.c:18851:21: warning: variable ‘dashes’ set but not used [-Wunused-but-set-variable] 18851 | Int4 dashes; | ^~~~~~ valid.c: In function ‘ValidateBioseqContextIndexed’: valid.c:20267:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 20267 | if (bvsp->is_mrna || cdscount == 1 && genecount < 2) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ valid.c:19476:65: warning: variable ‘cdsmgene’ set but not used [-Wunused-but-set-variable] 19476 | SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene; | ^~~~~~~~ valid.c:19476:33: warning: variable ‘cdspgene’ set but not used [-Wunused-but-set-variable] 19476 | SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene; | ^~~~~~~~ valid.c:19475:51: warning: variable ‘utr5minus’ set but not used [-Wunused-but-set-variable] 19475 | SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus; | ^~~~~~~~~ valid.c:19475:41: warning: variable ‘utr3plus’ set but not used [-Wunused-but-set-variable] 19475 | SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus; | ^~~~~~~~ valid.c:19442:41: warning: variable ‘utr3gene’ set but not used [-Wunused-but-set-variable] 19442 | SeqFeatPtr cdsgene, utr5gene, utr3gene; | ^~~~~~~~ valid.c: In function ‘ReportBadWGSGap’: valid.c:21153:18: warning: unused variable ‘is_wgs’ [-Wunused-variable] 21153 | Boolean is_wgs = FALSE; | ^~~~~~ valid.c: In function ‘ValidateBarcodeIndexNumber’: valid.c:21432:21: warning: variable ‘bin_len’ set but not used [-Wunused-but-set-variable] 21432 | Int4 bin_len; | ^~~~~~~ valid.c: In function ‘ValidateRptUnit’: valid.c:23411:32: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 23411 | Boolean badchars, found, just_nuc_letters, multi_rpt_unit, in_range; | ^~~~~ valid.c: In function ‘CheckForCommonCDSProduct’: valid.c:25628:19: warning: variable ‘is_nw’ set but not used [-Wunused-but-set-variable] 25628 | Boolean is_nw = FALSE; | ^~~~~ valid.c:25625:19: warning: variable ‘is_nc’ set but not used [-Wunused-but-set-variable] 25625 | Boolean is_nc = FALSE; | ^~~~~ valid.c: In function ‘CheckForIllegalDbxref’: valid.c:26017:16: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 26017 | Int4 id; | ^~ valid.c: In function ‘ValidateAnticodon’: valid.c:26781:53: warning: variable ‘circular’ set but not used [-Wunused-but-set-variable] 26781 | ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE; | ^~~~~~~~ valid.c:26780:19: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 26780 | Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE, | ^~~~~~ valid.c: In function ‘IsGeneXrefRedundant’: valid.c:28000:17: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 28000 | Int2 count; | ^~~~~ valid.c: In function ‘ValidateSeqFeat’: valid.c:28328:19: warning: unused variable ‘is_nc’ [-Wunused-variable] 28328 | Boolean is_nc = FALSE; | ^~~~~ valid.c:28308:19: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 28308 | Int2 count; | ^~~~~ valid.c:28286:19: warning: variable ‘pdp’ set but not used [-Wunused-but-set-variable] 28286 | PubdescPtr pdp; | ^~~ valid.c: In function ‘CdTransCheck’: valid.c:30490:19: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 30490 | GeneRefPtr grp; | ^~~ valid.c: In function ‘SpliceCheckEx’: valid.c:31313:19: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 31313 | SeqEntryPtr sep; | ^~~ valid.c: In function ‘CdsProductIdCheck’: valid.c:31689:15: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 31689 | GeneRefPtr grp; | ^~~ valid.c: In function ‘ValidateSeqLoc’: valid.c:31754:19: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 31754 | Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE, | ^~~~~~ valid.c:31753:24: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 31753 | SeqLocPtr tmp, prev; | ^~~~ valid.c: In function ‘SortSeqGraphProc’: valid.c:32156:26: warning: self-comparison always evaluates to false [-Wtautological-compare] 32156 | } else if (gip2->right < gip2->right) { | ^ valid.c: At top level: valid.c:30138:13: warning: ‘ValidateTranslExcept’ defined but not used [-Wunused-function] 30138 | static void ValidateTranslExcept ( | ^~~~~~~~~~~~~~~~~~~~ valid.c:27650:16: warning: ‘CouldExtendPartial’ defined but not used [-Wunused-function] 27650 | static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5) | ^~~~~~~~~~~~~~~~~~ valid.c:20878:28: warning: ‘MultiGeneOverlapFree’ defined but not used [-Wunused-function] 20878 | static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m) | ^~~~~~~~~~~~~~~~~~~~ valid.c:20828:19: warning: ‘ListFeaturesContainedInLocation’ defined but not used [-Wunused-function] 20828 | static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ valid.c:17541:16: warning: ‘IsEMBLAccn’ defined but not used [-Wunused-function] 17541 | static Boolean IsEMBLAccn (SeqEntryPtr sep, SeqLocPtr location) | ^~~~~~~~~~ valid.c:14642:16: warning: ‘CountryIsClosestToLatLon’ defined but not used [-Wunused-function] 14642 | static Boolean CountryIsClosestToLatLon ( | ^~~~~~~~~~~~~~~~~~~~~~~~ valid.c:14545:16: warning: ‘LatLonInRange’ defined but not used [-Wunused-function] 14545 | static Boolean LatLonInRange ( | ^~~~~~~~~~~~~ valid.c:13478:16: warning: ‘LatLonIsValid’ defined but not used [-Wunused-function] 13478 | static Boolean LatLonIsValid (CharPtr name) | ^~~~~~~~~~~~~ valid.c:10462:16: warning: ‘ConsistentWithC’ defined but not used [-Wunused-function] 10462 | static Boolean ConsistentWithC (Char ch) | ^~~~~~~~~~~~~~~ valid.c:6952:13: warning: ‘ReportLongSeqId’ defined but not used [-Wunused-function] 6952 | static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len) | ^~~~~~~~~~~~~~~ valid.c:5932:13: warning: ‘CheckMutSetSources’ defined but not used [-Wunused-function] 5932 | static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata) | ^~~~~~~~~~~~~~~~~~ valid.c:4360:13: warning: ‘FindLongIdsThatCollideWhenTruncated’ defined but not used [-Wunused-function] 4360 | static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ valid.c:1511:16: warning: ‘IsNotUnclassifiedExcept’ defined but not used [-Wunused-function] 1511 | static Boolean IsNotUnclassifiedExcept (ValidStructPtr vsp) | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF valapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from valapi.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valapi.c: In function ‘DoesStringMatchExpression’: valapi.c:263:15: warning: variable ‘errstr’ set but not used [-Wunused-but-set-variable] 263 | const char *errstr; | ^~~~~~ valapi.c: In function ‘DoesFieldValueMatchExpression’: valapi.c:292:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 292 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF alignmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/alignmgr.h:261, from alignmgr.c:584: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignmgr.c: In function ‘AlnMgrIndexParentSA’: alignmgr.c:1607:19: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1607 | sap->saip = (Pointer)AMAlignIndexFree(amaip); | ^ alignmgr.c: In function ‘AlnMgrGetNthBlockRange’: alignmgr.c:4182:21: warning: variable ‘amaip’ set but not used [-Wunused-but-set-variable] 4182 | AMAlignIndexPtr amaip; | ^~~~~ alignmgr.c: In function ‘AlnMgrMakeFakeMultipleEx’: alignmgr.c:5157:21: warning: variable ‘nogap’ set but not used [-Wunused-but-set-variable] 5157 | Boolean nogap; | ^~~~~ alignmgr.c: In function ‘AlnMgrMapBioseqToBioseq’: alignmgr.c:10840:19: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 10840 | Uint1 gap; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignmgr.c:10572:16: warning: ‘am_merge_after_edit’ defined but not used [-Wunused-function] 10572 | static Boolean am_merge_after_edit (SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~ alignmgr.c:6650:16: warning: ‘AlnMgrJaggedIndex’ defined but not used [-Wunused-function] 6650 | static Boolean AlnMgrJaggedIndex(SeqAlignPtr sap, AMmsmsPtr ams_head, AMmsmsPtr *ams_mhead, Int4 numrows) | ^~~~~~~~~~~~~~~~~ alignmgr.c:6123:18: warning: ‘AlnMgrConstructOverlaps’ defined but not used [-Wunused-function] 6123 | static AMmsmsPtr AlnMgrConstructOverlaps(AMmsmsPtr ams_head) | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:5405:13: warning: ‘AlnMgrMergeNeighbors’ defined but not used [-Wunused-function] 5405 | static void AlnMgrMergeNeighbors(SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~ alignmgr.c: In function ‘AlnMgrUnpackSeqAlign’: alignmgr.c:1149:33: warning: ‘sap_segs_prev’ may be used uninitialized [-Wmaybe-uninitialized] 1149 | sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:1117:17: note: ‘sap_segs_prev’ was declared here 1117 | SeqAlignPtr sap_segs_prev; | ^~~~~~~~~~~~~ alignmgr.c: In function ‘am_print_seqalign_indexes’: alignmgr.c:2436:27: warning: ‘amaip’ may be used uninitialized [-Wmaybe-uninitialized] 2436 | for (i=0; inumbsqs; i++) | ~~~~~^~~~~~~~~ alignmgr.c:2389:21: note: ‘amaip’ was declared here 2389 | AMAlignIndexPtr amaip; | ^~~~~ alignmgr.c:2409:31: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 2409 | printf("%d ", saip->aligncoords[i]); | ~~~~^~~~~~~~~~~~~ alignmgr.c:2393:21: note: ‘saip’ was declared here 2393 | SAIndexPtr saip; | ^~~~ alignmgr.c: In function ‘AlnMgrGetNthSeqRangeInSA’: alignmgr.c:4113:20: warning: ‘tmp_beg’ may be used uninitialized [-Wmaybe-uninitialized] 4113 | *start = tmp_beg; | ~~~~~~~^~~~~~~~~ alignmgr.c:3974:21: note: ‘tmp_beg’ was declared here 3974 | Int4 tmp_beg; | ^~~~~~~ alignmgr.c:4115:19: warning: ‘tmp_end’ may be used uninitialized [-Wmaybe-uninitialized] 4115 | *stop = tmp_end; | ~~~~~~^~~~~~~~~ alignmgr.c:3975:21: note: ‘tmp_end’ was declared here 3975 | Int4 tmp_end; | ^~~~~~~ alignmgr.c: In function ‘AlnMgrGetSubAlign’: alignmgr.c:9097:17: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 9097 | salp = am_cleanupsalp(salp); | ^~~~~~~~~~~~~~~~~~~~ alignmgr.c:8885:21: note: ‘salp’ was declared here 8885 | SeqAlignPtr salp; | ^~~~ In function ‘am_find_master’, inlined from ‘AlnMgrMakeMultByIntersectOnMaster’ at alignmgr.c:5588:17: alignmgr.c:5865:15: warning: ‘sip_head’ may be used uninitialized [-Wmaybe-uninitialized] 5865 | while (sip && !done) | ~~~~^~~~~~~~ alignmgr.c: In function ‘AlnMgrMakeMultByIntersectOnMaster’: alignmgr.c:5845:18: note: ‘sip_head’ was declared here 5845 | SeqIdPtr sip_head; | ^~~~~~~~ alignmgr.c:5589:7: warning: ‘sip_tmp’ may be used uninitialized [-Wmaybe-uninitialized] 5589 | if (sip_tmp == NULL) | ^ alignmgr.c:5553:17: note: ‘sip_tmp’ was declared here 5553 | SeqIdPtr sip_tmp; | ^~~~~~~ alignmgr.c: In function ‘am_is_consistent’: alignmgr.c:10114:13: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 10114 | AlnMgrGetNthUnalignedForNthRow(sap, n, i, &u_start, &u_stop); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:10009:21: note: ‘n’ was declared here 10009 | Int4 n; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF aliparse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/aliparse.h:12, from aliparse.c:9: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ aliparse.c: In function ‘s_IsInterleaved’: aliparse.c:929:51: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 929 | (s_configInfo.useMaybes == FALSE) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 930 | (seqLinePtr->maybe == FALSE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:823:20: warning: variable ‘isMaybe’ set but not used [-Wunused-but-set-variable] 823 | Boolean isMaybe; | ^~~~~~~ aliparse.c: In function ‘s_ProcessInterId’: aliparse.c:1000:15: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1000 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_ProcessInterSeq’: aliparse.c:1090:15: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1090 | ErrInfoPtr errPtr = NULL; | ^~~~~~ aliparse.c: In function ‘s_AnalyzeInterleaved’: aliparse.c:1193:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1193 | (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘s_ProcessContigId’: aliparse.c:1385:18: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1385 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_ProcessContigSeq’: aliparse.c:1476:18: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1476 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_AnalyzeContiguous’: aliparse.c:1603:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1603 | (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘s_CheckContext’: aliparse.c:2150:47: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2150 | (seqLinePtr->maybe == TRUE) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2151 | (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:2131:20: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 2131 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘PrintOutMultAlign’: aliparse.c:3161:10: warning: statement with no effect [-Wunused-value] 3161 | for (d; dnext = newSeqPart; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ aliparse.c:633:18: note: ‘lastSeqPart’ was declared here 633 | SeqPartPtr lastSeqPart; | ^~~~~~~~~~~ aliparse.c:641:10: warning: ‘newIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 641 | if (idStr != NULL) | ^ aliparse.c:543:20: note: ‘newIdStr’ was declared here 543 | CharPtr newIdStr; | ^~~~~~~~ aliparse.c:669:39: warning: ‘currentIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 669 | currentId->id = currentIdStr; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ aliparse.c:631:18: note: ‘currentIdStr’ was declared here 631 | CharPtr currentIdStr; | ^~~~~~~~~~~~ In function ‘s_CheckContext’, inlined from ‘Ali_Read’ at aliparse.c:2565:7: aliparse.c:2294:25: warning: ‘newIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 2294 | if ((lastRow != NULL) && | ~~~~~~~~~~~~~~~~~~^~ 2295 | ((idStr = s_GetRowIdString (lastRow)) != NULL) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:543:20: note: ‘newIdStr’ was declared here 543 | CharPtr newIdStr; | ^~~~~~~~ In function ‘s_DisplayRowList’, inlined from ‘Ali_Read’ at aliparse.c:2568:3: aliparse.c:760:17: warning: ‘cLineType’ may be used uninitialized [-Wmaybe-uninitialized] 760 | fprintf(stderr,"%04d: MAYBE SEQUENCE[%c] : %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 761 | seqLinePtr->rowNum, | ~~~~~~~~~~~~~~~~~~~ 762 | cLineType, | ~~~~~~~~~~ 763 | seqLinePtr->sequence); | ~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:723:20: note: ‘cLineType’ was declared here 723 | Char cLineType; | ^~~~~~~~~ In function ‘s_IsInterleaved’, inlined from ‘s_AnalyzeContents’ at aliparse.c:2004:7, inlined from ‘Ali_Read’ at aliparse.c:2572:3: aliparse.c:927:25: warning: ‘seqLinePtr’ may be used uninitialized [-Wmaybe-uninitialized] 927 | if (seqLinePtr->sequence != NULL) | ~~~~~~~~~~^~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:820:20: note: ‘seqLinePtr’ was declared here 820 | SeqLineInfoPtr seqLinePtr; | ^~~~~~~~~~ In function ‘s_AnalyzeInterleaved’, inlined from ‘s_AnalyzeContents’ at aliparse.c:2007:16, inlined from ‘Ali_Read’ at aliparse.c:2572:3: aliparse.c:1352:50: warning: ‘previousLength’ may be used uninitialized [-Wmaybe-uninitialized] 1352 | if ((s_configInfo.declaredInfo.seqLength != 0) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 1353 | (s_configInfo.declaredInfo.seqLength != previousLength)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:1154:20: note: ‘previousLength’ was declared here 1154 | Int4 previousLength; | ^~~~~~~~~~~~~~ aliparse.c: In function ‘ALI_ConvertToNCBIData’: aliparse.c:3276:4: warning: ‘sep_new’ may be used uninitialized [-Wmaybe-uninitialized] 3276 | SeqAlignAddInSeqEntry (sep_head, sanp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:2974:18: note: ‘sep_new’ was declared here 2974 | SeqEntryPtr sep_new; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF aliread.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from aliread.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/aliparse.h:15, from aliread.c:6: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF alignval.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from alignval.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignval.c: In function ‘ValidateSeqlengthInDenseSeg’: alignval.c:1267:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1267 | if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen) | ^ alignval.c: In function ‘PercentStringMatch’: alignval.c:1579:32: warning: variable ‘max_len’ set but not used [-Wunused-but-set-variable] 1579 | Int4 len1, len2, min_len, k, max_len; | ^~~~~~~ alignval.c: In function ‘CheckAlnSeqLens’: alignval.c:2004:12: warning: variable ‘aln_len’ set but not used [-Wunused-but-set-variable] 2004 | Int4 aln_len, start, stop; | ^~~~~~~ alignval.c: In function ‘ValidateSeqAlign’: alignval.c:2125:16: warning: variable ‘ans’ set but not used [-Wunused-but-set-variable] 2125 | MsgAnswer ans; | ^~~ alignval.c: In function ‘GetAlignmentColumnPercentIdentities’: alignval.c:2511:14: warning: variable ‘num_match’ set but not used [-Wunused-but-set-variable] 2511 | Int4 num_match; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from alignval.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignval.c:2002:13: warning: ‘CheckAlnSeqLens’ defined but not used [-Wunused-function] 2002 | static void CheckAlnSeqLens (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~ alignval.c:1560:16: warning: ‘IsSipContainedInStdseg’ defined but not used [-Wunused-function] 1560 | static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp) | ^~~~~~~~~~~~~~~~~~~~~~ alignval.c:602:13: warning: ‘delete_bioseqs’ defined but not used [-Wunused-function] 602 | static void delete_bioseqs (ValNodePtr ids, Uint2 entityID) | ^~~~~~~~~~~~~~ alignval.c: In function ‘ValMessage’: alignval.c:465:92: warning: ‘, the alignment claims to co...’ directive writing 195 bytes into a region of size between 155 and 493 [-Wformat-overflow=] 465 | sprintf(string2, "In sequence %s, segment %ld (near sequence position %ld) context %s, the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment", buf, (long) Intvalue, (long) pos, buf3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ValMessage’ at alignval.c:465:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 255 and 593 bytes into a destination of size 552 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ alignval.c: In function ‘ValMessage’: alignval.c:448:92: warning: ‘, the alignment claims to co...’ directive writing 195 bytes into a region of size between 155 and 493 [-Wformat-overflow=] 448 | sprintf(string2, "In sequence %s, segment %ld (near sequence position %ld) context %s, the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment", buf, (long) Intvalue, (long) pos, buf3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘ValMessage’ at alignval.c:448:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 255 and 593 bytes into a destination of size 552 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil1.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil1.c: In function ‘GeneExtendFunc’: sqnutil1.c:2012:18: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 2012 | GeneRefPtr grp; | ^~~ sqnutil1.c: In function ‘ParseAnticodon’: sqnutil1.c:3494:14: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 3494 | Uint1 strand; | ^~~~~~ sqnutil1.c: In function ‘ParseCodeBreak’: sqnutil1.c:3617:17: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 3617 | Uint1 strand; | ^~~~~~ sqnutil1.c: In function ‘CleanUpPubdescAuthors’: sqnutil1.c:9093:20: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 9093 | ValNodePtr PNTR prev; | ^~~~ sqnutil1.c: In function ‘FixWrongFuzzOnPlusStrand’: sqnutil1.c:11948:15: warning: unused variable ‘spp’ [-Wunused-variable] 11948 | SeqPntPtr spp; | ^~~ sqnutil1.c: In function ‘FixWrongFuzzOnMinusStrand’: sqnutil1.c:12007:15: warning: unused variable ‘spp’ [-Wunused-variable] 12007 | SeqPntPtr spp; | ^~~ sqnutil1.c: In function ‘ConsolidateBioSourceNotes’: sqnutil1.c:13250:21: warning: variable ‘note_mod’ set but not used [-Wunused-but-set-variable] 13250 | OrgModPtr mod, note_mod; | ^~~~~~~~ sqnutil1.c:13249:21: warning: variable ‘note_ssp’ set but not used [-Wunused-but-set-variable] 13249 | SubSourcePtr ssp, note_ssp; | ^~~~~~~~ sqnutil1.c: In function ‘RemoveUnnecessaryGeneXrefs’: sqnutil1.c:15059:24: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 15059 | Int2 count; | ^~~~~ sqnutil1.c: In function ‘LinkTwoFeatures’: sqnutil1.c:17930:25: warning: variable ‘prev_xref’ set but not used [-Wunused-but-set-variable] 17930 | SeqFeatXrefPtr xref, prev_xref, next_xref; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil1.c:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil1.c:10386:16: warning: ‘CleanUpSgml’ defined but not used [-Wunused-function] 10386 | static CharPtr CleanUpSgml ( | ^~~~~~~~~~~ sqnutil1.c:10272:13: warning: ‘SortGoTermsSfp’ defined but not used [-Wunused-function] 10272 | static void SortGoTermsSfp ( | ^~~~~~~~~~~~~~ sqnutil1.c:7405:16: warning: ‘IsStringSingleToken’ defined but not used [-Wunused-function] 7405 | static Boolean IsStringSingleToken (CharPtr str) | ^~~~~~~~~~~~~~~~~~~ sqnutil1.c:4942:13: warning: ‘CleanupConsSplice’ defined but not used [-Wunused-function] 4942 | static void CleanupConsSplice (GBQualPtr gbq) | ^~~~~~~~~~~~~~~~~ sqnutil1.c:2007:16: warning: ‘GeneExtendFunc’ defined but not used [-Wunused-function] 2007 | static Boolean GeneExtendFunc (GatherContextPtr gcp) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil2.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil2.c: In function ‘FindResidueByName’: sqnutil2.c:5223:11: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 5223 | Uint1 last; | ^~~~ sqnutil2.c: In function ‘ReadFeatureTableEx’: sqnutil2.c:7254:18: warning: variable ‘isnote’ set but not used [-Wunused-but-set-variable] 7254 | Boolean isnote; | ^~~~~~ sqnutil2.c:7246:18: warning: variable ‘endsinspace’ set but not used [-Wunused-but-set-variable] 7246 | Boolean endsinspace; | ^~~~~~~~~~~ sqnutil2.c: In function ‘SeqEntryCopyReplace’: sqnutil2.c:9270:15: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 9270 | Uint1 type = 0; | ^~~~ sqnutil2.c: In function ‘StreamingReadBioseq’: sqnutil2.c:10095:10: warning: variable ‘level’ set but not used [-Wunused-but-set-variable] 10095 | Int2 level; | ^~~~~ sqnutil2.c: In function ‘StreamAsnForDescriptors’: sqnutil2.c:10328:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 10328 | while (rval = StreamingReadSeqEntry (aip, sp, &sr)) { | ^~~~ sqnutil2.c: In function ‘WriteAsnWithReplacedDescriptors’: sqnutil2.c:10749:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 10749 | while (rval = StreamingReadWriteSeqEntry(desc_stream_list, aip_in, aip_out, sp)) { | ^~~~ sqnutil2.c: In function ‘ReadFeatureTableFile’: sqnutil2.c:11700:18: warning: variable ‘begin’ set but not used [-Wunused-but-set-variable] 11700 | Int4 begin; | ^~~~~ sqnutil2.c: In function ‘ReadFastaOnly’: sqnutil2.c:11894:18: warning: variable ‘seqid’ set but not used [-Wunused-but-set-variable] 11894 | Char seqid [2048]; | ^~~~~ sqnutil2.c: In function ‘ReadDeltaFastaWithEmptyDefline’: sqnutil2.c:12446:29: warning: variable ‘seqid’ set but not used [-Wunused-but-set-variable] 12446 | Char line [4096], seqid [2048]; | ^~~~~ sqnutil2.c: In function ‘SortSeqGraphProc’: sqnutil2.c:13002:26: warning: self-comparison always evaluates to false [-Wtautological-compare] 13002 | } else if (gip2->right < gip2->right) { | ^ sqnutil2.c: In function ‘PrintQualityScoresToBuffer’: sqnutil2.c:13052:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 13052 | Uint2 entityID; | ^~~~~~~~ sqnutil2.c: In function ‘GetScoresbySeqId’: sqnutil2.c:13461:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 13461 | Uint2 entityID; | ^~~~~~~~ sqnutil2.c: In function ‘RemoveGapsFromDeltaLocation’: sqnutil2.c:15480:15: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 15480 | Uint1 strand; | ^~~~~~ sqnutil2.c: In function ‘IsStringInSpanInList’: sqnutil2.c:16693:11: warning: variable ‘str_val’ set but not used [-Wunused-but-set-variable] 16693 | Int4 str_val; | ^~~~~~~ sqnutil2.c:16691:27: warning: variable ‘suffix_len’ set but not used [-Wunused-but-set-variable] 16691 | Int4 prefix_len = 0, suffix_len; | ^~~~~~~~~~ sqnutil2.c: In function ‘CreateStructuredCommentsFromFile’: sqnutil2.c:18415:35: warning: variable ‘vnp_h’ set but not used [-Wunused-but-set-variable] 18415 | ValNodePtr table, header, line, vnp_h, vnp_l, tmp; | ^~~~~ sqnutil2.c: In function ‘AlignmentIntervalToString’: sqnutil2.c:18779:14: warning: variable ‘target_strand’ set but not used [-Wunused-but-set-variable] 18779 | Uint1 target_strand; | ^~~~~~~~~~~~~ sqnutil2.c:18778:14: warning: variable ‘seq_len’ set but not used [-Wunused-but-set-variable] 18778 | Int4 seq_len; | ^~~~~~~ sqnutil2.c: In function ‘AdjustForConsensusSpliceCallback’: sqnutil2.c:20313:33: warning: variable ‘partial5_last’ set but not used [-Wunused-but-set-variable] 20313 | Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE; | ^~~~~~~~~~~~~ sqnutil2.c: In function ‘RemoveGIProc’: sqnutil2.c:20926:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 20926 | SeqIdPtr nextid, sip; | ^~~~~~ sqnutil2.c: In function ‘RemoveBadCodonRecognizedCallback’: sqnutil2.c:22812:13: warning: variable ‘rcodon’ set but not used [-Wunused-but-set-variable] 22812 | Uint1 rcodon [4]; | ^~~~~~ sqnutil2.c: In function ‘CompareStructuredComment’: sqnutil2.c:25151:23: warning: variable ‘ovp2’ set but not used [-Wunused-but-set-variable] 25151 | ObjValNodePtr ovp1, ovp2; | ^~~~ sqnutil2.c:25151:17: warning: variable ‘ovp1’ set but not used [-Wunused-but-set-variable] 25151 | ObjValNodePtr ovp1, ovp2; | ^~~~ sqnutil2.c: In function ‘UniqueAndCountValNodeCS’: sqnutil2.c:25546:17: warning: variable ‘curr’ set but not used [-Wunused-but-set-variable] 25546 | ValNodePtr curr; | ^~~~ sqnutil2.c: In function ‘PerformArticleQuery’: sqnutil2.c:25810:20: warning: variable ‘debug_mode’ set but not used [-Wunused-but-set-variable] 25810 | Boolean debug_mode = FALSE; | ^~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil2.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil2.c:18065:19: warning: ‘AuthAffilListFree’ defined but not used [-Wunused-function] 18065 | static ValNodePtr AuthAffilListFree (ValNodePtr list) | ^~~~~~~~~~~~~~~~~ sqnutil2.c:18044:21: warning: ‘AuthAffilNew’ defined but not used [-Wunused-function] 18044 | static AuthAffilPtr AuthAffilNew (CharPtr affil) | ^~~~~~~~~~~~ sqnutil2.c:16282:19: warning: ‘MakeTranscriptomeIDTokensFromLine’ defined but not used [-Wunused-function] 16282 | static ValNodePtr MakeTranscriptomeIDTokensFromLine (CharPtr line) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil2.c:16188:13: warning: ‘RevCompFeatsOnBioseq’ defined but not used [-Wunused-function] 16188 | static void RevCompFeatsOnBioseq (BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~ sqnutil2.c:8333:16: warning: ‘DoesSeqEntryAccessionMatchList’ defined but not used [-Wunused-function] 8333 | static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil2.c:4684:16: warning: ‘IsNonSeqChar’ defined but not used [-Wunused-function] 4684 | static Boolean IsNonSeqChar (Char ch, Boolean is_prot) | ^~~~~~~~~~~~ sqnutil2.c: In function ‘DoAddToSecAccn’: sqnutil2.c:2429:28: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 2429 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ sqnutil2.c:2429:27: note: directive argument in the range [-2147483648, 2147483647] 2429 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DoAddToSecAccn’ at sqnutil2.c:2429:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘DoAddToSeqHist’: sqnutil2.c:2593:28: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 2593 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ sqnutil2.c:2593:27: note: directive argument in the range [-2147483648, 2147483647] 2593 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In function ‘sprintf’, inlined from ‘DoAddToSeqHist’ at sqnutil2.c:2593:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘ReplaceLocalID’: sqnutil2.c:23605:22: warning: ‘%d’ directive writing between 1 and 6 bytes into a region of size between 5 and 68 [-Wformat-overflow=] 23605 | sprintf (tmp, "%s__%d", str, (int) count); | ^~ sqnutil2.c:23605:17: note: directive argument in the range [-32768, 32767] 23605 | sprintf (tmp, "%s__%d", str, (int) count); | ^~~~~~~~ In function ‘sprintf’, inlined from ‘ReplaceLocalID’ at sqnutil2.c:23605:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 72 bytes into a destination of size 70 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘AdjustSeqEntryForConsensusSpliceBioseqCallback’: sqnutil2.c:20313:48: warning: ‘partial3_last’ may be used uninitialized [-Wmaybe-uninitialized] 20313 | Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE; | ^~~~~~~~~~~~~ sqnutil2.c: In function ‘PrintQualityScoresToBuffer’: sqnutil2.c:13110:47: warning: ‘, Max: ’ directive writing 7 bytes into a region of size between 2 and 63 [-Wformat-overflow=] 13110 | sprintf (buf, ">%s %s (Length: %ld, Min: %ld, Max: %ld)\n", id, title, | ^~~~~~~ sqnutil2.c:13110:17: note: directive argument in the range [-2147483647, 2147483647] 13110 | sprintf (buf, ">%s %s (Length: %ld, Min: %ld, Max: %ld)\n", id, title, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintQualityScoresToBuffer’ at sqnutil2.c:13110:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 32 or more bytes (assuming 103) into a destination of size 84 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil3.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil3.c: In function ‘BspLinkCDSmRNAbyOverlap’: sqnutil3.c:528:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 528 | Int2 count; | ^~~~~ sqnutil3.c: In function ‘CautiousSeqEntryCleanup’: sqnutil3.c:2178:16: warning: variable ‘taxserver’ set but not used [-Wunused-but-set-variable] 2178 | Boolean taxserver; | ^~~~~~~~~ sqnutil3.c: In function ‘AddGapSeqLit’: sqnutil3.c:3127:19: warning: unused variable ‘gap_chars’ [-Wunused-variable] 3127 | CharPtr gap_chars = "NNNNNNNNNN" | ^~~~~~~~~ sqnutil3.c: In function ‘ConvertSegSetsToDeltaSequencesInt’: sqnutil3.c:3382:26: warning: variable ‘prev_sep’ set but not used [-Wunused-but-set-variable] 3382 | SeqEntryPtr sub_sep, prev_sep, next_sep; | ^~~~~~~~ sqnutil3.c: In function ‘MakeSequinDataFromAlignmentEx’: sqnutil3.c:4797:32: warning: variable ‘num_sets’ set but not used [-Wunused-but-set-variable] 4797 | Int4 index, curr_seg, num_sets; | ^~~~~~~~ sqnutil3.c:4791:26: warning: variable ‘salp_last’ set but not used [-Wunused-but-set-variable] 4791 | SeqAlignPtr salp_list, salp_last; | ^~~~~~~~~ sqnutil3.c:4791:15: warning: variable ‘salp_list’ set but not used [-Wunused-but-set-variable] 4791 | SeqAlignPtr salp_list, salp_last; | ^~~~~~~~~ sqnutil3.c: In function ‘ConvertContainedCDSToMiscFeat’: sqnutil3.c:12824:14: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 12824 | Uint1 strand; | ^~~~~~ sqnutil3.c: In function ‘OrgNameMatchExceptOldName’: sqnutil3.c:13713:28: warning: self-comparison always evaluates to false [-Wtautological-compare] 13713 | || onp2->mgcode != onp2->mgcode | ^~ sqnutil3.c: In function ‘FindMismatchedCitSubAffiliations’: sqnutil3.c:19281:14: warning: variable ‘has_seq_submit’ set but not used [-Wunused-but-set-variable] 19281 | Boolean has_seq_submit = TRUE; | ^~~~~~~~~~~~~~ sqnutil3.c: In function ‘GetCDSformRNA’: sqnutil3.c:20267:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 20267 | Int2 count; | ^~~~~ sqnutil3.c: In function ‘FindTextInFlatfileOncaller’: sqnutil3.c:22140:19: warning: variable ‘okay’ set but not used [-Wunused-but-set-variable] 22140 | Boolean okay; | ^~~~ sqnutil3.c: In function ‘CheckForTitleAuthorConflicts’: sqnutil3.c:23168:14: warning: variable ‘author_conflict’ set but not used [-Wunused-but-set-variable] 23168 | Boolean author_conflict = FALSE; | ^~~~~~~~~~~~~~~ sqnutil3.c: In function ‘SortVnpByBspProjectId’: sqnutil3.c:26956:31: warning: the comparison will always evaluate as ‘true’ for the address of ‘vnp2’ will never be NULL [-Waddress] 26956 | if (vnp1 != NULL &&& vnp2 != NULL) { | ^~ sqnutil3.c:26948:15: note: ‘vnp2’ declared here 26948 | ValNodePtr vnp2; | ^~~~ sqnutil3.c: In function ‘GetDiscrepancyItemTextEx’: sqnutil3.c:31033:21: warning: variable ‘special_flag’ set but not used [-Wunused-but-set-variable] 31033 | Boolean special_flag = FALSE; | ^~~~~~~~~~~~ sqnutil3.c: In function ‘CollectionDateIsInTheFuture’: sqnutil3.c:34586:20: warning: variable ‘time’ set but not used [-Wunused-but-set-variable] 34586 | CharPtr str, time; | ^~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil3.c:62: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35189:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35189 | system (cmmd); | ^~~~~~~~~~~~~ sqnutil3.c: At top level: sqnutil3.c:36777:13: warning: ‘TestLatLonFormatting’ defined but not used [-Wunused-function] 36777 | static void TestLatLonFormatting (FILE *fp) | ^~~~~~~~~~~~~~~~~~~~ sqnutil3.c:34406:22: warning: ‘BetterDateFree’ defined but not used [-Wunused-function] 34406 | static BetterDatePtr BetterDateFree (BetterDatePtr dp) | ^~~~~~~~~~~~~~ sqnutil3.c:33998:16: warning: ‘GetColon’ defined but not used [-Wunused-function] 33998 | static CharPtr GetColon (CharPtr str) | ^~~~~~~~ sqnutil3.c:17224:24: warning: ‘IntervalPairFree’ defined but not used [-Wunused-function] 17224 | static IntervalPairPtr IntervalPairFree (IntervalPairPtr i) | ^~~~~~~~~~~~~~~~ sqnutil3.c:10883:16: warning: ‘IsMitochondrionBioseq’ defined but not used [-Wunused-function] 10883 | static Boolean IsMitochondrionBioseq(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~~ sqnutil3.c: In function ‘tRNASameStrandBioseqCallback’: sqnutil3.c:16757:19: warning: ‘strand’ may be used uninitialized [-Wmaybe-uninitialized] 16757 | if ((strand == Seq_strand_minus && this_strand != Seq_strand_minus) sqnutil3.c:16728:22: note: ‘strand’ was declared here 16728 | Uint1 strand, this_strand; | ^~~~~~ sqnutil3.c: In function ‘CheckForDivConflicts’: sqnutil3.c:8137:21: warning: ‘sdp’ may be used uninitialized [-Wmaybe-uninitialized] 8137 | ValNodeAddPointer(&(grp_sdp_sfp[i]), OBJ_SEQDESC, sdp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil3.c:8087:17: note: ‘sdp’ was declared here 8087 | SeqDescrPtr sdp; | ^~~ sqnutil3.c:8138:15: warning: ‘sfp’ may be used uninitialized [-Wmaybe-uninitialized] 8138 | else ValNodeAddPointer(&(grp_sdp_sfp[i]), OBJ_SEQFEAT, sfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil3.c:8088:17: note: ‘sfp’ was declared here 8088 | SeqFeatPtr sfp; | ^~~ sqnutil3.c: In function ‘FindMismatchedComments’: sqnutil3.c:26612:47: warning: ‘sdp’ may be used uninitialized [-Wmaybe-uninitialized] 26612 | sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue); | ~~~~~~~~~^~~~~~~~~ sqnutil3.c:26580:15: note: ‘sdp’ was declared here 26580 | SeqDescrPtr sdp; | ^~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35188:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 252 [-Wformat-overflow=] 35188 | sprintf (cmmd, "%s -i %s -o %s", tracefetchcmd, path_in, path_out); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FillInMissingTraces’ at sqnutil3.c:35188:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 9 or more bytes (assuming 8199) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35188:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 252 [-Wformat-overflow=] 35188 | sprintf (cmmd, "%s -i %s -o %s", tracefetchcmd, path_in, path_out); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘FillInMissingTraces’ at sqnutil3.c:35188:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 9 or more bytes (assuming 8199) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sqnutil4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil4.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil4.c: In function ‘ListClauses’: sqnutil4.c:8566:43: warning: variable ‘twobefore’ set but not used [-Wunused-but-set-variable] 8566 | FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter; | ^~~~~~~~~ sqnutil4.c: In function ‘SmashOneTallClause’: sqnutil4.c:9900:20: warning: variable ‘subclause_featlist’ set but not used [-Wunused-but-set-variable] 9900 | ValNodePtr subclause_featlist; | ^~~~~~~~~~~~~~~~~~ sqnutil4.c: In function ‘GetFeatureClauseForSeg’: sqnutil4.c:10787:21: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 10787 | Int4 start, stop; | ^~~~~ sqnutil4.c: In function ‘RemoveAutodefObjectsForDesc’: sqnutil4.c:13618:18: warning: unused variable ‘bssp’ [-Wunused-variable] 13618 | BioseqSetPtr bssp; | ^~~~ sqnutil4.c:13617:15: warning: unused variable ‘bsp’ [-Wunused-variable] 13617 | BioseqPtr bsp; | ^~~ sqnutil4.c: In function ‘ConvertProtToImpFunc’: sqnutil4.c:15072:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 15072 | Uint2 entityID; | ^~~~~~~~ sqnutil4.c: In function ‘ExtraCDSCreationActions’: sqnutil4.c:15989:28: warning: variable ‘nsep’ set but not used [-Wunused-but-set-variable] 15989 | SeqEntryPtr psep, nsep; | ^~~~ sqnutil4.c: In function ‘TESTDisplayQualCombo’: sqnutil4.c:17099:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 17099 | Int4 val; | ^~~ sqnutil4.c: In function ‘ConvertCDSToMatPeptideForOverlappingCDS’: sqnutil4.c:18589:15: warning: variable ‘crp’ set but not used [-Wunused-but-set-variable] 18589 | CdRegionPtr crp; | ^~~ sqnutil4.c: In function ‘AddNewUniqueAnnotations’: sqnutil4.c:18780:39: warning: variable ‘sap_tmp_next’ set but not used [-Wunused-but-set-variable] 18780 | SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap; | ^~~~~~~~~~~~ sqnutil4.c: In function ‘AssignBioseqToLineageGroup’: sqnutil4.c:19443:27: warning: variable ‘vnp_last’ set but not used [-Wunused-but-set-variable] 19443 | ValNodePtr list, vnp, vnp_last = NULL; | ^~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from sqnutil4.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sqnutil4.c:64: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sqnutil4.c:17248:13: warning: ‘TESTDisplayList’ defined but not used [-Wunused-function] 17248 | static void TESTDisplayList (ValNodePtr new_list) | ^~~~~~~~~~~~~~~ sqnutil4.c:17219:19: warning: ‘ExpandOneComboListUsingAllPresentQuals’ defined but not used [-Wunused-function] 17219 | static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil4.c:16930:16: warning: ‘RemoveFieldFromUniqBioSrcGrpList’ defined but not used [-Wunused-function] 16930 | static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil4.c:10029:19: warning: ‘RemoveAllButLastCDS’ defined but not used [-Wunused-function] 10029 | static ValNodePtr RemoveAllButLastCDS ( | ^~~~~~~~~~~~~~~~~~~ sqnutil4.c:9998:13: warning: ‘SmashTallClauses’ defined but not used [-Wunused-function] 9998 | static void SmashTallClauses ( | ^~~~~~~~~~~~~~~~ sqnutil4.c:9834:13: warning: ‘RemoveFeats’ defined but not used [-Wunused-function] 9834 | static void RemoveFeats ( | ^~~~~~~~~~~ sqnutil4.c:5211:13: warning: ‘CountFeatures’ defined but not used [-Wunused-function] 5211 | static Int4 CountFeatures ( | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF subutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from ../include/subutil.h:50, from subutil.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ subutil.c: In function ‘AddSeqLitToBioseq’: subutil.c:769:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 769 | ValNodePtr vnp; | ^~~ subutil.c: In function ‘AddReferenceToSegmentedEntry’: subutil.c:1163:22: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 1163 | SeqEntryPtr tmp, prev; | ^~~~ subutil.c: In function ‘GetDNAConv’: subutil.c:1624:16: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1624 | dnaconv[*ptr] = *ptr; | ^~~~ subutil.c: In function ‘GetProteinConv’: subutil.c:1646:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1646 | protconv[*ptr] = *ptr; | ^~~~ subutil.c: In function ‘AddBasesToByteStore’: subutil.c:1669:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1669 | residue = dnaconv[ch]; | ^ subutil.c: In function ‘AddAAsToByteStore’: subutil.c:1700:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1700 | residue = aaconv[ch]; | ^ subutil.c: In function ‘CitArtBuild’: subutil.c:2683:21: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 2683 | ValNodePtr vnp, tmp; | ^~~ subutil.c: In function ‘MakeRNAFeature’: subutil.c:3639:29: warning: comparison between pointer and zero character constant [-Wpointer-compare] 3639 | if (AA_for_tRNA != '\0') | ^~ subutil.c:3639:17: note: did you mean to dereference the pointer? 3639 | if (AA_for_tRNA != '\0') | ^ subutil.c: At top level: subutil.c:3546:20: warning: ‘TranslateCdRegionNew’ defined but not used [-Wunused-function] 3546 | static SeqEntryPtr TranslateCdRegionNew ( | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF edutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/edutil.h:188, from edutil.c:365: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ edutil.c: In function ‘SeqLocsToDeltaSeqs’: edutil.c:795:14: warning: variable ‘sip’ set but not used [-Wunused-but-set-variable] 795 | SeqIdPtr sip; | ^~~ edutil.c: In function ‘SeqLocCopyPart’: edutil.c:2243:13: warning: variable ‘done’ set but not used [-Wunused-but-set-variable] 2243 | Boolean done, started, wasa_null, hada_null; | ^~~~ edutil.c: In function ‘IndexedSeqFeatsCopy’: edutil.c:2400:16: warning: variable ‘region’ set but not used [-Wunused-but-set-variable] 2400 | ValNodePtr region; | ^~~~~~ edutil.c: In function ‘SeqFeatsCopy’: edutil.c:2504:16: warning: variable ‘region’ set but not used [-Wunused-but-set-variable] 2504 | ValNodePtr region; | ^~~~~~ edutil.c: In function ‘SeqLocInsert’: edutil.c:3686:10: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 3686 | Int4 diff, numpnt, i, tpos; | ^~~~ edutil.c: In function ‘SeqEdRecreateDeletedFeats’: edutil.c:4212:19: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 4212 | SeqFeatPtr sfp; | ^~~ edutil.c: In function ‘SeqEdSeqLocInsert’: edutil.c:4512:8: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 4512 | Int4 diff, numpnt, i, tpos; | ^~~~ edutil.c: In function ‘SeqEdSeqLocDelete’: edutil.c:5069:10: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 5069 | Int4 diff; | ^~~~ edutil.c: In function ‘SeqEdInsertAdjustFeat’: edutil.c:5300:7: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 5300 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c: In function ‘SeqEdDeleteFromBsp’: edutil.c:6485:11: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6485 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c:6548:11: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6548 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c:6437:21: warning: variable ‘merge_mode’ set but not used [-Wunused-but-set-variable] 6437 | Boolean merge_mode; | ^~~~~~~~~~ edutil.c:6428:21: warning: variable ‘feats_altered’ set but not used [-Wunused-but-set-variable] 6428 | Boolean feats_altered = FALSE; | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from asn2ff1.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff1.c: In function ‘asn2ff_print’: asn2ff1.c:289:25: warning: unused variable ‘dsp’ [-Wunused-variable] 289 | DescrStructPtr dsp = NULL; | ^~~ asn2ff1.c: In function ‘Asn2ffJobCreate’: asn2ff1.c:351:25: warning: unused variable ‘itemID’ [-Wunused-variable] 351 | Uint4 itemID = 0; | ^~~~~~ asn2ff1.c: In function ‘SeqEntryToEntrez’: asn2ff1.c:498:41: warning: unused variable ‘slp’ [-Wunused-variable] 498 | SeqLocPtr slp = NULL; | ^~~ asn2ff1.c: In function ‘SeqLocToFlat’: asn2ff1.c:1518:26: warning: unused variable ‘itemID’ [-Wunused-variable] 1518 | Uint4 itemID=0; | ^~~~~~ asn2ff1.c: In function ‘asn2ff_setup’: asn2ff1.c:1579:19: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 1579 | BioseqPtr bsp; | ^~~ asn2ff1.c: In function ‘PrintStatusLine’: asn2ff1.c:2197:36: warning: unused variable ‘ptr’ [-Wunused-variable] 2197 | CharPtr u, ptr=NULL; | ^~~ asn2ff1.c: In function ‘asn2gb_setup’: asn2ff1.c:2403:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2403 | if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) { asn2ff1.c: At top level: asn2ff1.c:2189:13: warning: ‘PrintStatusLine’ defined but not used [-Wunused-function] 2189 | static void PrintStatusLine(Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~~~~~~ asn2ff1.c:2171:16: warning: ‘find_user_object’ defined but not used [-Wunused-function] 2171 | static Boolean find_user_object(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~ asn2ff1.c:816:19: warning: ‘SeqEntryToLinkStrEx’ defined but not used [-Wunused-function] 816 | static LinkStrPtr SeqEntryToLinkStrEx(Asn2ffJobPtr ajp, SeqEntryPtr sep, LinkStrPtr lsp, Uint1 format) | ^~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from asn2ff1.c:45: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff1.c: In function ‘print_taxinfo’: asn2ff1.c:4356:33: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 4356 | sprintf(tmp, "%d", gcode); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘print_taxinfo’ at asn2ff1.c:4356:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff1.c: In function ‘asn2embl_setup’: asn2ff1.c:2753:36: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized] 2753 | for (index=0; index< max; index++) { | ~~~~~^~~~~ asn2ff1.c:2642:21: note: ‘max’ was declared here 2642 | Int4 index, max, total, pub_num, seqblks_num; | ^~~ asn2ff1.c: In function ‘asn2gp_setup’: asn2ff1.c:2942:45: warning: ‘feat_num’ may be used uninitialized [-Wmaybe-uninitialized] 2942 | for (index=0; index < feat_num; index++) { | ~~~~~~^~~~~~~~~~ asn2ff1.c:2795:14: note: ‘feat_num’ was declared here 2795 | Int4 feat_num; | ^~~~~~~~ asn2ff1.c: In function ‘SeqEntryToGBFlatNoSeq’: asn2ff1.c:1307:20: warning: ‘rsult’ may be used uninitialized [-Wmaybe-uninitialized] 1307 | return rsult; | ^~~~~ asn2ff1.c:1292:19: note: ‘rsult’ was declared here 1292 | Boolean rsult; | ^~~~~ asn2ff1.c: In function ‘PrintSequence’: asn2ff1.c:5218:67: warning: ‘%9ld’ directive writing between 9 and 11 bytes into a region of size 10 [-Wformat-overflow=] 5218 | sprintf(num_ptr, "%9ld", (long) (total+1 - loc_start)); | ^~~~ asn2ff1.c:5218:66: note: directive argument in the range [-2147483648, 2147483647] 5218 | sprintf(num_ptr, "%9ld", (long) (total+1 - loc_start)); | ^~~~~~ In function ‘sprintf’, inlined from ‘PrintSequence’ at asn2ff1.c:5218:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 10 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from asn2ff2.c:216: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff2.c: In function ‘GetStrForBankit’: asn2ff2.c:518:33: warning: unused variable ‘i’ [-Wunused-variable] 518 | Int2 i=0, ptrlen = 0; | ^ asn2ff2.c: In function ‘GetCommentByChoice’: asn2ff2.c:769:41: warning: unused variable ‘string’ [-Wunused-variable] 769 | CharPtr buf = NULL, ptr = NULL, string=NULL, new_string=NULL, str=NULL; | ^~~~~~ asn2ff2.c: In function ‘GP_GetSeqDescrComms’: asn2ff2.c:1163:17: warning: unused variable ‘got_comment’ [-Wunused-variable] 1163 | Boolean got_comment=FALSE; | ^~~~~~~~~~~ asn2ff2.c: At top level: asn2ff2.c:1358:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 1358 | static ChoicePID(SeqIdPtr sid) | ^~~~~~~~~ asn2ff2.c: In function ‘GetGibbsqCommentLength’: asn2ff2.c:1600:14: warning: unused variable ‘gibbsq’ [-Wunused-variable] 1600 | Int4 gibbsq=0, total; | ^~~~~~ asn2ff2.c: In function ‘GatherDescrByChoice’: asn2ff2.c:1864:15: warning: variable ‘bspID’ set but not used [-Wunused-but-set-variable] 1864 | Uint2 bspID; | ^~~~~ asn2ff2.c: At top level: asn2ff2.c:1190:16: warning: ‘GetSPBlock’ defined but not used [-Wunused-function] 1190 | static CharPtr GetSPBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~ asn2ff2.c:680:16: warning: ‘GetEvidence’ defined but not used [-Wunused-function] 680 | static CharPtr GetEvidence(Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~~ asn2ff2.c:232:16: warning: ‘has_comment’ defined but not used [-Wunused-variable] 232 | static Boolean has_comment; | ^~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from asn2ff2.c:218: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff2.c: In function ‘GetCommentByChoice’: asn2ff2.c:829:36: warning: ‘is_other’ may be used uninitialized [-Wmaybe-uninitialized] 829 | if (is_other == TRUE && mfp->completeness) { | ^ asn2ff2.c:772:17: note: ‘is_other’ was declared here 772 | Boolean is_other; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff3.c:39: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff3.c: In function ‘PutGeneFirst’: asn2ff3.c:1073:33: warning: unused variable ‘qual_temp’ [-Wunused-variable] 1073 | GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL; | ^~~~~~~~~ asn2ff3.c:1072:17: warning: unused variable ‘still_looking’ [-Wunused-variable] 1072 | Boolean still_looking=TRUE; | ^~~~~~~~~~~~~ asn2ff3.c: In function ‘mRNAEvidenceComment’: asn2ff3.c:1157:33: warning: unused variable ‘Locus_id’ [-Wunused-variable] 1157 | Int4 Locus_id = 0; | ^~~~~~~~ asn2ff3.c: In function ‘Add_gene_id’: asn2ff3.c:2717:31: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘Nlm_VoidPtr’ {aka ‘void *’} [-Wformat=] 2717 | sprintf(val, "GeneID:%s", vnp->data.ptrvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | char * Nlm_VoidPtr {aka void *} | %p asn2ff3.c: In function ‘Add_trid’: asn2ff3.c:3123:16: warning: unused variable ‘gi’ [-Wunused-variable] 3123 | BIG_ID gi = -1; | ^~ asn2ff3.c: At top level: asn2ff3.c:2702:13: warning: ‘Add_gene_id’ defined but not used [-Wunused-function] 2702 | static void Add_gene_id (GeneStructPtr gsp, SeqFeatPtr sfp_out) | ^~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff3.c: In function ‘Add_dbxref’: asn2ff3.c:269:24: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 269 | if (val[0] != '\0') { | ~~~^~~ asn2ff3.c:216:17: note: ‘val’ was declared here 216 | CharPtr val; | ^~~ asn2ff3.c: In function ‘GettRNAaa’: asn2ff3.c:1618:28: warning: ‘seq_code’ may be used uninitialized [-Wmaybe-uninitialized] 1618 | if ((table=SeqCodeTableFind (seq_code)) != NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2ff3.c:1596:15: note: ‘seq_code’ was declared here 1596 | Uint1 seq_code; | ^~~~~~~~ In file included from ../include/ncbi.h:62: asn2ff3.c: In function ‘mRNAEvidenceComment’: ../include/ncbistr.h:331:25: warning: ‘ne_name’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen asn2ff3.c:1153:53: note: ‘ne_name’ was declared here 1153 | CharPtr method = NULL, ptr, ne_name; | ^~~~~~~ asn2ff3.c: In function ‘ConvertToNAImpFeat’: asn2ff3.c:2254:51: warning: ‘%ld’ directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=] 2254 | sprintf(buf_ptr, "%ld", (long) (cdr->frame)); | ^~~ asn2ff3.c:2254:50: note: directive argument in the range [1, 255] 2254 | sprintf(buf_ptr, "%ld", (long) (cdr->frame)); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ConvertToNAImpFeat’ at asn2ff3.c:2254:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 2 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff4.c:273: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff4.c: In function ‘FlatLocPoint’: asn2ff4.c:437:22: warning: variable ‘order’ set but not used [-Wunused-but-set-variable] 437 | static Uint1 order[NUM_SEQID]; | ^~~~~ asn2ff4.c: In function ‘FlatLocElement’: asn2ff4.c:778:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 778 | if (ASN2FF_SHOW_ERROR_MSG == TRUE) | ^~ asn2ff4.c:781:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 781 | break; | ^~~~~ asn2ff4.c: In function ‘do_FlatLoc’: asn2ff4.c:1122:28: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1122 | if ( ! FlatVirtLoc( bsp, slp)) | ^ asn2ff4.c: At top level: asn2ff4.c:1347:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 1347 | static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) | ^~~~~~~~~~ asn2ff4.c: In function ‘CreateImpFeatFromProt’: asn2ff4.c:1659:33: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 1659 | GeneRefPtr grp; | ^~~ asn2ff4.c: In function ‘is_embl’: asn2ff4.c:2069:43: warning: the comparison will always evaluate as ‘false’ for the address of ‘accession’ will never be NULL [-Waddress] 2069 | if (gbp == NULL || gbp->accession == NULL) | ^~ ../include/asn2ffg.h:339:14: note: ‘accession’ declared here 339 | Char accession[60]; /* primary accession */ | ^~~~~~~~~ asn2ff4.c: In function ‘MatchNAGeneToFeat’: asn2ff4.c:2196:25: warning: variable ‘nsp’ set but not used [-Wunused-but-set-variable] 2196 | NoteStructPtr nsp; /* UNUSED */ | ^~~ asn2ff4.c: In function ‘MatchAAGeneToFeat’: asn2ff4.c:2367:33: warning: variable ‘nsp’ set but not used [-Wunused-but-set-variable] 2367 | NoteStructPtr nsp; /* UNUSED */ | ^~~ asn2ff4.c: In function ‘SortOrganizeFeat’: asn2ff4.c:2457:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2457 | if (ofp == NULL) | ^~ asn2ff4.c:2459:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2459 | if (ofp->sfpListsize > 0 && ofp->sortListsize < ofp->sfpListsize) { | ^~ asn2ff4.c: In function ‘OrganizeSeqFeat’: asn2ff4.c:2578:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2578 | if (ajp->ignore_top) | ^~ asn2ff4.c:2580:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2580 | gsc.seglevels = 1; | ^~~ asn2ff4.c: In function ‘GetSeqFeat’: asn2ff4.c:2660:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘locus’ will never be NULL [-Waddress] 2660 | if (gbp->locus) { | ^~~ ../include/asn2ffg.h:338:14: note: ‘locus’ declared here 338 | Char locus[25]; /* locus */ | ^~~~~ asn2ff4.c:2664:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘accession’ will never be NULL [-Waddress] 2664 | if (gbp->accession) { | ^~~ ../include/asn2ffg.h:339:14: note: ‘accession’ declared here 339 | Char accession[60]; /* primary accession */ | ^~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h: At top level: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff4.c: In function ‘CheckNewSfpLoc’: asn2ff4.c:1766:13: warning: ‘slp’ may be used uninitialized [-Wmaybe-uninitialized] 1766 | if (SeqIdForSameBioseq(SeqLocId(slp), bsp->id)) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2ff4.c:1761:19: note: ‘slp’ was declared here 1761 | SeqLocPtr slp, slp1 = NULL; | ^~~ asn2ff4.c: In function ‘FlatLocHalfCaret’: asn2ff4.c:388:63: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 2 and 22 [-Wformat-overflow=] 388 | sprintf(localbuf,"(%ld.%ld)..(%ld.%ld)", | ^~~ asn2ff4.c:388:50: note: directive argument in the range [-2147483648, 2147483647] 388 | sprintf(localbuf,"(%ld.%ld)..(%ld.%ld)", | ^~~~~~~~~~~~~~~~~~~~~~ asn2ff4.c:388:50: note: directive argument in the range [-2147483648, 2147483647] In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FlatLocHalfCaret’ at asn2ff4.c:388:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 53 bytes into a destination of size 30 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff4.c: In function ‘CreateImpFeatFromProt’: asn2ff4.c:1723:39: warning: ‘%d’ directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=] 1723 | sprintf(buf, "%d", cdr->frame); | ^~ asn2ff4.c:1723:38: note: directive argument in the range [1, 255] 1723 | sprintf(buf, "%d", cdr->frame); | ^~~~ In function ‘sprintf’, inlined from ‘CreateImpFeatFromProt’ at asn2ff4.c:1723:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 2 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff5.c:177: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff5.c: In function ‘format_cit_sub’: asn2ff5.c:1023:78: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1023 | format == EMBLPEPT_FMT && afp->choice == 1) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ asn2ff5.c:926:41: warning: variable ‘need_space’ set but not used [-Wunused-but-set-variable] 926 | Boolean need_comma = FALSE, /*UNUSED*/need_space = TRUE; | ^~~~~~~~~~ asn2ff5.c: In function ‘format_thesis’: asn2ff5.c:1213:27: warning: variable ‘embl_format’ set but not used [-Wunused-but-set-variable] 1213 | Boolean /*UNUSED*/embl_format = FALSE; | ^~~~~~~~~~~ asn2ff5.c: In function ‘format_book’: asn2ff5.c:1296:17: warning: variable ‘embl_format’ set but not used [-Wunused-but-set-variable] 1296 | Boolean embl_format = FALSE; | ^~~~~~~~~~~ asn2ff5.c: In function ‘format_jourarticle’: asn2ff5.c:1680:28: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1680 | if (ip->pages != NULL) | ^ asn2ff5.c: In function ‘StripParanthesis’: asn2ff5.c:2124:33: warning: value computed is not used [-Wunused-value] 2124 | temp++; *ptr_in++; | ^~~~~~~~~ asn2ff5.c: In function ‘PostARefErrMessage’: asn2ff5.c:3005:27: warning: variable ‘ignore_this’ set but not used [-Wunused-but-set-variable] 3005 | Boolean /*UNUSED*/ignore_this, submit=FALSE, error; | ^~~~~~~~~~~ asn2ff5.c: At top level: asn2ff5.c:188:26: warning: ‘GetSubmitterName’ declared ‘static’ but never defined [-Wunused-function] 188 | static CharPtr /*UNUSED*/GetSubmitterName PROTO ((Uint1 format, ValNodePtr pub)); | ^~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff5.c: In function ‘CheckPubs’: asn2ff5.c:2768:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 2768 | if (status < 0) | ^ asn2ff5.c:2746:24: note: ‘status’ was declared here 2746 | Int2 retval=0, status; | ^~~~~~ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1121:40: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1121 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1121:37: note: directive argument in the range [1, 2147483647] 1121 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘format_patent’ at asn2ff5.c:1121:4, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1115:40: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1115 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1115:37: note: directive argument in the range [1, 2147483647] 1115 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘format_patent’ at asn2ff5.c:1115:4, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1140:31: warning: ‘afp’ may be used uninitialized [-Wmaybe-uninitialized] 1140 | if (ap == NULL || afp == NULL) { | ^ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1051:18: note: ‘afp’ was declared here 1051 | AffilPtr afp; | ^~~ In file included from ../include/ncbi.h:62: In function ‘format_general’, inlined from ‘FlatJournal’ at asn2ff5.c:844:17: ../include/ncbistr.h:349:25: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized] 349 | #define StringMove Nlm_StringMove asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1946:23: note: ‘temp’ was declared here 1946 | CharPtr affil=NULL, temp, dup_pages=NULL, retval=NULL; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2ff6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ff6.h:134, from asn2ff6.c:347: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff6.c: In function ‘AddGBQual’: asn2ff6.c:1327:25: warning: variable ‘note’ set but not used [-Wunused-but-set-variable] 1327 | GBQualPtr curq, note = NULL; | ^~~~ asn2ff6.c: In function ‘FlatOrganelle’: asn2ff6.c:1483:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1483 | if (! retval ) | ^~ asn2ff6.c:1486:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1486 | break; | ^~~~~ asn2ff6.c: In function ‘BioseqGetGBDivCodeEx’: asn2ff6.c:1700:30: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 1700 | Int2 tech, /*UNUSED*/diff, retval = 0; | ^~~~ asn2ff6.c: In function ‘GR_PrintPubs’: asn2ff6.c:2297:48: warning: unused variable ‘stop’ [-Wunused-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~ asn2ff6.c:2297:39: warning: unused variable ‘start’ [-Wunused-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~~ asn2ff6.c:2297:20: warning: variable ‘pmid’ set but not used [-Wunused-but-set-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~ asn2ff6.c:2296:17: warning: unused variable ‘descr’ [-Wunused-variable] 2296 | CharPtr descr = NULL; | ^~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2786:24: warning: variable ‘base_locus_max’ set but not used [-Wunused-but-set-variable] 2786 | Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits; | ^~~~~~~~~~~~~~ asn2ff6.c: In function ‘ValidateOtherAccession’: asn2ff6.c:2886:36: warning: unused variable ‘FiveNum’ [-Wunused-variable] 2886 | Boolean FirstLetter=FALSE, FiveNum = FALSE; | ^~~~~~~ asn2ff6.c:2886:17: warning: unused variable ‘FirstLetter’ [-Wunused-variable] 2886 | Boolean FirstLetter=FALSE, FiveNum = FALSE; | ^~~~~~~~~~~ asn2ff6.c: In function ‘AddExtraAccessions’: asn2ff6.c:3498:27: warning: variable ‘ncbi’ set but not used [-Wunused-but-set-variable] 3498 | Boolean /*UNUSED*/ncbi = FALSE; | ^~~~ asn2ff6.c: At top level: asn2ff6.c:2883:13: warning: ‘ValidateOtherAccession’ defined but not used [-Wunused-function] 2883 | static Int2 ValidateOtherAccession(CharPtr new_buf, CharPtr orig_buf) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2866:61: warning: ‘%ld’ directive writing between 1 and 6 bytes into a region of size 4 [-Wformat-overflow=] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^~~ asn2ff6.c:2866:60: note: directive argument in the range [-32768, 32767] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ValidateLocus’ at asn2ff6.c:2866:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 7 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2866:54: warning: ‘exp’ may be used uninitialized [-Wmaybe-uninitialized] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^ asn2ff6.c:2786:51: note: ‘exp’ was declared here 2786 | Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits; | ^~~ asn2ff6.c: In function ‘MakeBaseLocusAwp’: asn2ff6.c:3093:45: warning: ‘num_of_digits’ may be used uninitialized [-Wmaybe-uninitialized] 3093 | base_locus_max = MAX_LOCUS_NAME_LEN - num_of_digits; asn2ff6.c:3070:56: note: ‘num_of_digits’ was declared here 3070 | Int2 index, length, base_locus_max, name_len, num_of_digits, num_seg; | ^~~~~~~~~~~~~ asn2ff6.c: In function ‘GetLocusPartsAwp’: asn2ff6.c:3313:53: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3313 | sprintf(gbp->locus, "%-16s", buf_acc); | ^ In function ‘sprintf’, inlined from ‘GetLocusPartsAwp’ at asn2ff6.c:3313:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 26 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff6.c: In function ‘GetLocusPartsAwp’: asn2ff6.c:3311:53: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3311 | sprintf(gbp->locus, "%-10s", buf_acc); | ^ In function ‘sprintf’, inlined from ‘GetLocusPartsAwp’ at asn2ff6.c:3311:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 11 and 26 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff6.c: In function ‘GetLocusPartsAwp’: asn2ff6.c:3270:61: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3270 | sprintf(gbp->locus, "%-16s", buf_acc); | ^ In function ‘sprintf’, inlined from ‘GetLocusPartsAwp’ at asn2ff6.c:3270:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 26 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff6.c: In function ‘GetLocusPartsAwp’: asn2ff6.c:3268:61: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3268 | sprintf(gbp->locus, "%-10s", buf_acc); | ^ In function ‘sprintf’, inlined from ‘GetLocusPartsAwp’ at asn2ff6.c:3268:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 11 and 26 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb1.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb1.c: In function ‘IsWholeWordSubstr’: asn2gnb1.c:2202:19: warning: variable ‘right’ set but not used [-Wunused-but-set-variable] 2202 | Boolean left, right; | ^~~~~ asn2gnb1.c: In function ‘s_LocusGetBaseName’: asn2gnb1.c:2350:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 2350 | else | ^~~~ asn2gnb1.c:2352:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 2352 | newLength = segNameLen - deleteChars; | ^~~~~~~~~ asn2gnb1.c: In function ‘DoOneSection’: asn2gnb1.c:2522:24: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 2522 | IntAsn2gbSectPtr iasp; | ^~~~ asn2gnb1.c:2514:24: warning: variable ‘bkmask’ set but not used [-Wunused-but-set-variable] 2514 | BlockMask bkmask; | ^~~~~~ asn2gnb1.c: In function ‘Count2Seg’: asn2gnb1.c:3438:18: warning: variable ‘to’ set but not used [-Wunused-but-set-variable] 3438 | Int4 to; | ^~ asn2gnb1.c:3436:18: warning: variable ‘parent’ set but not used [-Wunused-but-set-variable] 3436 | BioseqPtr parent; | ^~~~~~ asn2gnb1.c: At top level: asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] 3714 | static ModeFlags flagTable [] = { | ^ asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c: In function ‘SeqIdWriteForTable’: asn2gnb1.c:5808:13: warning: variable ‘pdb’ set but not used [-Wunused-but-set-variable] 5808 | pdb = NULL, general = NULL, gi = NULL; | ^~~ asn2gnb1.c:5807:40: warning: variable ‘patent’ set but not used [-Wunused-but-set-variable] 5807 | SeqIdPtr accn = NULL, local = NULL, patent = NULL, | ^~~~~~ In file included from ../include/ncbi.h:58: asn2gnb1.c: In function ‘DoImmediateFormat’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb1.c:6951:19: note: in expansion of macro ‘MAX’ 6951 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb1.c:6930:20: warning: variable ‘is_www’ set but not used [-Wunused-but-set-variable] 6930 | Boolean is_www; | ^~~~~~ asn2gnb1.c: In function ‘asn2gnbk_format’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb1.c:7072:19: note: in expansion of macro ‘MAX’ 7072 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb1.c: In function ‘asn2gnbk_cleanup’: asn2gnb1.c:7118:21: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 7118 | IntAsn2gbSectPtr iasp; | ^~~~ asn2gnb1.c: In function ‘SeqEntryToGnbk’: asn2gnb1.c:7304:22: warning: variable ‘userdata’ set but not used [-Wunused-but-set-variable] 7304 | Pointer userdata = NULL; | ^~~~~~~~ asn2gnb1.c:7299:22: warning: variable ‘gbseq’ set but not used [-Wunused-but-set-variable] 7299 | GBSeqPtr gbseq = NULL; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb1.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb1.c: In function ‘PrintFtableIntervals’: asn2gnb1.c:5463:28: warning: ‘ ’ directive writing 1 byte into a region of size between 0 and 62 [-Wformat-overflow=] 5463 | sprintf (str, "%s\t%s\t%s\n", str1, str2, label); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintFtableIntervals’ at asn2gnb1.c:5463:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 4 or more bytes (assuming 66) into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb1.c: In function ‘PrintFtableIntervals’: asn2gnb1.c:5487:30: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5487 | sprintf (str, "%s\t%s\n", str1, str2); | ^ In function ‘sprintf’, inlined from ‘PrintFtableIntervals’ at asn2gnb1.c:5487:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 65 bytes into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb2.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb2.c: In function ‘s_LocusAddSuffix’: asn2gnb2.c:217:11: warning: variable ‘ch’ set but not used [-Wunused-but-set-variable] 217 | Char ch; | ^~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1361:66: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1361 | } else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘IsSuccessor’: asn2gnb2.c:1742:15: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1742 | while (accp != '\0' && prevp != '\0') { | ^~ asn2gnb2.c:1742:10: note: did you mean to dereference the pointer? 1742 | while (accp != '\0' && prevp != '\0') { | ^ asn2gnb2.c:1742:34: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1742 | while (accp != '\0' && prevp != '\0') { | ^~ asn2gnb2.c:1742:28: note: did you mean to dereference the pointer? 1742 | while (accp != '\0' && prevp != '\0') { | ^ asn2gnb2.c: In function ‘IsProjectAccn’: asn2gnb2.c:1767:38: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue; | ^~ asn2gnb2.c:1767:34: note: did you mean to dereference the pointer? 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue; | ^ asn2gnb2.c: In function ‘AddDblinkBlock’: asn2gnb2.c:2892:22: warning: variable ‘parentID’ set but not used [-Wunused-but-set-variable] 2892 | Int4 parentID; | ^~~~~~~~ asn2gnb2.c: In function ‘AddSPBlock’: asn2gnb2.c:3409:14: warning: implicit declaration of function ‘PrintDate’ [-Wimplicit-function-declaration] 3409 | string = PrintDate (spb->created); | ^~~~~~~~~ asn2gnb2.c:3409:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3409 | string = PrintDate (spb->created); | ^ asn2gnb2.c:3417:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3417 | string = PrintDate (spb->sequpd); | ^ asn2gnb2.c:3424:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3424 | string = PrintDate (spb->annotupd); | ^ asn2gnb2.c: In function ‘AddSourceOrganismBlock’: asn2gnb2.c:5056:22: warning: variable ‘common’ set but not used [-Wunused-but-set-variable] 5056 | CharPtr common; | ^~~~~~ asn2gnb2.c: In function ‘GetRefsOnBioseq’: asn2gnb2.c:5893:22: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 5893 | Uint1 strand; | ^~~~~~ asn2gnb2.c:5890:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 5890 | Boolean split; | ^~~~~ asn2gnb2.c:5884:22: warning: variable ‘right’ set but not used [-Wunused-but-set-variable] 5884 | Int4 right; | ^~~~~ asn2gnb2.c:5878:22: warning: variable ‘left’ set but not used [-Wunused-but-set-variable] 5878 | Int4 left; | ^~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:239:24: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 6 [-Wformat-overflow=] 239 | sprintf(segCountStr,"%d",awp->numsegs); | ^~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:239:23: note: directive argument in the range [2, 2147483647] 239 | sprintf(segCountStr,"%d",awp->numsegs); | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:239:3, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:244:25: warning: ‘%0*d’ directive writing between 1 and 32768 bytes into a region of size 4 [-Wformat-overflow=] 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg); | ^~~~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:244:23: note: directive argument in the range [0, 65535] 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg); | ^~~~~~~ In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:244:5, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 32770 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:246:24: warning: ‘%0*d’ directive writing between 1 and 32768 bytes into a region of size 5 [-Wformat-overflow=] 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg); | ^~~~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:246:23: note: directive argument in the range [0, 65535] 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg); | ^~~~~~ In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:246:5, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1514:48: warning: ‘" title="Jump to the comment...’ directive writing 69 bytes into a region of size between 66 and 106 [-Wformat-overflow=] 1514 | sprintf (sect, "
  • Comment
    • ", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1514:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 92 and 132 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1518:46: warning: ‘" title="Jump to the feature...’ directive writing 68 bytes into a region of size between 66 and 106 [-Wformat-overflow=] 1518 | sprintf (sect, "
  • Features
    • ", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1518:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 91 and 131 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1527:117: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1527 | sprintf (sect, "
  • Genome
    • ", | ^ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1527:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 89 and 129 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1532:117: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1532 | sprintf (sect, "
  • Contig
    • ", | ^ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1532:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 89 and 129 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1579:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 68 and 77 [-Wformat-overflow=] 1579 | sprintf (sect, "
  • Next
    • ", (long) nextGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1579:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 67 and 203 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1587:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 67 and 77 [-Wformat-overflow=] 1587 | sprintf (sect, "
  • Next
    • ", (long) awp->nextGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1587:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 67 and 204 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1608:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 67 and 77 [-Wformat-overflow=] 1608 | sprintf (sect, "
  • Previous
    • ", (long) awp->prevGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1608:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 71 and 208 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1600:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 68 and 77 [-Wformat-overflow=] 1600 | sprintf (sect, "
  • Previous
    • ", (long) prevGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1600:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 71 and 207 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb3.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb3.c: In function ‘GetStatusForRefTrack’: asn2gnb3.c:796:22: warning: variable ‘urf’ set but not used [-Wunused-but-set-variable] 796 | UserFieldPtr ufp, urf = NULL; | ^~~ asn2gnb3.c: In function ‘AddCommentBlock’: asn2gnb3.c:2656:22: warning: variable ‘is_wgs’ set but not used [-Wunused-but-set-variable] 2656 | Boolean is_wgs = FALSE; | ^~~~~~ asn2gnb3.c: In function ‘GetSourcesOnBioseq’: asn2gnb3.c:5472:22: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 5472 | Uint1 strand; | ^~~~~~ asn2gnb3.c:5470:22: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5470 | Int4 start; | ^~~~~ asn2gnb3.c:5468:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 5468 | Boolean split; | ^~~~~ asn2gnb3.c: In function ‘AddSourceFeatBlock’: asn2gnb3.c:5989:22: warning: unused variable ‘sip’ [-Wunused-variable] 5989 | SeqIdPtr sip; | ^~~ asn2gnb3.c: In function ‘GetFeatsOnCdsProduct’: asn2gnb3.c:6446:22: warning: variable ‘isRefSeq’ set but not used [-Wunused-but-set-variable] 6446 | Boolean isRefSeq; | ^~~~~~~~ asn2gnb3.c: In function ‘GetRemoteFeatsOnCdsProduct’: asn2gnb3.c:6595:20: warning: variable ‘lastsfp’ set but not used [-Wunused-but-set-variable] 6595 | SeqFeatPtr lastsfp; | ^~~~~~~ asn2gnb3.c:6594:20: warning: variable ‘lastsap’ set but not used [-Wunused-but-set-variable] 6594 | SeqAnnotPtr lastsap; | ^~~~~~~ asn2gnb3.c:6593:20: warning: variable ‘lastright’ set but not used [-Wunused-but-set-variable] 6593 | Int4 lastright; | ^~~~~~~~~ asn2gnb3.c:6592:20: warning: variable ‘lastleft’ set but not used [-Wunused-but-set-variable] 6592 | Int4 lastleft; | ^~~~~~~~ asn2gnb3.c:6591:20: warning: variable ‘isRefSeq’ set but not used [-Wunused-but-set-variable] 6591 | Boolean isRefSeq; | ^~~~~~~~ asn2gnb3.c: In function ‘GetFeatsOnBioseq’: asn2gnb3.c:6895:22: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 6895 | Int4 start; | ^~~~~ asn2gnb3.c:6866:22: warning: variable ‘icp’ set but not used [-Wunused-but-set-variable] 6866 | IntCdsBlockPtr icp; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb3.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb3.c:1582:16: warning: ‘nsWGSGapsString’ defined but not used [-Wunused-variable] 1582 | static CharPtr nsWGSGapsString = "The strings of n's in this record represent gaps between contigs or uncallable bases."; | ^~~~~~~~~~~~~~~ asn2gnb3.c:1581:16: warning: ‘nsAreGapsString’ defined but not used [-Wunused-variable] 1581 | static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap."; | ^~~~~~~~~~~~~~~ asn2gnb3.c: In function ‘AddCommentBlock’: asn2gnb3.c:3429:29: warning: ‘nm’ may be used uninitialized [-Wmaybe-uninitialized] 3429 | if (IS_protdb_accession (nm)) { | ^~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb3.c:2676:22: note: ‘nm’ was declared here 2676 | CharPtr nm; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb4.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockQuals’: asn2gnb4.c:3723:50: warning: "/*" within comment [-Wcomment] 3723 | StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) { | asn2gnb4.c:3101:24: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 3101 | Boolean split; | ^~~~~ asn2gnb4.c:3042:24: warning: variable ‘at_end’ set but not used [-Wunused-but-set-variable] 3042 | Boolean at_end = FALSE; | ^~~~~~ asn2gnb4.c: In function ‘FF_asn2gb_www_featkey_Ex’: asn2gnb4.c:5325:16: warning: variable ‘prefix’ set but not used [-Wunused-but-set-variable] 5325 | CharPtr prefix = "?"; | ^~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockEx’: asn2gnb4.c:6572:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 6572 | Boolean split; | ^~~~~ In file included from ../include/ncbi.h:58: asn2gnb4.c: In function ‘DoImmediateRemoteFeatureFormat’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb4.c:8796:19: note: in expansion of macro ‘MAX’ 8796 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb4.c: In function ‘FormatFeatureQuals’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb4.c:8869:19: note: in expansion of macro ‘MAX’ 8869 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb4.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockEx’: asn2gnb4.c:7695:26: warning: ‘sep’ may be used uninitialized [-Wmaybe-uninitialized] 7695 | oldscope = SeqEntrySetScope (sep); | ^~~~~~~~~~~~~~~~~~~~~~ asn2gnb4.c:6566:22: note: ‘sep’ was declared here 6566 | SeqEntryPtr sep; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb5.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb5.c: In function ‘FormatCitBookArt’: asn2gnb5.c:2108:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2108 | ValNodePtr vnp; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb5.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb5.c: In function ‘FormatReferenceBlock’: asn2gnb5.c:2553:22: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2553 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~ In function ‘FormatCitPat’, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: asn2gnb5.c:2553:19: note: directive argument in the range [1, 2147483647] 2553 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FormatCitPat’ at asn2gnb5.c:2553:7, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb5.c: In function ‘FormatReferenceBlock’: asn2gnb5.c:2550:22: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2550 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~ In function ‘FormatCitPat’, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: asn2gnb5.c:2550:19: note: directive argument in the range [1, 2147483647] 2550 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘FormatCitPat’ at asn2gnb5.c:2550:7, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2gnb6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb6.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb6.c: In function ‘FlatLocElement’: asn2gnb6.c:2546:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2546 | if (sintp->to > 0 && | ~~~~~~~~~~~~~~^~ 2547 | (sintp->to != sintp->from || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2548 | sintp->if_from != NULL || | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2549 | sintp->if_to != NULL) || | ~~~~~~~~~~~~~~~~~~~~~ asn2gnb6.c: In function ‘FormatContigBlock’: asn2gnb6.c:5701:20: warning: variable ‘dspnext’ set but not used [-Wunused-but-set-variable] 5701 | DeltaSeqPtr dspnext; | ^~~~~~~ asn2gnb6.c: In function ‘ProcessGapSpecialFormat’: asn2gnb6.c:6041:13: warning: unused variable ‘sip’ [-Wunused-variable] 6041 | SeqIdPtr sip; | ^~~ asn2gnb6.c: In function ‘FormatSequenceBlock’: asn2gnb6.c:6168:21: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 6168 | IntAsn2gbSectPtr iasp; | ^~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb6.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb6.c:76:16: warning: ‘link_lat_lon’ defined but not used [-Wunused-variable] 76 | static CharPtr link_lat_lon = "https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html?"; | ^~~~~~~~~~~~ asn2gnb6.c: In function ‘FormatBasecountBlock’: asn2gnb6.c:5365:58: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 10 and 50 [-Wformat-overflow=] 5365 | sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;", | ^~~ asn2gnb6.c:5365:19: note: directive argument in the range [-2147483648, 2147483647] 5365 | sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb6.c:5365:19: note: directive argument in the range [-2147483648, 2147483647] In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FormatBasecountBlock’ at asn2gnb6.c:5365:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 44 and 104 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ftusrstr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ftusrstr.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gbfeat.c gbfeat.c: In function ‘CkLabelType’: gbfeat.c:1465:47: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1465 | for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str) x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gbftglob.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gbparint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/parsegb.h:57, from gbparint.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gbparint.c: In function ‘Nlm_gbparselex’: gbparint.c:2134:24: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2134 | if (*current_col != '\0') | ^ gbparint.c: In function ‘Nlm_gbparselex_ver’: gbparint.c:2520:24: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2520 | if (*current_col != '\0') | ^ gbparint.c: In function ‘Nlm_gbparselex’: gbparint.c:1903:9: warning: array subscript 0 is outside array bounds of ‘char[0:]’ [-Warray-bounds=] 1903 | *(current_col +1) = Saved_ch; | ^~~~~~~~~~~~~~~~~ cc1: note: source object is likely at address zero gbparint.c: In function ‘Nlm_gbparselex_ver’: gbparint.c:1903:9: warning: array subscript 0 is outside array bounds of ‘char[0:]’ [-Warray-bounds=] 1903 | *(current_col +1) = Saved_ch; | ^~~~~~~~~~~~~~~~~ cc1: note: source object is likely at address zero x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF utilpars.c utilpars.c:112:39: warning: missing braces around initializer [-Wmissing-braces] 112 | ParFlat_AA_array[ParFlat_TOTAL_AA] = { | ^ 113 | "Ala", 'A', | { } 114 | "Asx", 'B', | { } 115 | "Cys", 'C', | { } 116 | "Asp", 'D', | { } 117 | "Glu", 'E', | { } 118 | "Phe", 'F', | { } 119 | "Gly", 'G', | { } 120 | "His", 'H', | { } 121 | "Ile", 'I', | { } 122 | "Xle", 'J', /* was - notice no 'J', breaks naive meaning of index -Karl */ | { } 123 | "Lys", 'K', | { } 124 | "Leu", 'L', | { } 125 | "Met", 'M', | { } 126 | "Asn", 'N', | { } 127 | "Pyl", 'O', /* was - no 'O' */ | { } 128 | "Pro", 'P', | { } 129 | "Gln", 'Q', | { } 130 | "Arg", 'R', | { } 131 | "Ser", 'S', | { } 132 | "Thr", 'T', | { } 133 | "Val", 'V', | { } 134 | "Trp", 'W', | { } 135 | "Sec", 'U', /* was - not in iupacaa */ | { } 136 | "Xxx", 'X', | { } 137 | "Tyr", 'Y', | { } 138 | "Glx", 'Z', | { } 139 | "TERM", '*', /* not in iupacaa */ /*changed by Tatiana 06.07.95?`*/ | { } 140 | "OTHER", 'X'}; | { } x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF utilpub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from utilpub.c:13: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ utilpub.c: In function ‘FindCit’: utilpub.c:998:43: warning: variable ‘ifp’ set but not used [-Wunused-but-set-variable] 998 | ImpFeatPtr /*UNUSED*/ifp; | ^~~ utilpub.c: In function ‘ChangeCitQual’: utilpub.c:1053:72: warning: variable ‘pub’ set but not used [-Wunused-but-set-variable] 1053 | ValNodePtr vnp, pubset = NULL, pub_min, /*UNUSED*/pub; | ^~~ utilpub.c:1052:41: warning: variable ‘descr’ set but not used [-Wunused-but-set-variable] 1052 | ValNodePtr PNTR vnpp, /*UNUSED*/descr; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ffprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from ffprint.c:127: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ffprint.c: In function ‘FFBSPrint’: ffprint.c:347:19: warning: unused variable ‘byte_sp’ [-Wunused-variable] 347 | ByteStorePtr byte_sp = NULL; | ^~~~~~~ ffprint.c: At top level: ffprint.c:420:16: warning: ‘ff_print_insert’ defined but not used [-Wunused-function] 420 | static CharPtr ff_print_insert(CharPtr str, CharPtr ins) | ^~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF wprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from wprint.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ wprint.c: In function ‘LocPrintGenome’: wprint.c:1696:21: warning: unused variable ‘sep’ [-Wunused-variable] 1696 | SeqEntryPtr sep = NULL; | ^~~ wprint.c:1695:37: warning: unused variable ‘b’ [-Wunused-variable] 1695 | BioseqPtr bsp = NULL, b = NULL; | ^ wprint.c:1695:25: warning: unused variable ‘bsp’ [-Wunused-variable] 1695 | BioseqPtr bsp = NULL, b = NULL; | ^~~ wprint.c:1692:52: warning: unused variable ‘temp’ [-Wunused-variable] 1692 | static Char buf[14], val[166], temp[166]; | ^~~~ wprint.c: At top level: wprint.c:79:13: warning: ‘link_gdb_map’ defined but not used [-Wunused-variable] 79 | static Char link_gdb_map[MAX_WWWBUF]; | ^~~~~~~~~~~~ wprint.c:77:13: warning: ‘link_pir’ defined but not used [-Wunused-variable] 77 | static Char link_pir[MAX_WWWBUF]; | ^~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from wprint.c:51: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ wprint.c: In function ‘PrintDate’: wprint.c:188:41: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 188 | sprintf(day, "%d", (int) (date -> data[3] )); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintDate’ at wprint.c:188:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ wprint.c: In function ‘www_db_xref’: wprint.c:969:48: warning: ‘%d’ directive writing between 1 and 6 bytes into a region of size between 4 and 9 [-Wformat-overflow=] 969 | sprintf(id, "%d%d", id1, id2); | ^~ In function ‘www_db_xref’, inlined from ‘www_db_xref’ at wprint.c:679:28: wprint.c:969:45: note: directive argument in the range [-32768, 32767] 969 | sprintf(id, "%d%d", id1, id2); | ^~~~~~ In function ‘sprintf’, inlined from ‘www_db_xref’ at wprint.c:969:5, inlined from ‘www_db_xref’ at wprint.c:679:28: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ../include/ncbi.h:62: wprint.c: In function ‘www_xref’: ../include/ncbistr.h:331:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1358:20: note: ‘link’ was declared here 1358 | CharPtr s, link, prefix, ss; | ^~~~ ../include/ncbistr.h:331:25: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1358:26: note: ‘prefix’ was declared here 1358 | CharPtr s, link, prefix, ss; | ^~~~~~ wprint.c: In function ‘www_xref_button’: ../include/ncbistr.h:331:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1398:20: note: ‘link’ was declared here 1398 | CharPtr s, link, prefix, ss; | ^~~~ ../include/ncbistr.h:331:25: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1398:26: note: ‘prefix’ was declared here 1398 | CharPtr s, link, prefix, ss; | ^~~~~~ wprint.c: In function ‘PrintSPBlock’: wprint.c:1570:41: warning: ‘s’ may be used uninitialized [-Wmaybe-uninitialized] 1570 | AddLink(s); | ^~~~~~~~~~ wprint.c:1443:31: note: ‘s’ was declared here 1443 | CharPtr link, prefix, s; | ^ In function ‘sprintf’, inlined from ‘PrintSPBlock’ at wprint.c:1601:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ wprint.c: In function ‘PrintSPBlock’: wprint.c:1443:23: note: ‘prefix’ was declared here 1443 | CharPtr link, prefix, s; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF satutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/satutil.h:12, from satutil.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ satutil.c: In function ‘CopyFeatureFromAlign’: satutil.c:1011:17: warning: variable ‘check_gap’ set but not used [-Wunused-but-set-variable] 1011 | Boolean check_gap; | ^~~~~~~~~ satutil.c: At top level: satutil.c:168:16: warning: ‘bk_map_one_location’ defined but not used [-Wunused-function] 168 | static Boolean bk_map_one_location(SeqLocPtr source_loc, SeqAlignPtr align, SeqIdPtr target_sip, Boolean check_gap, Int4Ptr r_start, Int4Ptr r_stop, SeqLocPtr PNTR head_slp) | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from seqmgr.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqmgr.c: In function ‘SeqEntrySetScope’: seqmgr.c:311:13: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 311 | Boolean found; | ^~~~~ seqmgr.c: In function ‘ClearBioseqFindCache’: seqmgr.c:897:14: warning: variable ‘smp’ set but not used [-Wunused-but-set-variable] 897 | SeqMgrPtr smp; | ^~~ seqmgr.c: In function ‘GetUniGeneIDForSeqId’: seqmgr.c:3676:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3676 | if(StringCmp(db_tag->db, "BSNR") == 0) | ^~ seqmgr.c:3678:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3678 | if(StringCmp(db_tag->db, "HUMGEN") == 0) | ^~ seqmgr.c: In function ‘SeqMgrGetExtraDataForOmdp’: seqmgr.c:3736:14: warning: variable ‘omp’ set but not used [-Wunused-but-set-variable] 3736 | ObjMgrPtr omp; | ^~~ seqmgr.c: In function ‘CheckForTransSplice’: seqmgr.c:5657:14: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 5657 | SeqLocPtr prev, tmp; | ^~~~ seqmgr.c: In function ‘SeqEntryAsnOut’: seqmgr.c:11799:41: warning: variable ‘aopp_desc’ set but not used [-Wunused-but-set-variable] 11799 | AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL; | ^~~~~~~~~ seqmgr.c:11799:23: warning: variable ‘aopp_feat’ set but not used [-Wunused-but-set-variable] 11799 | AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from seqmgr.c:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from objmgr.c:51: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmgr.c: In function ‘ObjMgrReapOne’: objmgr.c:2727:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2727 | if (omp->reaping) /* protect against recursion caused by ObjMgrSendMsg */ | ^~ objmgr.c:2730:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2730 | lowest = UINT4_MAX; | ^~~~~~ objmgr.c: In function ‘ObjMgrDeSelectStructFunc’: objmgr.c:3767:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3767 | if (next != NULL) | ^~ objmgr.c:3770:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3770 | ObjMgrSendDeSelMsg (omp, ssp->entityID, ssp->itemID, ssp->itemtype, ssp->regiontype, ssp->region); | ^~~~~~~~~~~~~~~~~~ objmgr.c: In function ‘ObjMgrSelectFunc2’: objmgr.c:4031:22: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 4031 | Boolean retval = FALSE; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gather.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from gather.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gather.c: In function ‘AttachDataProc’: gather.c:4827:30: warning: variable ‘into_seqentry’ set but not used [-Wunused-but-set-variable] 4827 | Boolean no_good = FALSE, into_seqentry = FALSE; | ^~~~~~~~~~~~~ In file included from ../include/ncbi.h:59: gather.c: In function ‘GatherSeqFeat’: ../include/ncbimem.h:232:23: warning: ‘lrdp’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree gather.c:1404:38: note: ‘lrdp’ was declared here 1404 | GatherRangePtr rdp = NULL, trdp, lrdp; | ^~~~ gather.c:1527:32: warning: ‘max_interval’ may be used uninitialized [-Wmaybe-uninitialized] 1527 | if (ctr >= max_interval) | ^ gather.c:1407:15: note: ‘max_interval’ was declared here 1407 | Int2 ctr, max_interval, i, numcheck, j; | ^~~~~~~~~~~~ gather.c: In function ‘gather_align_data’: gather.c:2441:70: warning: ‘mag_val’ may be used uninitialized [-Wmaybe-uninitialized] 2441 | t_range.right = t_range.left+len / mag_val -1; | ~~~~^~~~~~~~~ gather.c:2218:10: note: ‘mag_val’ was declared here 2218 | Int4 mag_val; /*the magnification value */ | ^~~~~~~ gather.c:2450:34: warning: ‘master_loc’ may be used uninitialized [-Wmaybe-uninitialized] 2450 | c_stop = SeqLocStop(master_loc); | ^~~~~~~~~~~~~~~~~~~~~~ gather.c:2219:15: note: ‘master_loc’ was declared here 2219 | SeqLocPtr master_loc, m_loc; | ^~~~~~~~~~ gather.c: In function ‘GatherBioseqFunc’: gather.c:3307:53: warning: ‘tlen’ may be used uninitialized [-Wmaybe-uninitialized] 3307 | rdp->right = offset + tlen - 1; | ~~~~~~~^~~~~~ gather.c:3022:35: note: ‘tlen’ was declared here 3022 | Int4 offset, toffset, seglen, tlen; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF accmmdbs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from accmmdbs.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF acccn3ds.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from acccn3ds.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF lsqfetch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from ../include/lsqfetch.h:110, from lsqfetch.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ lsqfetch.c: In function ‘ChangeLocalToGenbank’: lsqfetch.c:1403:21: warning: ‘%s’ directive writing up to 40 bytes into a region of size 38 [-Wformat-overflow=] 1403 | sprintf (tmp, "gb|%s", id); | ^~ ~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ChangeLocalToGenbank’ at lsqfetch.c:1403:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 44 bytes into a destination of size 41 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF findrepl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from findrepl.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF codon.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/codon.h:61, from codon.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ codon.c: In function ‘make_cds_paragraph’: codon.c:262:14: warning: variable ‘space_len’ set but not used [-Wunused-but-set-variable] 262 | Int4 space_len, i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF jzcoll.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from jzcoll.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ jzcoll.c: In function ‘load_default_matrix’: jzcoll.c:99:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 99 | ss[pchars[i]][pchars[j]] = webb_blosum62[i][j]; | ~~~~~~^~~ jzcoll.c:99:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 99 | ss[pchars[i]][pchars[j]] = webb_blosum62[i][j]; | ~~~~~~^~~ jzcoll.c:101:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 101 | ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4; | ~~~~~~^~~ jzcoll.c:101:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 101 | ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4; | ~~~~~~^~~ jzcoll.c: In function ‘GetUseThisGi’: jzcoll.c:143:17: warning: unused variable ‘retval’ [-Wunused-variable] 143 | Boolean retval=FALSE; | ^~~~~~ jzcoll.c: In function ‘buffer_for_feature’: jzcoll.c:514:14: warning: unused variable ‘i’ [-Wunused-variable] 514 | Int2 i=0; | ^ jzcoll.c: In function ‘ProcessTextInsertion’: jzcoll.c:878:14: warning: variable ‘last_ins’ set but not used [-Wunused-but-set-variable] 878 | Int4 last_ins; | ^~~~~~~~ jzcoll.c: In function ‘satcollfunc’: jzcoll.c:1748:27: warning: the comparison will always evaluate as ‘false’ for the address of ‘features’ will never be NULL [-Waddress] 1748 | if(csop->features == NULL && afp->all_feature == FALSE) | ^~ ../include/jzcoll.h:206:17: note: ‘features’ declared here 206 | Boolean features[FEATDEF_ANY]; /*for filtering unwanted features*/ | ^~~~~~~~ jzcoll.c:1723:19: warning: variable ‘head’ set but not used [-Wunused-but-set-variable] 1723 | SeqLocPtr head; | ^~~~ jzcoll.c:1721:15: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 1721 | Uint1 strand; | ^~~~~~ jzcoll.c:1720:14: warning: variable ‘current_pos’ set but not used [-Wunused-but-set-variable] 1720 | Int4 current_pos; | ^~~~~~~~~~~ jzcoll.c:1714:19: warning: unused variable ‘slp’ [-Wunused-variable] 1714 | SeqLocPtr slp = NULL; | ^~~ jzcoll.c: In function ‘coll_align_data’: jzcoll.c:2631:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 2631 | sprintf(buf, "%d", gilist->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld jzcoll.c: In function ‘collect_anpnode_with_option’: jzcoll.c:3053:20: warning: unused variable ‘prev’ [-Wunused-variable] 3053 | ValNodePtr prev = NULL; | ^~~~ jzcoll.c: In function ‘ck_seqfeat_extra’: jzcoll.c:3414:17: warning: unused variable ‘has_gb’ [-Wunused-variable] 3414 | Boolean has_gb = FALSE, has_med = FALSE; | ^~~~~~ jzcoll.c: In function ‘collseqfunc’: jzcoll.c:3768:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3768 | if(omtp->labelfunc !=NULL) | ^~ jzcoll.c:3770:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3770 | fnp->landmark = check_feature_for_landmark(chp->thislabel, chp->gdata, sfp, gcp, chp->priority); | ^~~ jzcoll.c: In function ‘load_open_close_sts_mark’: jzcoll.c:4010:17: warning: variable ‘collected’ set but not used [-Wunused-but-set-variable] 4010 | Boolean collected = FALSE; | ^~~~~~~~~ jzcoll.c: In function ‘FeatNodeCompProc’: jzcoll.c:4225:22: warning: variable ‘gr2’ set but not used [-Wunused-but-set-variable] 4225 | GatherRange gr1, gr2; | ^~~ jzcoll.c:4225:17: warning: variable ‘gr1’ set but not used [-Wunused-but-set-variable] 4225 | GatherRange gr1, gr2; | ^~~ jzcoll.c: At top level: jzcoll.c:2316:16: warning: ‘stop_collecting_alignment’ defined but not used [-Wunused-function] 2316 | static Boolean stop_collecting_alignment(ValNodePtr anp_list, Int4 max_num) | ^~~~~~~~~~~~~~~~~~~~~~~~~ jzcoll.c:1654:16: warning: ‘collect_sequence_label’ defined but not used [-Wunused-function] 1654 | static Boolean collect_sequence_label(Uint1 format) | ^~~~~~~~~~~~~~~~~~~~~~ jzcoll.c: In function ‘load_text.isra.0’: jzcoll.c:421:41: warning: ‘smtp’ may be used uninitialized [-Wmaybe-uninitialized] 421 | stdaa_res = SeqMapTableConvert(smtp, m_res); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jzcoll.c:274:20: note: ‘smtp’ was declared here 274 | SeqMapTablePtr smtp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF jzmisc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/jzmisc.h:86, from jzmisc.c:23: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF maputil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from maputil.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ maputil.c: In function ‘load_gene_list’: maputil.c:690:15: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 690 | Uint1 val; | ^~~ maputil.c: In function ‘gmarkfunc’: maputil.c:985:20: warning: variable ‘syn’ set but not used [-Wunused-but-set-variable] 985 | ValNodePtr syn = NULL; | ^~~ maputil.c: In function ‘get_location_for_query’: maputil.c:1265:1: warning: function may return address of local variable [-Wreturn-local-addr] 1265 | } | ^ maputil.c:1190:16: note: declared here 1190 | SeqLoc sl; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mconsist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/mconsist.h:4, from mconsist.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF macroapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from macroapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ macroapi.c: In function ‘AdvancedStringCompare’: macroapi.c:4463:23: warning: variable ‘init_target_match_len’ set but not used [-Wunused-but-set-variable] 4463 | Int4 len1, len2, init_target_match_len = 0, target_match_len = 0; | ^~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘RemoveGBQualMatch’: macroapi.c:6981:27: warning: variable ‘does_match’ set but not used [-Wunused-but-set-variable] 6981 | Boolean rval = FALSE, does_match, do_remove; | ^~~~~~~~~~ macroapi.c: In function ‘ParseCodonsRecognizedFromCommaDelimitedList’: macroapi.c:7726:41: warning: pointer targets in passing argument 1 of ‘ExpandWobbleCodon’ differ in signedness [-Wpointer-sign] 7726 | wobble_list = ExpandWobbleCodon(codon); | ^~~~~ | | | Nlm_Uint1 * {aka unsigned char *} macroapi.c:7636:46: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} 7636 | static ValNodePtr ExpandWobbleCodon (CharPtr codon) macroapi.c: In function ‘GetQualFromFeatureAnyType’: macroapi.c:8537:8: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 8536 | if (str == NULL | ~~~~~~~~~~~ 8537 | && (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:8681:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 8681 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘SetNameInPrimerList’: macroapi.c:10682:21: warning: variable ‘prev_pp’ set but not used [-Wunused-but-set-variable] 10682 | PCRPrimerPtr pp, prev_pp = NULL; | ^~~~~~~ macroapi.c: In function ‘SetSeqInPrimerList’: macroapi.c:10703:21: warning: variable ‘prev_pp’ set but not used [-Wunused-but-set-variable] 10703 | PCRPrimerPtr pp, prev_pp = NULL; | ^~~~~~~ macroapi.c: In function ‘GetGenomeProjectIdFromBioseq’: macroapi.c:12881:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12881 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘RemoveGenomeProjectIdFromBioseq’: macroapi.c:12916:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12916 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘SetGenomeProjectIdOnBioseq’: macroapi.c:12957:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12957 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘GetPubFieldFromPub’: macroapi.c:15043:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15043 | sprintf (str, "%d", the_pub->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘GetCitListsForSeqEntry’: macroapi.c:15825:19: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 15825 | Uint2 entityID; | ^~~~~~~~ macroapi.c:15823:19: warning: variable ‘okay’ set but not used [-Wunused-but-set-variable] 15823 | Boolean okay; | ^~~~ macroapi.c: In function ‘GetPubclassQualFromPub’: macroapi.c:18324:11: warning: unused variable ‘str’ [-Wunused-variable] 18324 | CharPtr str = NULL; | ^~~ macroapi.c: In function ‘GetPubMLStatus’: macroapi.c:18681:14: warning: variable ‘csp’ set but not used [-Wunused-but-set-variable] 18681 | CitSubPtr csp; | ^~~ macroapi.c: In function ‘CollectDBLinkObjectsForApply’: macroapi.c:20029:72: warning: unused variable ‘tmp_tail’ [-Wunused-variable] 20029 | ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp; | ^~~~~~~~ macroapi.c:20029:55: warning: unused variable ‘tmp_list’ [-Wunused-variable] 20029 | ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp; | ^~~~~~~~ macroapi.c: In function ‘DoConvertActionToObjectListEx’: macroapi.c:20844:20: warning: unused variable ‘already_added’ [-Wunused-variable] 20844 | Boolean already_added, field_change; | ^~~~~~~~~~~~~ macroapi.c: In function ‘ApplyPartial5SetActionToSeqFeat’: macroapi.c:25749:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25749 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘ApplyPartial3SetActionToSeqFeat’: macroapi.c:25872:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25872 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘ApplyPartialBothSetActionToSeqFeat’: macroapi.c:25939:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25939 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘FindPosBeforeFeat’: macroapi.c:26236:15: warning: variable ‘regulator’ set but not used [-Wunused-but-set-variable] 26236 | SeqFeatPtr regulator = NULL, candidate; | ^~~~~~~~~ macroapi.c: In function ‘PerformAutofixInSeqEntry’: macroapi.c:29471:8: warning: unused variable ‘num_created’ [-Wunused-variable] 29471 | Int4 num_created = 0; | ^~~~~~~~~~~ macroapi.c: In function ‘AddFileDescriptors’: macroapi.c:29871:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 29871 | while (sdp = SeqDescAsnRead (aip, NULL)) { | ^~~ macroapi.c: In function ‘ApplyMacroToSeqEntryExEx’: macroapi.c:31907:28: warning: too many arguments for format [-Wformat-extra-args] 31907 | fprintf (log_fp, "Instantiated protein titles\n", num); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘PreprocessAddDescriptorListMacro’: macroapi.c:32020:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 32020 | while (sdp = SeqDescAsnRead (aip, NULL)) { | ^~~ macroapi.c: In function ‘FieldTypeFromString’: macroapi.c:32370:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 32370 | if (ft == NULL && StringsAreEquivalent(str, "location") || StringsAreEquivalent(str, "genome")) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘SummarizeRemoveOutsideAction’: macroapi.c:32939:11: warning: unused variable ‘case_insensitive’ [-Wunused-variable] 32939 | CharPtr case_insensitive = " (case insensitive)"; | ^~~~~~~~~~~~~~~~ macroapi.c: In function ‘GetObjectTableForTabTable’: macroapi.c:37508:63: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 37508 | ValNodePtr obj_table = NULL, obj_row, last_obj = NULL, tmp, last = NULL; | ^~~~ macroapi.c: In function ‘FormatMultipleDestinationErrorMessage’: macroapi.c:37987:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 37987 | sprintf (buf, "%d", vnp->data.intvalue + 1); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘CheckObjTableForExistingText’: macroapi.c:38084:14: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 38084 | Uint2 entityID; | ^~~~~~~~ macroapi.c: In function ‘FixSuspectProductNamesInEntrezGene’: macroapi.c:40352:18: warning: variable ‘prefix’ set but not used [-Wunused-but-set-variable] 40352 | CharPtr prefix = NULL; | ^~~~~~ In file included from ../include/tax3api.h:51, from macroapi.c:67: ../include/objtax3.h: At top level: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ macroapi.c:37233:16: warning: ‘IsFieldTypeProteinDesc’ defined but not used [-Wunused-function] 37233 | static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft) | ^~~~~~~~~~~~~~~~~~~~~~ macroapi.c:27097:13: warning: ‘GetDescriptorTypeFromDescriptorChoice’ defined but not used [-Wunused-function] 27097 | static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:21298:13: warning: ‘GetFieldsFromAECR’ defined but not used [-Wunused-function] 21298 | static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair) | ^~~~~~~~~~~~~~~~~ macroapi.c:20787:16: warning: ‘NoFieldChange’ defined but not used [-Wunused-function] 20787 | static Boolean NoFieldChange (CharPtr new_val, ValNodePtr vnp, FieldTypePtr field_from, StringConstraintPtr scp, BatchExtraPtr batch_extra) | ^~~~~~~~~~~~~ macroapi.c:16014:13: warning: ‘InitBatchExtraForAECRActionAndObjectList’ defined but not used [-Wunused-function] 16014 | static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:10389:16: warning: ‘HasMultiplePrimerSets’ defined but not used [-Wunused-function] 10389 | static Boolean HasMultiplePrimerSets (CharPtr value) | ^~~~~~~~~~~~~~~~~~~~~ macroapi.c:5482:16: warning: ‘DoesLocationMatchConstraint’ defined but not used [-Wunused-function] 5482 | static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:4590:13: warning: ‘TestAdvancedStringMatch’ defined but not used [-Wunused-function] 4590 | static void TestAdvancedStringMatch (void) | ^~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:2806:13: warning: ‘OriginFromOriginName’ defined but not used [-Wunused-function] 2806 | static Int4 OriginFromOriginName (CharPtr origin_name) | ^~~~~~~~~~~~~~~~~~~~ macroapi.c:1200:16: warning: ‘IsObjectAppropriateForFieldPair’ defined but not used [-Wunused-function] 1200 | static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘ReadNameFromString’, inlined from ‘ReadNameListFromString’ at macroapi.c:14060:9: macroapi.c:14037:14: warning: ‘ch_r1’ may be used uninitialized [-Wmaybe-uninitialized] 14037 | *p_repl1 = ch_r1; | ~~~~~~~~~^~~~~~~ macroapi.c: In function ‘ReadNameListFromString’: macroapi.c:13946:11: note: ‘ch_r1’ was declared here 13946 | Char ch_r1, ch_r2, ch_r3; | ^~~~~ macroapi.c: In function ‘AlsoChangeMrnaForObject’: macroapi.c:20637:10: warning: ‘mrna’ may be used uninitialized [-Wmaybe-uninitialized] 20637 | if (mrna != NULL) { | ^ macroapi.c:20618:19: note: ‘mrna’ was declared here 20618 | SeqFeatPtr sfp, mrna, cds; | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘fprintf’, inlined from ‘ApplyMacroToSeqEntryExEx’ at macroapi.c:31907:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: ‘num’ may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘ApplyMacroToSeqEntryExEx’: macroapi.c:31469:37: note: ‘num’ was declared here 31469 | Int4 num_AECR = 0, num_parse = 0, num; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salpedit.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salpedit.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpedit.c: In function ‘SeqAlignInsert’: salpedit.c:162:19: warning: variable ‘ssp’ set but not used [-Wunused-but-set-variable] 162 | StdSegPtr ssp; | ^~~ salpedit.c:161:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 161 | DenseDiagPtr ddp; | ^~~ salpedit.c: At top level: salpedit.c:4120:18: warning: ‘build_slp_for_gcontig’ defined but not used [-Wunused-function] 4120 | static SeqLocPtr build_slp_for_gcontig (BioseqPtr gcontig_bsp, SeqIdPtr gcontig_sip) | ^~~~~~~~~~~~~~~~~~~~~ salpedit.c:4073:17: warning: ‘get_best_id’ defined but not used [-Wunused-function] 4073 | static SeqIdPtr get_best_id(BioseqPtr bsp) | ^~~~~~~~~~~ salpedit.c:4046:16: warning: ‘second_seq_has_gap’ defined but not used [-Wunused-function] 4046 | static Boolean second_seq_has_gap(BioseqPtr s_bsp) | ^~~~~~~~~~~~~~~~~~ salpedit.c:4016:18: warning: ‘dup_mul_locs’ defined but not used [-Wunused-function] 4016 | static SeqLocPtr dup_mul_locs(SeqLocPtr slp) | ^~~~~~~~~~~~ salpedit.c:3968:18: warning: ‘create_fake_bioseq’ defined but not used [-Wunused-function] 3968 | static BioseqPtr create_fake_bioseq(SeqLocPtr seq_loc, CharPtr fake_name) | ^~~~~~~~~~~~~~~~~~ salpedit.c:3937:13: warning: ‘reverse_seqloc’ defined but not used [-Wunused-function] 3937 | static void reverse_seqloc (SeqLocPtr s_loc) | ^~~~~~~~~~~~~~ salpedit.c:3850:13: warning: ‘save_output’ defined but not used [-Wunused-function] 3850 | static void save_output (SeqIdPtr sip, CharPtr f_name, SeqAlignPtr align) | ^~~~~~~~~~~ salpedit.c:3836:13: warning: ‘get_align_list_len’ defined but not used [-Wunused-function] 3836 | static Int4 get_align_list_len(SeqAlignPtr align) | ^~~~~~~~~~~~~~~~~~ salpedit.c:2939:20: warning: ‘open_annot’ defined but not used [-Wunused-function] 2939 | static SeqAnnotPtr open_annot(CharPtr f_name) | ^~~~~~~~~~ salpedit.c:2835:13: warning: ‘SeqAnnotWrite’ defined but not used [-Wunused-function] 2835 | static void SeqAnnotWrite(SeqAlignPtr align) | ^~~~~~~~~~~~~ salpedit.c:2653:16: warning: ‘FigureAlignRange’ defined but not used [-Wunused-function] 2653 | static Boolean FigureAlignRange(SeqAlignPtr align, SeqLocPtr m_loc, SeqLocPtr s_loc) | ^~~~~~~~~~~~~~~~ salpedit.c:1665:16: warning: ‘free_diag_in_list’ defined but not used [-Wunused-function] 1665 | static Boolean free_diag_in_list(ValNodePtr ddp_list, DenseDiagPtr ddp) | ^~~~~~~~~~~~~~~~~ salpedit.c:1605:16: warning: ‘is_overlap’ defined but not used [-Wunused-function] 1605 | static Boolean is_overlap(BoolPtr status, Int4 from, Int4 len) | ^~~~~~~~~~ salpedit.c:1560:13: warning: ‘filter_wrong_orientation’ defined but not used [-Wunused-function] 1560 | static void filter_wrong_orientation (SeqAlignPtr align, Boolean same_orient) | ^~~~~~~~~~~~~~~~~~~~~~~~ salpedit.c:1479:16: warning: ‘filter_this_seg’ defined but not used [-Wunused-function] 1479 | static Boolean filter_this_seg (DenseDiagPtr curr, DenseDiagPtr PNTR h_list, Int2 order) | ^~~~~~~~~~~~~~~ salpedit.c:1422:16: warning: ‘convert_ddp_to_array’ defined but not used [-Wunused-function] 1422 | static Int4Ptr convert_ddp_to_array (ValNodePtr ddp_list, Uint1 strand, Int2 s_order, Int4Ptr p_num) | ^~~~~~~~~~~~~~~~~~~~ salpedit.c:1387:14: warning: ‘has_too_much_overlap’ defined but not used [-Wunused-function] 1387 | static Uint1 has_too_much_overlap (Int4 start_1, Int4 stop_1, Int4 start_2, Int4 stop_2) | ^~~~~~~~~~~~~~~~~~~~ salpedit.c:1281:13: warning: ‘attach_new_align’ defined but not used [-Wunused-function] 1281 | static void attach_new_align(SeqAlignPtr new_salp, SeqAlignPtr PNTR old) { | ^~~~~~~~~~~~~~~~ salpedit.c:1169:20: warning: ‘JZSeqAlignMerge’ defined but not used [-Wunused-function] 1169 | static SeqAlignPtr JZSeqAlignMerge(SeqAlignPtr f_align, SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr t_align) | ^~~~~~~~~~~~~~~ salpedit.c:254:16: warning: ‘is_gap_segment’ defined but not used [-Wunused-function] 254 | static Boolean is_gap_segment(Int4Ptr c_starts, Int2 dim) | ^~~~~~~~~~~~~~ salpedit.c:158:20: warning: ‘SeqAlignInsert’ defined but not used [-Wunused-function] 158 | static SeqAlignPtr SeqAlignInsert(SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr head, Boolean merge, Boolean add_insertion) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salpstat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salpstat.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpstat.c: In function ‘DenseSegStats’: salpstat.c:310:10: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 310 | if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c: In function ‘SeqAlignScoreFix’: salpstat.c:162:27: warning: ‘sp_last’ may be used uninitialized [-Wmaybe-uninitialized] 162 | sp_last->next = (ScorePtr) MemNew(sizeof(Score)); salpstat.c:121:20: note: ‘sp_last’ was declared here 121 | ScorePtr sp=NULL,sp_last; | ^~~~~~~ salpstat.c: In function ‘DenseSegStats’: salpstat.c:345:23: warning: ‘spp_1’ may be used uninitialized [-Wmaybe-uninitialized] 345 | SeqPortSeek(spp_1,start_1,SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c:307:14: note: ‘spp_1’ was declared here 307 | SeqPortPtr spp_1, spp_2; | ^~~~~ salpstat.c:352:23: warning: ‘spp_2’ may be used uninitialized [-Wmaybe-uninitialized] 352 | SeqPortSeek(spp_2,start_2,SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c:307:21: note: ‘spp_2’ was declared here 307 | SeqPortPtr spp_1, spp_2; | ^~~~~ salpstat.c: In function ‘SeqAlignWindowScoreFN’: salpstat.c:2038:45: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 2038 | residue_score[pos]=score; | ~~~~~~~~~~~~~~~~~~^~~~~~ salpstat.c:1915:8: note: ‘score’ was declared here 1915 | Int4 score,win_score,gap_score; | ^~~~~ salpstat.c: In function ‘SeqAlignWindowScore’: salpstat.c:2214:12: warning: ‘scoreptr’ may be used uninitialized [-Wmaybe-uninitialized] 2214 | return scoreptr; | ^~~~~~~~ salpstat.c:2142:16: note: ‘scoreptr’ was declared here 2142 | FloatHiPtr scoreptr; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salpacc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salpacc.h:33, from salpacc.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpacc.c: In function ‘SeqAlignStrand’: salpacc.c:334:20: warning: unused variable ‘this_strand’ [-Wunused-variable] 334 | Uint1Ptr this_strand=Seq_strand_unknown; | ^~~~~~~~~~~ salpacc.c: In function ‘SeqAlignStop’: salpacc.c:561:13: warning: ‘this_stop’ may be used uninitialized [-Wmaybe-uninitialized] 561 | if(this_stop!=-1) | ^ salpacc.c:545:12: note: ‘this_stop’ was declared here 545 | Int4 this_stop; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salprop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salprop.h:46, from salprop.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salprop.c: In function ‘CopySeqLocFromSeqAlign’: salprop.c:398:13: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 398 | else | ^~~~ salprop.c:401:16: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 401 | if(crp != NULL) /*for coding region features*/ | ^~ salprop.c:291:12: warning: variable ‘check_gap’ set but not used [-Wunused-but-set-variable] 291 | Boolean check_gap; | ^~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:867:43: warning: the comparison will always evaluate as ‘true’ for the address of ‘label’ will never be NULL [-Waddress] 867 | if (af.protName==NULL && sesp->label) | ^~ ../include/salsa.h:171:20: note: ‘label’ declared here 171 | Char label[101]; | ^~~~~ salprop.c: In function ‘FeatListToProp’: salprop.c:1336:20: warning: variable ‘feat_itemID’ set but not used [-Wunused-but-set-variable] 1336 | Uint4 feat_itemID; | ^~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from salprop.c:46: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ../include/salprop.h:50:16: warning: ‘GBFeat’ defined but not used [-Wunused-variable] 50 | static CharPtr GBFeat[number_GBFeat] = { | ^~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:861:40: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 861 | if ((val2=is_id_unique (entityID, SeqLocId(sfp->product)))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c:785:20: note: ‘entityID’ was declared here 785 | Uint2 entityID; | ^~~~~~~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:737:12: warning: ‘ppp.p3’ may be used uninitialized [-Wmaybe-uninitialized] 737 | SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:679:17: note: ‘ppp.p3’ was declared here 679 | ParTials ppp; | ^~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:711:6: warning: ‘sfp’ may be used uninitialized [-Wmaybe-uninitialized] 711 | if (sfp != NULL) | ^ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:674:17: note: ‘sfp’ was declared here 674 | SeqFeatPtr sfp; | ^~~ In function ‘CheckPartialInterval’, inlined from ‘ApplyBioFeatToSeqEntry’ at salprop.c:731:12, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:620:11: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 620 | j = stop - SeqLocStop(sfp_location); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:514:17: note: ‘stop’ was declared here 514 | stop, | ^~~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:733:24: warning: ‘ppp.p5’ may be used uninitialized [-Wmaybe-uninitialized] 733 | if (!sfp_p5 && ppp.p5) | ~~~~~~~~^~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:679:17: note: ‘ppp.p5’ was declared here 679 | ParTials ppp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salsap.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salsap.h:57, from salsap.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salsap.c: In function ‘DenseDiagToDenseSegFunc’: salsap.c:2912:30: warning: variable ‘slpstop2’ set but not used [-Wunused-but-set-variable] 2912 | slpstop1 = 0, slpstop2 = 0; | ^~~~~~~~ salsap.c:2912:16: warning: variable ‘slpstop1’ set but not used [-Wunused-but-set-variable] 2912 | slpstop1 = 0, slpstop2 = 0; | ^~~~~~~~ salsap.c:2911:31: warning: variable ‘slpstart2’ set but not used [-Wunused-but-set-variable] 2911 | Int4 slpstart1 = 0, slpstart2 = 0, | ^~~~~~~~~ salsap.c:2911:16: warning: variable ‘slpstart1’ set but not used [-Wunused-but-set-variable] 2911 | Int4 slpstart1 = 0, slpstart2 = 0, | ^~~~~~~~~ salsap.c:2909:28: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2909 | Int4 start1 = 0, start2 = 0, | ^~~~~~ salsap.c:2909:16: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2909 | Int4 start1 = 0, start2 = 0, | ^~~~~~ In file included from ../include/sqnutils.h:51, from salsap.c:47: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salsap.c:3631:13: warning: ‘FindSeqAlignCallback’ defined but not used [-Wunused-function] 3631 | static void FindSeqAlignCallback (SeqEntryPtr sep, Pointer mydata, | ^~~~~~~~~~~~~~~~~~~~ salsap.c:2157:16: warning: ‘AreDenseSegSegmentsValid’ defined but not used [-Wunused-function] 2157 | static Boolean AreDenseSegSegmentsValid (DenseSegPtr dsp, Int4 start, Int4 num) | ^~~~~~~~~~~~~~~~~~~~~~~~ salsap.c: In function ‘CleanStrandsSeqAlign’: salsap.c:1610:15: warning: ‘lenp’ may be used uninitialized [-Wmaybe-uninitialized] 1610 | Int4Ptr lenp; | ^~~~ salsap.c:1611:15: warning: ‘startp’ may be used uninitialized [-Wmaybe-uninitialized] 1611 | Int4Ptr startp; | ^~~~~~ salsap.c:1662:29: warning: ‘numseg’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++) | ~~~~~~^~~~ salsap.c:1613:15: note: ‘numseg’ was declared here 1613 | Int4 numseg; | ^~~~~~ salsap.c:1662:29: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++) | ~~~~~~^~~~ salsap.c:1614:15: note: ‘dim’ was declared here 1614 | Int2 dim; | ^~~ salsap.c: In function ‘LocalAlignToSeqAnnotDimn’: salsap.c:1735:13: warning: ‘the_lens’ may be used uninitialized [-Wmaybe-uninitialized] 1735 | while ( j < lens ) | ~~^~~~~~ salsap.c:1705:25: note: ‘the_lens’ was declared here 1705 | Int4 lenstmp, the_lens; | ^~~~~~~~ salsap.c: In function ‘multseqalign_from_pairseqalign’: salsap.c:4245:6: warning: ‘ok’ may be used uninitialized [-Wmaybe-uninitialized] 4245 | if (!ok) | ^ salsap.c:4209:20: note: ‘ok’ was declared here 4209 | Boolean ok; | ^~ salsap.c:4353:22: warning: ‘strandp’ may be used uninitialized [-Wmaybe-uninitialized] 4353 | strandtmp = *strandp; | ~~~~~~~~~~^~~~~~~~~~ salsap.c:4185:20: note: ‘strandp’ was declared here 4185 | Uint1Ptr strandp; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salstruc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salstruc.h:56, from salstruc.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salstruc.c: In function ‘prot_to_rputprot’: salstruc.c:734:18: warning: comparison between pointer and zero character constant [-Wpointer-compare] 734 | if (strptmp == '\0') break; | ^~ salstruc.c:734:10: note: did you mean to dereference the pointer? 734 | if (strptmp == '\0') break; | ^ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:1338:22: warning: variable ‘maxscroll’ set but not used [-Wunused-but-set-variable] 1338 | Int4 maxscroll; | ^~~~~~~~~ salstruc.c: In function ‘slpfeatcollfunc’: salstruc.c:1999:21: warning: the comparison will always evaluate as ‘false’ for the address of ‘features’ will never be NULL [-Waddress] 1999 | if(csop->features == NULL) | ^~ In file included from ../include/txalign.h:228, from ../include/salstruc.h:57: ../include/jzcoll.h:206:17: note: ‘features’ declared here 206 | Boolean features[FEATDEF_ANY]; /*for filtering unwanted features*/ | ^~~~~~~~ salstruc.c: In function ‘ShowAlignmentText’: salstruc.c:2203:29: warning: variable ‘itemtype’ set but not used [-Wunused-but-set-variable] 2203 | Uint2 entityID, itemtype; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from salstruc.c:40: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from salstruc.c:41: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salstruc.c: In function ‘prot_to_rputprot’: salstruc.c:707:11: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 707 | Int4 j, k; | ^ In function ‘update_fromalignnode’, inlined from ‘data_collect_arrange’ at salstruc.c:1363:13: salstruc.c:1064:46: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 1064 | adp->caret.entityID = entityID; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:1005:17: note: ‘entityID’ was declared here 1005 | Uint2 entityID; | ^~~~~~~~ In function ‘arrange_buffer’, inlined from ‘data_collect_arrange’ at salstruc.c:1433:6: salstruc.c:918:52: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 918 | if (OBJ_(tdp->feattype) == OBJ_BIOSEQ && (is_seqvisible(entityID, itemID, adp->seq_info)) ) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:872:19: note: ‘entityID’ was declared here 872 | Uint2 entityID; | ^~~~~~~~ salstruc.c: In function ‘ShowAlignmentText’: salstruc.c:2258:16: warning: ‘bspsip’ may be used uninitialized [-Wmaybe-uninitialized] 2258 | print_line (fout, tdp->label, bufstr, leftmargin, adp->columnpcell, bspsip, html_option, FALSE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salstruc.c:2194:19: note: ‘bspsip’ was declared here 2194 | SeqIdPtr bspsip; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salutil.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salutil.c: In function ‘ReadBufferFromSap’: salutil.c:128:24: warning: variable ‘buffstart’ set but not used [-Wunused-but-set-variable] 128 | Int4 bufflen, buffstart; | ^~~~~~~~~ salutil.c:127:15: warning: variable ‘sumstart’ set but not used [-Wunused-but-set-variable] 127 | Int4 sumstart; | ^~~~~~~~ salutil.c: In function ‘IS_protSeqLoc’: salutil.c:594:11: warning: variable ‘seq’ set but not used [-Wunused-but-set-variable] 594 | CharPtr seq; | ^~~ salutil.c: In function ‘ReplaceSeqIdWithSeqId’: salutil.c:1236:20: warning: variable ‘oldscope’ set but not used [-Wunused-but-set-variable] 1236 | SeqEntryPtr oldscope; | ^~~~~~~~ salutil.c: In function ‘del_ssp_fromid’: salutil.c:1722:24: warning: variable ‘pressp’ set but not used [-Wunused-but-set-variable] 1722 | SelEdStructPtr ssp, pressp = NULL; | ^~~~~~ salutil.c: In function ‘checkCDSselect_forprotein’: salutil.c:2510:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2510 | if (feat != NULL) | ^ salutil.c: In function ‘NoMoreSegGapForOneAlignment’: salutil.c:3647:8: warning: implicit declaration of function ‘AlnMgr2IndexSingleChildSeqAlign’ [-Wimplicit-function-declaration] 3647 | AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from salutil.c:53: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salutil.c: In function ‘sesp_to_slp’: salutil.c:1974:14: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 1974 | while (j>0) { | ~^~ salutil.c:1927:18: note: ‘j’ was declared here 1927 | Int2 j,k; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF udvseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udvseq.h:100, from udvseq.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvseq.c: In function ‘UDV_EncodeIdxFeat’: udvseq.c:448:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 448 | return *((Int4Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~ udvseq.c: In function ‘UDV_BigEncodeIdxFeat’: udvseq.c:473:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 473 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ udvseq.c: In function ‘UDV_EncodeIdxFeat’: udvseq.c:448:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 448 | return *((Int4Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~ udvseq.c:443:7: note: ‘index_g’ declared here 443 | Uint2 index_g[2]; | ^~~~~~~ udvseq.c: In function ‘UDV_BigEncodeIdxFeat’: udvseq.c:473:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 473 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ udvseq.c:466:7: note: ‘index_g’ declared here 466 | Uint2 index_g[4]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blocks.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/blocks.h:88, from blocks.c:93: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blocks.c: In function ‘IndexBlocks’: blocks.c:928:19: warning: operation on ‘segp_align->to’ may be undefined [-Wsequence-point] 928 | segp_align->to = segp_align->to = -1; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blocks.c: In function ‘IndexNewBlocks’: blocks.c:1084:19: warning: operation on ‘segp_align->to’ may be undefined [-Wsequence-point] 1084 | segp_align->to = segp_align->to = -1; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blocks.c: In function ‘GetBlockOrientation’: blocks.c:2383:11: warning: ‘orient’ may be used uninitialized [-Wmaybe-uninitialized] 2383 | return orient; | ^~~~~~ blocks.c:2259:10: note: ‘orient’ was declared here 2259 | Int4 orient; | ^~~~~~ blocks.c: In function ‘SAMergeBlocks’: blocks.c:2071:27: warning: ‘tmp_curr’ may be used uninitialized [-Wmaybe-uninitialized] 2071 | tmp2->prev = tmp_curr; | ~~~~~~~~~~~^~~~~~~~~~ blocks.c:1317:16: note: ‘tmp_curr’ was declared here 1317 | SegmentPtr tmp_curr; | ^~~~~~~~ blocks.c:1882:34: warning: ‘tmp_head’ may be used uninitialized [-Wmaybe-uninitialized] 1882 | tmp_head->next = tmp_curr; | ~~~~~~~~~~~~~~~^~~~~~~~~~ blocks.c:1318:16: note: ‘tmp_head’ was declared here 1318 | SegmentPtr tmp_head; | ^~~~~~~~ blocks.c:1709:27: warning: ‘prev’ may be used uninitialized [-Wmaybe-uninitialized] 1709 | tmp1->prev = prev; | ~~~~~~~~~~~^~~~~~ blocks.c:1311:16: note: ‘prev’ was declared here 1311 | SegmentPtr prev; | ^~~~ blocks.c:1638:29: warning: ‘new_sabp1’ may be used uninitialized [-Wmaybe-uninitialized] 1638 | new_sabp1->prev = merged; | ~~~~~~~~~~~~~~~~^~~~~~~~ blocks.c:1307:16: note: ‘new_sabp1’ was declared here 1307 | SABlockPtr new_sabp1; | ^~~~~~~~~ blocks.c:2162:30: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized] 2162 | tmp2->prev = tmp_curr; | ~~~~~~~~~~~^~~~~~~~~~ blocks.c:1320:16: note: ‘tmp2’ was declared here 1320 | SegmentPtr tmp2; | ^~~~ blocks.c: In function ‘SASplitBlock’: blocks.c:2796:25: warning: ‘segp2_prev’ may be used uninitialized [-Wmaybe-uninitialized] 2796 | segp2->prev = segp2_prev; | ~~~~~~~~~~~~^~~~~~~~~~~~ blocks.c:2765:16: note: ‘segp2_prev’ was declared here 2765 | SegmentPtr segp2_prev; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pgppop.c pgppop.c:58:2: warning: missing braces around initializer [-Wmissing-braces] 58 | { | ^ 59 | /* Red Grn Blue Color ColorID Old Hex New Hex */ 60 | 255, 255, 255, /* default 0 0xffffff - */ | { } 61 | 255, 00, 153, /* hotpink 1 0xff1493 0xff0099 */ | { } 62 | 255, 0, 255, /* magenta 2 0xff00ff - */ | { } 63 | 153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */ | { } 64 | 0, 0, 255, /* blue 4 0x0000ff - */ | { } 65 | 00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */ | { } 66 | 0, 255, 255, /* cyan 6 0x00ffff - */ | { } 67 | 0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */ | { } 68 | 0, 255, 0, /* green 8 0x00ff00 - */ | { } 69 | 255, 255, 0, /* yellow 9 0xffff00 - */ | { } 70 | 255, 204, 0, /* gold 10 0xffa500 0xffcc00 */ | { } 71 | 255, 102, 0, /* orange 11 0xff4500 0xff6600 */ | { } 72 | 255, 0, 0, /* red 12 0xff0000 - */ | { } 73 | 255, 153, 153, /* pink 13 0xff7256 0xff9999 */ | { } 74 | 255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */ | { } 75 | 255, 255, 255, /* white 15 0xffffff -*/ | { } 76 | 0, 0, 0, /* black 16 0x000000 - */ | { } 77 | 204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/ | { } 78 | 153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */ | { } 79 | 255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */ | { } 80 | 102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */ | { } 81 | 153, 102, 51, /* brown 21 0x8b5742 01x996633 */ | { } 82 | 255, 0, 0, /* perm colors 22: red 0xff0000 - */ | { } 83 | 0, 255, 0, /* perm colors 23: green 0x00ff00 - */ | { } 84 | 255, 0, 255, /* perm colors 24: magenta 0xff00ff - */ | { } 85 | 00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */ | { } 86 | 153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */ | { } 87 | 0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */ | { } 88 | 255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */ | { } 89 | 255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */ | { } 90 | 0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */ | { } 91 | 255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */ | { } 92 | 0, 0, 0 /* background colors 32: black 0x000000 - */ | { 93 | }; | } pgppop.c: In function ‘DDV_WWW_get_CDS_minus’: pgppop.c:329:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 329 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ pgppop.c:327:33: warning: variable ‘numivals2’ set but not used [-Wunused-but-set-variable] 327 | numivals2=0; | ^~~~~~~~~ pgppop.c: In function ‘DDV_WWW_get_CDS_plus’: pgppop.c:451:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 451 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ pgppop.c: In function ‘DDV_DisplayTopScale’: pgppop.c:1300:9: warning: unused variable ‘szBlank’ [-Wunused-variable] 1300 | Char szBlank[TABLE_LEFT_MARGIN+5]={""}; | ^~~~~~~ pgppop.c: In function ‘DDV_GetBLASTCompLine_1’: pgppop.c:1736:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1736 | if (matrix[s][q]>0){ | ^ pgppop.c:1736:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1736 | if (matrix[s][q]>0){ | ^ pgppop.c: In function ‘DDV_DisplayDefaultAlign’: pgppop.c:3169:25: warning: unused variable ‘sabp’ [-Wunused-variable] 3169 | SABlockPtr sabp=NULL;/*indexed SeqAlign*/ | ^~~~ pgppop.c: In function ‘DDV_ShowSeqAlign’: pgppop.c:3512:10: warning: unused variable ‘szPopSetAuth’ [-Wunused-variable] 3512 | Char szPopSetAuth[INFO_SIZE+1]={""}; | ^~~~~~~~~~~~ pgppop.c:3510:10: warning: unused variable ‘szPopSetName’ [-Wunused-variable] 3510 | Char szPopSetName[INFO_SIZE+1]={""};/*article title of the Pop-Set*/ | ^~~~~~~~~~~~ pgppop.c: In function ‘DDV_PrintPopSetSummary’: pgppop.c:3683:9: warning: variable ‘bPairwise’ set but not used [-Wunused-but-set-variable] 3683 | Boolean bPairwise=TRUE,bPrintTax,bPrintCom; | ^~~~~~~~~ In file included from ../include/sqnutils.h:51, from pgppop.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/ddvcreate.h:143, from pgppop.c:54: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ pgppop.c:2664:13: warning: ‘DDV_PrintFastaGappedSequence’ defined but not used [-Wunused-function] 2664 | static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pgppop.c:2617:13: warning: ‘DDV_GetGappedSequence’ defined but not used [-Wunused-function] 2617 | static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence, | ^~~~~~~~~~~~~~~~~~~~~ pgppop.c:1841:13: warning: ‘DDV_HideMaskedLetters’ defined but not used [-Wunused-function] 1841 | static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask) | ^~~~~~~~~~~~~~~~~~~~~ pgppop.c:314:13: warning: ‘DDV_WWW_get_CDS_minus’ defined but not used [-Wunused-function] 314 | static void DDV_WWW_get_CDS_minus(SeqMgrFeatContextPtr context,Int4 start, | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from pgppop.c:51: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ pgppop.c: In function ‘DDV_GetPubValues’: pgppop.c:2873:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2873 | sprintf(szBuf,"%d",year); | ^ In file included from /usr/include/stdio.h:980, from pgppop.c:41: In function ‘sprintf’, inlined from ‘DDV_GetPubValues’ at pgppop.c:2873:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 7 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pgppop.c: In function ‘DDV_PopDisplay2’: pgppop.c:1004:42: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1004 | vnp->next=NULL; | ^ pgppop.c:774:17: note: ‘vnp’ was declared here 774 | ValNodePtr vnp,vnp2;/*used to delete additional ParaG nodes, if needed; | ^~~ pgppop.c:997:36: warning: ‘pgp2’ may be used uninitialized [-Wmaybe-uninitialized] 997 | if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) { | ^ pgppop.c:776:15: note: ‘pgp2’ was declared here 776 | ParaGPtr pgp1,pgp2;/*used to create new ParaGs*/ | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF samutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/samutil.h:230, from samutil.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ samutil.c: In function ‘SAM_AlignIdComp’: samutil.c:796:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 796 | if ((a == NULL) || (b == NULL)) | ^~ samutil.c:799:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 799 | choice = a->choice; | ^~~~~~ samutil.c: In function ‘SAM_AlignIdDup’: samutil.c:852:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 852 | if (oldid == NULL) | ^~ samutil.c:855:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 855 | newid = ValNodeNew(NULL); | ^~~~~ samutil.c: In function ‘DDE_FreeStack’: samutil.c:1556:11: warning: operation on ‘Index’ may be undefined [-Wsequence-point] 1556 | Index = ++Index % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Add’: samutil.c:1611:22: warning: operation on ‘pStack->StackMin’ may be undefined [-Wsequence-point] 1611 | pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE; samutil.c:1622:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1622 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Prev’: samutil.c:1686:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1686 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Next’: samutil.c:1717:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1717 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_ShowRow’: samutil.c:1984:26: warning: variable ‘NumRows’ set but not used [-Wunused-but-set-variable] 1984 | Int4 i, NumRows, HiRow, LowRow, tmp1, tmp2; | ^~~~~~~ samutil.c: In function ‘DDE_AddGapToEndOfAllRows’: samutil.c:3106:41: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 3106 | ValNodePtr ptxtList, last_vnp, vnp; | ^~~ samutil.c: In function ‘DDE_RightAddNode’: samutil.c:3707:33: warning: variable ‘new_vnp’ set but not used [-Wunused-but-set-variable] 3707 | ValNodePtr vnp, next_vnp, new_vnp; | ^~~~~~~ samutil.c: In function ‘DDE_LeftMergeAndAddNodeList’: samutil.c:3757:24: warning: variable ‘RetVal2’ set but not used [-Wunused-but-set-variable] 3757 | Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted; | ^~~~~~~ samutil.c: In function ‘DDE_RightMergeAndAddNodeList’: samutil.c:3813:38: warning: variable ‘RetVal2’ set but not used [-Wunused-but-set-variable] 3813 | Boolean RetVal=FALSE, RetVal1, RetVal2, HeadChanged; | ^~~~~~~ samutil.c: In function ‘DDE_ShiftRightBoundaryLeft1’: samutil.c:4592:41: warning: variable ‘Index’ set but not used [-Wunused-but-set-variable] 4592 | Int4 NumBlocks, i, NumRows, Index, BlockCount=0; | ^~~~~ samutil.c: In function ‘DDE_CreateArraysForDenseSeg’: samutil.c:5028:22: warning: variable ‘NumSegs’ set but not used [-Wunused-but-set-variable] 5028 | Int4 NumRows, NumSegs, i, StartIndex, StopIndex, ArrayIndex=0; | ^~~~~~~ samutil.c: In function ‘DDE_GetLastVNP’: samutil.c:3143:9: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3143 | return(last_vnp); | ^ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_GetNumResidues’: samutil.c:3166:13: warning: ‘to’ may be used uninitialized [-Wmaybe-uninitialized] 3166 | return((to-from) + 1); | ~~~^~~~~~ samutil.c:3153:27: note: ‘to’ was declared here 3153 | Int4 from=-1, to; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvcolor.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvcolor.c:160: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvcolor.c: In function ‘DDV_GetColor’: ddvcolor.c:1422:10: warning: unused variable ‘retval’ [-Wunused-variable] 1422 | Int4 retval = 0; | ^~~~~~ In file included from ../include/samutil.h:234, from ddvcolor.c:165: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF viewmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/viewmgr.h:111, from viewmgr.c:165: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from viewmgr.c:167: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from viewmgr.c:168: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ viewmgr.c:683:13: warning: ‘ViewMgr_Swap’ defined but not used [-Wunused-function] 683 | static void ViewMgr_Swap(SeqAlign *salp1, SeqAlign *salp2) | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvcreate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ddvcreate.h:142, from ddvcreate.c:245: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvcreate.c:290:2: warning: missing braces around initializer [-Wmissing-braces] 290 | { | ^ 291 | /* Red Grn Blue Color ColorID Old Hex New Hex */ 292 | 255, 255, 255, /* default 0 0xffffff - */ | { } 293 | 255, 0, 153, /* hotpink 1 0xff1493 0xff0099 */ | { } 294 | 255, 0, 255, /* magenta 2 0xff00ff - */ | { } 295 | 153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */ | { } 296 | 0, 0, 255, /* blue 4 0x0000ff - */ | { } 297 | 00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */ | { } 298 | 0, 255, 255, /* cyan 6 0x00ffff - */ | { } 299 | 0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */ | { } 300 | 0, 192, 0, /* green 8 0x00ff00 - */ | { } 301 | 255, 255, 0, /* yellow 9 0xffff00 - */ | { } 302 | 255, 204, 0, /* gold 10 0xffa500 0xffcc00 */ | { } 303 | 255, 102, 0, /* orange 11 0xff4500 0xff6600 */ | { } 304 | 255, 0, 0, /* red 12 0xff0000 - */ | { } 305 | 255, 153, 153, /* pink 13 0xff7256 0xff9999 */ | { } 306 | 255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */ | { } 307 | 255, 255, 255, /* white 15 0xffffff -*/ | { } 308 | 0, 0, 0, /* black 16 0x000000 - */ | { } 309 | 204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/ | { } 310 | 153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */ | { } 311 | 255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */ | { } 312 | 102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */ | { } 313 | 153, 102, 51, /* brown 21 0x8b5742 01x996633 */ | { } 314 | 255, 0, 0, /* perm colors 22: red 0xff0000 - */ | { } 315 | 0, 255, 0, /* perm colors 23: green 0x00ff00 - */ | { } 316 | 255, 0, 255, /* perm colors 24: magenta 0xff00ff - */ | { } 317 | 00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */ | { } 318 | 153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */ | { } 319 | 0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */ | { } 320 | 255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */ | { } 321 | 255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */ | { } 322 | 0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */ | { } 323 | 255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */ | { } 324 | 0, 0, 0 /* background colors 32: black 0x000000 - */ | { 325 | }; | } ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_1’: ddvcreate.c:493:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 493 | while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) | ^~~~ ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_2’: ddvcreate.c:529:21: warning: variable ‘more’ set but not used [-Wunused-but-set-variable] 529 | Boolean more; | ^~~~ ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_EX2’: ddvcreate.c:779:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 779 | while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) | ^~~~ ddvcreate.c:690:21: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 690 | Boolean last; | ^~~~ ddvcreate.c:686:21: warning: variable ‘PopulateTo’ set but not used [-Wunused-but-set-variable] 686 | Int4 PopulateTo; | ^~~~~~~~~~ ddvcreate.c: In function ‘DDV_DisplayNewBLAST’: ddvcreate.c:1942:16: warning: variable ‘what’ set but not used [-Wunused-but-set-variable] 1942 | Uint1 what; | ^~~~ ddvcreate.c: In function ‘UDV_BigEncodeIdxFeat4’: ddvcreate.c:2878:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2878 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/ddvcreate.h:143: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ddvcreate.c:249: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:2362:16: warning: ‘DDV_DisplayBlastSAP’ defined but not used [-Wunused-function] 2362 | static Boolean DDV_DisplayBlastSAP(SeqAlignPtr sap, ValNodePtr mask, | ^~~~~~~~~~~~~~~~~~~ ddvcreate.c:525:16: warning: ‘DDV_CreateDisplayFromIndex_2’ defined but not used [-Wunused-function] 525 | static Boolean DDV_CreateDisplayFromIndex_2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c: In function ‘UDV_BigEncodeIdxFeat4’: ddvcreate.c:2878:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 2878 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:2873:7: note: ‘index_g’ declared here 2873 | Uint4 index_g[2]; | ^~~~~~~ ddvcreate.c: In function ‘DDV_PopulateDisplayForDisc’: ddvcreate.c:1048:30: warning: ‘vnp_para’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | vnp_list[n-1]=vnp_para; | ~~~~~~~~~~~~~^~~~~~~~~ ddvcreate.c:845:31: note: ‘vnp_para’ was declared here 845 | ValNodePtr vnp,vnp2,vnp3,vnp_para,vnp_mtdp=NULL; | ^~~~~~~~ ddvcreate.c: In function ‘UABuildDescriptor2’: ddvcreate.c:1541:27: warning: ‘stopcopy’ may be used uninitialized [-Wmaybe-uninitialized] 1541 | *TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/ | ^~ ddvcreate.c:1484:57: note: ‘stopcopy’ was declared here 1484 | Int4 length,r,cumulpop,StartLetter,startcopy,stopcopy,pop,UAnum; | ^~~~~~~~ ddvcreate.c: In function ‘DDV_DumpSAPInAFile’: ddvcreate.c:1798:9: warning: ‘matrix’ may be used uninitialized [-Wmaybe-uninitialized] 1798 | DDV_AffichageParaG(mpplp,0,0,mpplp->LengthAli-1,mpplp->LengthAli,0,option, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1799 | LineSize,hFile,byteSpp,matrix,gclr,NULL); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:1781:17: note: ‘matrix’ was declared here 1781 | Int4Ptr PNTR matrix ; | ^~~~~~ ddvcreate.c: In function ‘DDV_ReadSeqBin’: ddvcreate.c:2593:16: warning: ‘btr’ may be used uninitialized [-Wmaybe-uninitialized] 2593 | return btr; | ^~~ ddvcreate.c:2571:13: note: ‘btr’ was declared here 2571 | Uint1Ptr btr; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF jsavlt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/jsavlt.h:4, from jsavlt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF needleman.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/needleman.h:40, from needleman.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ needleman.c: In function ‘NeedlemanWunschQuadraticByLoc’: needleman.c:281:24: warning: variable ‘bestDbPos’ set but not used [-Wunused-but-set-variable] 281 | Int4 bestQueryPos, bestDbPos; /*position ending best score in | ^~~~~~~~~ needleman.c:281:10: warning: variable ‘bestQueryPos’ set but not used [-Wunused-but-set-variable] 281 | Int4 bestQueryPos, bestDbPos; /*position ending best score in | ^~~~~~~~~~~~ needleman.c: In function ‘FetchSequenceByLoc’: needleman.c:243:12: warning: ‘query’ may be used uninitialized [-Wmaybe-uninitialized] 243 | return query; | ^~~~~ needleman.c:202:13: note: ‘query’ was declared here 202 | Uint1 * query; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF txalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from ../include/txalign.h:228, from txalign.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ txalign.c: In function ‘addLinkoutForDefline’: txalign.c:188:13: warning: variable ‘hasLinkout’ set but not used [-Wunused-but-set-variable] 188 | Boolean hasLinkout=FALSE; | ^~~~~~~~~~ txalign.c: In function ‘addLinkoutForBioseq’: txalign.c:256:13: warning: variable ‘hasLinkout’ set but not used [-Wunused-but-set-variable] 256 | Boolean hasLinkout=FALSE; | ^~~~~~~~~~ txalign.c: In function ‘DrawTextToBuffer’: txalign.c:1254:123: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 1254 | snprintf(checkboxBuf, 200, "", sip->data.intvalue, query_number_glb); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld txalign.c: In function ‘load_align_sum_for_StdSeg’: txalign.c:2230:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2230 | if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) { | ^~~ txalign.c: In function ‘ShowAlignNodeText2Ex’: txalign.c:3030:13: warning: variable ‘is_end’ set but not used [-Wunused-but-set-variable] 3030 | Boolean is_end, strip_semicolon=TRUE; | ^~~~~~ txalign.c: In function ‘Tx_PrintDefLine’: txalign.c:4079:14: warning: unused variable ‘seqid_length’ [-Wunused-variable] 4079 | Int4 seqid_length = 0, total_length = 0; | ^~~~~~~~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4494:39: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 4494 | } else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ txalign.c:4498:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 4498 | if (bsp = BioseqLockById(bestid)) { | ^~~ txalign.c:4200:10: warning: unused variable ‘ColumnDistance’ [-Wunused-variable] 4200 | Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2; | ^~~~~~~~~~~~~~ txalign.c:4192:43: warning: unused variable ‘sip_list’ [-Wunused-variable] 4192 | SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id; | ^~~~~~~~ txalign.c:4188:17: warning: variable ‘ptr_start’ set but not used [-Wunused-but-set-variable] 4188 | Char *ptr, *ptr_start, *eval_buff_ptr, *bit_score_buff_ptr; | ^~~~~~~~~ txalign.c: In function ‘FormatScoreFromSeqAlignEx’: txalign.c:4817:25: warning: unused variable ‘t_adj’ [-Wunused-variable] 4817 | Int4 m_adj = 0, t_adj = 0; | ^~~~~ txalign.c:4816:29: warning: unused variable ‘last_t_to’ [-Wunused-variable] 4816 | Int4 last_m_to = 0, last_t_to = 0; | ^~~~~~~~~ txalign.c: In function ‘FSFPrintOneDefline’: txalign.c:4925:14: warning: variable ‘seqid_len’ set but not used [-Wunused-but-set-variable] 4925 | Int4 gi, seqid_len = 0; | ^~~~~~~~~ txalign.c: In function ‘FormatScoreFunc’: txalign.c:5142:13: warning: variable ‘allocated’ set but not used [-Wunused-but-set-variable] 5142 | Boolean allocated, first; | ^~~~~~~~~ txalign.c: In function ‘OOFShowSingleAlignment’: txalign.c:5808:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 5808 | else if(matrix[line1[line_index]][line2[line_index]] > 0) | ~~~~~^~~~~~~~~~~~ txalign.c:5808:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 5808 | else if(matrix[line1[line_index]][line2[line_index]] > 0) | ~~~~~^~~~~~~~~~~~ txalign.c:5575:13: warning: variable ‘lines’ set but not used [-Wunused-but-set-variable] 5575 | Int4 i, lines, k, shift_info = 0; | ^~~~~ txalign.c: In function ‘OOFDisplayTraceBack1’: txalign.c:6063:33: warning: unused variable ‘st’ [-Wunused-variable] 6063 | tmp[10] = " ", *st; | ^~ txalign.c:6063:9: warning: unused variable ‘tmp’ [-Wunused-variable] 6063 | tmp[10] = " ", *st; | ^~~ txalign.c: In function ‘OOFDisplayTraceBack2’: txalign.c:6137:33: warning: unused variable ‘st’ [-Wunused-variable] 6137 | tmp[10] = " ", *st; | ^~ txalign.c: In function ‘FDGetTaxNamesFromBioseq’: txalign.c:6239:21: warning: variable ‘bdsp’ set but not used [-Wunused-but-set-variable] 6239 | BlastDefLinePtr bdsp; | ^~~~ txalign.c: At top level: txalign.c:310:19: warning: ‘ProcessTextInsertion’ declared ‘static’ but never defined [-Wunused-function] 310 | static ValNodePtr ProcessTextInsertion PROTO((AlignNodePtr anp, Int4 m_left, Int4 m_right, BioseqPtr bsp, Int4 line_len, Int1 frame)); | ^~~~~~~~~~~~~~~~~~~~ txalign.c:2915:1: warning: ‘get_seq_id’ defined but not used [-Wunused-function] 2915 | get_seq_id(SeqAlignPtr sap, Int2 index) | ^~~~~~~~~~ txalign.c:1820:16: warning: ‘has_hit_in_region’ defined but not used [-Wunused-function] 1820 | static Boolean has_hit_in_region(Uint1Ptr all_frame) | ^~~~~~~~~~~~~~~~~ txalign.c:112:16: warning: ‘getNameInitials’ defined but not used [-Wunused-function] 112 | static CharPtr getNameInitials(CharPtr name){ | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘snprintf’, inlined from ‘DrawTextToBuffer’ at txalign.c:1288:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: warning: ‘HTML_buffer’ may be used uninitialized [-Wmaybe-uninitialized] 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ txalign.c: In function ‘DrawTextToBuffer’: txalign.c:1094:17: note: ‘HTML_buffer’ was declared here 1094 | CharPtr HTML_buffer; | ^~~~~~~~~~~ txalign.c: In function ‘OOFShowSingleAlignment.isra.0’: txalign.c:5719:12: warning: ‘dna_line_start’ may be used uninitialized [-Wmaybe-uninitialized] 5719 | if (dna_line_start == 0) | ^ txalign.c:5571:32: note: ‘dna_line_start’ was declared here 5571 | Int4 dna_index, pro_index, dna_line_start, pro_line_start; | ^~~~~~~~~~~~~~ txalign.c:5722:11: warning: ‘pro_line_start’ may be used uninitialized [-Wmaybe-uninitialized] 5722 | if(pro_line_start == 0) | ^ txalign.c:5571:48: note: ‘pro_line_start’ was declared here 5571 | Int4 dna_index, pro_index, dna_line_start, pro_line_start; | ^~~~~~~~~~~~~~ In function ‘load_align_sum_for_DenseDiag’, inlined from ‘find_score_in_align’ at txalign.c:2404:21: txalign.c:1941:14: warning: ‘m_spp’ may be used uninitialized [-Wmaybe-uninitialized] 1941 | if(m_spp == NULL || t_spp == NULL) { | ^ txalign.c: In function ‘find_score_in_align’: txalign.c:1876:16: note: ‘m_spp’ was declared here 1876 | SeqPortPtr m_spp, t_spp; | ^~~~~ In function ‘load_align_sum_for_DenseDiag’, inlined from ‘find_score_in_align’ at txalign.c:2404:21: txalign.c:1941:31: warning: ‘t_spp’ may be used uninitialized [-Wmaybe-uninitialized] 1941 | if(m_spp == NULL || t_spp == NULL) { | ^ txalign.c: In function ‘find_score_in_align’: txalign.c:1876:23: note: ‘t_spp’ was declared here 1876 | SeqPortPtr m_spp, t_spp; | ^~~~~ In function ‘load_align_sum_for_DenseSeg’, inlined from ‘find_score_in_align’ at txalign.c:2413:13: txalign.c:2080:35: warning: ‘smtp’ may be used uninitialized [-Wmaybe-uninitialized] 2080 | stdaa_res = SeqMapTableConvert(smtp, t_res); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ txalign.c: In function ‘find_score_in_align’: txalign.c:1980:20: note: ‘smtp’ was declared here 1980 | SeqMapTablePtr smtp; | ^~~~ In file included from ../include/ncbi.h:58: In function ‘translate_faked_cds’, inlined from ‘ShowAlignNodeText2Ex.isra.0’ at txalign.c:3457:46: txalign.c:1753:63: warning: ‘m_len’ may be used uninitialized [-Wmaybe-uninitialized] 1753 | n = MAX(0, (master_len-1 - m_stop)/3 -1); | ~~~~~~~~~~^~ txalign.c: In function ‘ShowAlignNodeText2Ex.isra.0’: txalign.c:3025:10: note: ‘m_len’ was declared here 3025 | Int4 m_len; /*length of the master sequence*/ | ^~~~~ txalign.c: In function ‘ShowTextAlignFromAnnot3’: txalign.c:949:12: warning: ‘retval’ may be used uninitialized [-Wmaybe-uninitialized] 949 | return retval; | ^~~~~~ txalign.c:726:13: note: ‘retval’ was declared here 726 | Boolean retval, matrix_loaded=FALSE; | ^~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4647:50: warning: ‘%s’ directive writing up to 2048 bytes into a region of size 2038 [-Wformat-overflow=] 4647 | sprintf(buffer1, "%s", id_buffer, bit_score_buff_ptr); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintDefLinesFromSeqAlignWithPath’ at txalign.c:4647:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 2074 bytes into a destination of size 2049 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4645:51: warning: ‘%s’ directive writing up to 2048 bytes into a region of size 2037 [-Wformat-overflow=] 4645 | sprintf(buffer1, " %s", id_buffer, bit_score_buff_ptr); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintDefLinesFromSeqAlignWithPath’ at txalign.c:4645:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 2074 bytes into a destination of size 2049 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF fdlobj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from fdlobj.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ fdlobj.c: In function ‘BlastDefLineSetAsnRead’: fdlobj.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ fdlobj.c: In function ‘BlastDefLineAsnRead’: fdlobj.c:202:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 202 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF alignmgr2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/alignmgr2.h:110, from alignmgr2.c:242: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignmgr2.c: In function ‘AlnMgr2IndexSingleDenseSegSA’: alignmgr2.c:885:13: warning: statement with no effect [-Wunused-value] 885 | for (j; jnumseg && next == -1; j++) | ^~~ alignmgr2.c: In function ‘AlnMgr2CopySeg’: alignmgr2.c:2984:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2984 | if (ldelta = ABS(s->beg - beg)) { | ^~~~~~ alignmgr2.c: In function ‘AlnMgr2AddInNewPairwiseSA’: alignmgr2.c:3221:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3221 | while (a = AlnMgr2GetNextSeqPiece(a)) { | ^ alignmgr2.c:3223:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3223 | while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) { | ^ alignmgr2.c:3233:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3233 | while (A = AlnMgr2GetNextSeqPiece(A)) { | ^ alignmgr2.c:3237:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3237 | while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {}; | ^ alignmgr2.c: In function ‘AlnMgr2SetUnaln’: alignmgr2.c:5410:22: warning: variable ‘dsp’ set but not used [-Wunused-but-set-variable] 5410 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2PrintSeqAlign’: alignmgr2.c:5623:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 5623 | while (more = AlnMgr2GetNextAlnBit(sap, amp)) | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNextAlnBit’: alignmgr2.c:5719:21: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 5719 | Boolean found; | ^~~~~ alignmgr2.c: In function ‘AlnMgr2GetUnalignedInfo’: alignmgr2.c:6085:22: warning: variable ‘saip’ set but not used [-Wunused-but-set-variable] 6085 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetInterruptInfo’: alignmgr2.c:6331:7: warning: statement with no effect [-Wunused-value] 6331 | for (i; isegnum; i++) | ^~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLength’: alignmgr2.c:6774:20: warning: comparison between pointer and zero character constant [-Wpointer-compare] 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ^~ alignmgr2.c:6774:8: note: did you mean to dereference the pointer? 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ^ alignmgr2.c: In function ‘AlnMgr2ComputeScoreForSeqAlign’: alignmgr2.c:8341:17: warning: variable ‘numseqs’ set but not used [-Wunused-but-set-variable] 8341 | Int4 numseqs; | ^~~~~~~ alignmgr2.c:8339:17: warning: variable ‘mismatch’ set but not used [-Wunused-but-set-variable] 8339 | Int4 mismatch; | ^~~~~~~~ alignmgr2.c:8338:17: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 8338 | Int4 len; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignmgr2.c:3557:13: warning: ‘AlnMgr2AddInNewSA’ defined but not used [-Wunused-function] 3557 | static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~ alignmgr2.c:2368:18: warning: ‘AlnMgr2GetEdgeList’ defined but not used [-Wunused-function] 2368 | static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used) | ^~~~~~~~~~~~~~~~~~ alignmgr2.c:2140:13: warning: ‘AlnMgr2SortVerticesByNumEdges’ defined but not used [-Wunused-function] 2140 | static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:1061:13: warning: ‘AlnMgr2UnpackSeqAlignChain’ defined but not used [-Wunused-function] 1061 | static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘AlnMgr2UnpackSeqAlign’, inlined from ‘AlnMgr2IndexLite’ at alignmgr2.c:1169:9: alignmgr2.c:1001:33: warning: ‘sap_segs_prev’ may be used uninitialized [-Wmaybe-uninitialized] 1001 | sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2IndexLite’: alignmgr2.c:968:17: note: ‘sap_segs_prev’ was declared here 968 | SeqAlignPtr sap_segs_prev; | ^~~~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2GetUnalignedInfo’: alignmgr2.c:6106:26: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6106 | if (dsp->starts[dsp->dim*i+row-1] != -1) | ~~~^~~~~ alignmgr2.c:6082:21: note: ‘dsp’ was declared here 6082 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2GetMaxUnalignedLength’: alignmgr2.c:7066:23: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7066 | for (row=0; rowdim && !found; row++) | ~~~^~~~~ alignmgr2.c:7042:21: note: ‘dsp’ was declared here 7042 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7068:23: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7068 | for (i=0; isrdp[row]->numunaln && !found; i++) | ~~~~^~~~~~ alignmgr2.c:7048:22: note: ‘saip’ was declared here 7048 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetInterruptInfo’: alignmgr2.c:6178:11: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6178 | if (dsp->numseg < interrupt->segnum) | ~~~^~~~~~~~ alignmgr2.c:6148:22: note: ‘dsp’ was declared here 6148 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6180:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6180 | if (saip->anchor > 0) | ~~~~^~~~~~~~ alignmgr2.c:6157:22: note: ‘saip’ was declared here 6157 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c:6353:16: warning: ‘iip’ may be used uninitialized [-Wmaybe-uninitialized] 6353 | iip->strand = strand; | ~~~~~~~~~~~~^~~~~~~~ alignmgr2.c:6150:22: note: ‘iip’ was declared here 6150 | AMInterrInfoPtr iip; | ^~~ In function ‘AlnMgr2GetNthSeqRangeInSASet’, inlined from ‘AlnMgr2GetNthSeqRangeInSA’ at alignmgr2.c:6470:10: alignmgr2.c:6595:14: warning: ‘from’ may be used uninitialized [-Wmaybe-uninitialized] 6595 | *start = from; | ~~~~~~~^~~~~~ alignmgr2.c: In function ‘AlnMgr2GetNthSeqRangeInSA’: alignmgr2.c:6567:22: note: ‘from’ declared here 6567 | Int4 from; | ^~~~ In function ‘AlnMgr2GetNthSeqRangeInSASet’, inlined from ‘AlnMgr2GetNthSeqRangeInSA’ at alignmgr2.c:6470:10: alignmgr2.c:6595:14: warning: ‘from’ may be used uninitialized [-Wmaybe-uninitialized] 6595 | *start = from; | ~~~~~~~^~~~~~ alignmgr2.c: In function ‘AlnMgr2GetNthSeqRangeInSA’: alignmgr2.c:6567:22: note: ‘from’ declared here 6567 | Int4 from; | ^~~~ alignmgr2.c:6490:62: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6490 | end = dsp->starts[srdp->sect[0]*(dsp->dim) + n-1] + dsp->lens[srdp->sect[0]] - 1; | ~~~^~~~~~ alignmgr2.c:6449:21: note: ‘dsp’ was declared here 6449 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6476:16: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6476 | if (n > saip->numrows || n <= 0) | ~~~~^~~~~~~~~ alignmgr2.c:6451:22: note: ‘saip’ was declared here 6451 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthRowSpanInSA’: alignmgr2.c:6558:41: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6558 | *stop = saip->aligncoords[i] + dsp->lens[srdp->sect[srdp->numsect-1]] - 1; | ~~~^~~~~~ alignmgr2.c:6510:21: note: ‘dsp’ was declared here 6510 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6533:16: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6533 | if (n > saip->numrows || n <= 0) | ~~~~^~~~~~~~~ alignmgr2.c:6512:22: note: ‘saip’ was declared here 6512 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLength’: alignmgr2.c:6786:22: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6786 | for (i=0; inumseg; i++) | ~~~^~~~~~~~ alignmgr2.c:6751:21: note: ‘dsp’ was declared here 6751 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6774:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ~~~~^~~~~~~ alignmgr2.c:6755:22: note: ‘saip’ was declared here 6755 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c:6789:17: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 6789 | len += AlnMgr2GetMaxUnalignedLength(salp, i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:6756:21: note: ‘salp’ was declared here 6756 | SeqAlignPtr salp; | ^~~~ In file included from ../include/ncbi.h:59: alignmgr2.c: In function ‘AlnMgr2GetNextAlnBit’: alignmgr2.c:5787:35: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 5787 | trans = (Uint2Ptr)MemNew(dsp->numseg*sizeof(Uint2)); | ~~~^~~~~~~~ alignmgr2.c:5717:21: note: ‘dsp’ was declared here 5717 | DenseSegPtr dsp; | ^~~ alignmgr2.c:5759:27: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 5759 | if (amp->row_num > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:5727:22: note: ‘saip’ was declared here 5727 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2IsSAPDiscAli’: alignmgr2.c:6813:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6813 | if (saip->numunaln > 0) | ~~~~^~~~~~~~~~ alignmgr2.c:6799:22: note: ‘saip’ was declared here 6799 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNumAlnBlocks’: alignmgr2.c:6836:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6836 | if (saip->numunaln >= 0) | ~~~~^~~~~~~~~~ alignmgr2.c:6822:22: note: ‘saip’ was declared here 6822 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthBlockRange’: alignmgr2.c:6866:17: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6866 | if (n >= saip->numunaln) | ~~~~^~~~~~~~~~ alignmgr2.c:6848:22: note: ‘saip’ was declared here 6848 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthUnalignedForNthRow’: alignmgr2.c:6927:57: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6927 | if (i == -1 || saip->srdp[row-1]->unaligned[i] >= dsp->numseg-1) | ~~~^~~~~~~~ alignmgr2.c:6887:22: note: ‘dsp’ was declared here 6887 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6907:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6907 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:6889:22: note: ‘saip’ was declared here 6889 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNextLengthBit’: alignmgr2.c:7021:25: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7021 | maxseg = dsp->numseg-1; | ~~~^~~~~~~~ alignmgr2.c:6954:22: note: ‘dsp’ was declared here 6954 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6974:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6974 | if (saip->numunaln == -1) /* the whole thing is just one big aligned segment */ | ~~~~^~~~~~~~~~ alignmgr2.c:6958:22: note: ‘saip’ was declared here 6958 | SAIndex2Ptr saip; | ^~~~ In function ‘binary_search_on_uint4_list’, inlined from ‘AlnMgr2GetNumSegsInRange’ at alignmgr2.c:7185:12: alignmgr2.c:6038:13: warning: ‘aligncoords’ may be used uninitialized [-Wmaybe-uninitialized] 6038 | if (list == NULL || listlen == 0) | ^ alignmgr2.c: In function ‘AlnMgr2GetNumSegsInRange’: alignmgr2.c:7150:21: note: ‘aligncoords’ was declared here 7150 | Uint4Ptr aligncoords; | ^~~~~~~~~~~ alignmgr2.c:7185:62: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7185 | start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg); | ~~~^~~~~~~~ alignmgr2.c:7152:21: note: ‘dsp’ was declared here 7152 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2MapBioseqToSeqAlign’: alignmgr2.c:7649:51: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7649 | offset = pos - dsp->starts[(srdp->sect[L])*(dsp->dim)+row-1]; | ~~~~^~~~~~ alignmgr2.c:7590:21: note: ‘dsp’ was declared here 7590 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7619:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7619 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:7596:22: note: ‘saip’ was declared here 7596 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2MapSeqAlignToBioseq’: alignmgr2.c:7730:55: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7730 | return (dsp->starts[sect*(dsp->dim)+row-1] + dsp->lens[sect] - 1 - offset); | ~~~^~~~~~ alignmgr2.c:7685:21: note: ‘dsp’ was declared here 7685 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7712:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7712 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:7688:21: note: ‘saip’ was declared here 7688 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetSubAlign’: alignmgr2.c:8036:13: warning: ‘sap_real’ may be used uninitialized [-Wmaybe-uninitialized] 8036 | if ((a = AlnMgr2FindAnchor(sap_real)) > 0) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:7999:21: note: ‘sap_real’ was declared here 7999 | SeqAlignPtr sap_real; | ^~~~~~~~ alignmgr2.c: In function ‘AlnMgr2FillInUnaligned’: alignmgr2.c:9869:12: warning: ‘offset’ may be used uninitialized [-Wmaybe-uninitialized] 9869 | curr = curr + 1 + offset; | ~~~~~^~~~~~~~~~~~~~~~~~~ alignmgr2.c:9754:17: note: ‘offset’ was declared here 9754 | Int4 offset; | ^~~~~~ alignmgr2.c: In function ‘AlnMgr2MapBioseqToSeqAlignStdSeg’: alignmgr2.c:10175:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10175 | stop1 = SeqLocStop(slp_longest); | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2MapSeqAlignToBioseqStdSeg’: alignmgr2.c:10209:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10209 | stop1 = SeqLocStop(slp_longest); | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLengthStdSeg’: alignmgr2.c:10236:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10236 | return (SeqLocLen(slp_longest)); | ~^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF alnread.c In function ‘s_AddDeflineFromOrganismLine’, inlined from ‘s_ReadOrgNamesFromText’ at alnread.c:2949:9: alnread.c:2876:17: warning: ‘free’ called on pointer ‘clp_145->end’ with nonzero offset 1 [-Wfree-nonheap-object] 2876 | free (defline); | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF acerdapi.c acerdapi.c: In function ‘DoesSeqStringMatchBsp’: acerdapi.c:201:30: warning: variable ‘seq_len’ set but not used [-Wunused-but-set-variable] 201 | Int4 ctr, pos = 0, i, len, seq_len; | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from acerdapi.c:40: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF aceread.c aceread.c:3308:12: warning: ‘s_GetUngappedPosition’ defined but not used [-Wunused-function] 3308 | static int s_GetUngappedPosition (int gapped_pos, char *seq) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:276:13: warning: ‘AdjustGapInfoFor3Trim’ defined but not used [-Wunused-function] 276 | static void AdjustGapInfoFor3Trim (TGapInfoPtr gap_info, int new_len) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:247:13: warning: ‘AdjustGapInfoFor5Trim’ defined but not used [-Wunused-function] 247 | static void AdjustGapInfoFor5Trim (TGapInfoPtr gap_info, int trim) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:134:12: warning: ‘s_IsGapChar’ defined but not used [-Wunused-function] 134 | static int s_IsGapChar (char ch, char *gap_chars) | ^~~~~~~~~~~ aceread.c: In function ‘ReadListFree’: aceread.c:2148:11: warning: pointer ‘r_next_11’ used after ‘free’ [-Wuse-after-free] 2148 | r = r_next; | ~~^~~~~~~~ aceread.c:2147:9: note: call to ‘free’ here 2147 | free (r); | ^~~~~~~~ aceread.c: In function ‘s_ReadContig’: aceread.c:1477:12: warning: ‘linestring’ may be used uninitialized [-Wmaybe-uninitialized] 1477 | if (linestring != NULL) free (linestring); | ^ aceread.c:1384:16: note: ‘linestring’ was declared here 1384 | char *linestring; | ^~~~~~~~~~ rm -f libncbiobj.a ar cru libncbiobj.a objacces.o objalign.o objall.o objbibli.o objfeat.o objgen.o objloc.o objmedli.o objpub.o objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o objsub.o objprt.o objfdef.o objalignloc.o objtable.o objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o objvalid.o mimapi.o cddapi.o seqport.o sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o valid.o valapi.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o acerdapi.o aceread.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiobj.a ../lib ranlib ../lib/libncbiobj.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cdentrez.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from cdentrez.c:162: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdentrez.c:283:23: warning: ‘CdEntMlSumGet’ declared ‘static’ but never defined [-Wunused-function] 283 | static DocSumPtr NEAR CdEntMlSumGet PROTO((Int4 uid)); | ^~~~~~~~~~~~~ cdentrez.c:310:23: warning: ‘CdEntSeqSumGet’ declared ‘static’ but never defined [-Wunused-function] 310 | static DocSumPtr NEAR CdEntSeqSumGet PROTO((Int4 uid, DocType type)); | ^~~~~~~~~~~~~~ cdentrez.c:2935:23: warning: ‘MedSumAsnRead’ defined but not used [-Wunused-function] 2935 | static DocSumPtr NEAR MedSumAsnRead (AsnIoPtr aip, DocUid uid) | ^~~~~~~~~~~~~ cdentrez.c:1616:26: warning: ‘FreePostingList’ defined but not used [-Wunused-function] 1616 | static ByteStorePtr NEAR FreePostingList (ByteStorePtr lst) | ^~~~~~~~~~~~~~~ cdentrez.c:307:20: warning: ‘BIOSEQ_id_E’ defined but not used [-Wunused-variable] 307 | static AsnTypePtr BIOSEQ_id_E = NULL; | ^~~~~~~~~~~ cdentrez.c: In function ‘CdEntrezMergeTerm’: cdentrez.c:2637:12: warning: ‘termpage’ may be used uninitialized [-Wmaybe-uninitialized] 2637 | if (termpage >= 0) { | ^ cdentrez.c:2573:9: note: ‘termpage’ was declared here 2573 | Int4 termpage; | ^~~~~~~~ cdentrez.c:2672:17: warning: ‘special’ may be used uninitialized [-Wmaybe-uninitialized] 2672 | *spcl = special; | ~~~~~~^~~~~~~~~ cdentrez.c:2570:9: note: ‘special’ was declared here 2570 | Int4 special; | ^~~~~~~ cdentrez.c:2665:18: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 2665 | if (scanOk && total > 0) { | ~~~~~~~^~~~~~~~~~~~ cdentrez.c:2572:9: note: ‘total’ was declared here 2572 | Int4 total; | ^~~~~ cdentrez.c: In function ‘CdLinkUidList’: cdentrez.c:938:16: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 938 | return count; | ^~~~~ cdentrez.c:926:14: note: ‘count’ was declared here 926 | Int4 count; | ^~~~~ cdentrez.c: In function ‘CdTermListByTerm’: cdentrez.c:1023:24: warning: ‘first’ may be used uninitialized [-Wmaybe-uninitialized] 1023 | the_first_page = first; | ~~~~~~~~~~~~~~~^~~~~~~ cdentrez.c:1011:15: note: ‘first’ was declared here 1011 | Int4 first; | ^~~~~ In file included from ../include/ncbi.h:62: cdentrez.c: In function ‘CdEntTLAddTerm’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ In function ‘FindTermNode’, inlined from ‘CdEntTLAddTerm’ at cdentrez.c:617:14: cdentrez.c:1895:24: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 1895 | if (scanOk && total > 0) { | ~~~~~~~^~~~~~~~~~~~ cdentrez.c: In function ‘CdEntTLAddTerm’: cdentrez.c:1787:13: note: ‘total’ was declared here 1787 | Int4 total; | ^~~~~ cdentrez.c: In function ‘CdEntrezFindTerm’: cdentrez.c:1119:20: warning: ‘ctp’ may be used uninitialized [-Wmaybe-uninitialized] 1119 | if (ctp == NULL) | ^ cdentrez.c:1100:19: note: ‘ctp’ was declared here 1100 | CdTermPtr ctp; | ^~~ cdentrez.c: In function ‘CdEntMedlineEntryListGet’: cdentrez.c:2715:20: warning: ‘aip’ may be used uninitialized [-Wmaybe-uninitialized] 2715 | if (aip != NULL) | ^ cdentrez.c:2697:18: note: ‘aip’ was declared here 2697 | AsnIoPtr aip; | ^~~ cdentrez.c: In function ‘CdSeqSumAsnRead’: cdentrez.c:3424:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3424 | sprintf (cds, " cds%d", (int) proteins); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘CdSeqSumAsnRead’ at cdentrez.c:3424:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cdromlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objacces.h:64, from ../include/cdromlib.h:71, from cdromlib.c:73: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cdnewlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objacces.h:64, from ../include/cdromlib.h:71, from cdnewlib.c:208: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdnewlib.c:600:27: warning: missing braces around initializer [-Wmissing-braces] 600 | struct CdFInfo _finfo[] = { | ^ 601 | "", 0, 0, | { } 602 | "hca", MAGIC_hca, FORMAT_hca, | { } 603 | "sum", MAGIC_sum, FORMAT_sum, | { } 604 | "lnk", MAGIC_lnk, FORMAT_lnk, | { } 605 | "ofs", MAGIC_ofs, FORMAT_ofs, | { } 606 | "oix", MAGIC_oix, FORMAT_oix, | { } 607 | "trm", MAGIC_trm, FORMAT_trm, | { } 608 | "tix", MAGIC_tix, FORMAT_tix, | { } 609 | "pst", MAGIC_pst, FORMAT_pst, | { } 610 | "inf", MAGIC_inf, FORMAT_inf | { 611 | }; | } cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces] 614 | struct CdDirInfo _dir[] = { | ^ cdnewlib.c: In function ‘cd3_CdDocAsnOpen’: cdnewlib.c:1342:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1342 | return (AsnIo*) CatastrophicFailure(1); | ^ cdnewlib.c:1327:23: warning: unused variable ‘fdir’ [-Wunused-variable] 1327 | char *fdir = NULL; | ^~~~ cdnewlib.c: In function ‘UidIndex_ReadPage’: cdnewlib.c:1937:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1937 | return (long*)CatastrophicFailure(1); | ^ cdnewlib.c:1945:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1945 | return (long*)CatastrophicFailure(1); | ^ cdnewlib.c: In function ‘CdDevice_Init’: cdnewlib.c:2739:13: warning: variable ‘cd_num’ set but not used [-Wunused-but-set-variable] 2739 | int cd_num; | ^~~~~~ cdnewlib.c: At top level: cdnewlib.c:3605:13: warning: ‘Cache_Purge’ defined but not used [-Wunused-function] 3605 | static void Cache_Purge (Cache *cache) | ^~~~~~~~~~~ cdnewlib.c:3592:14: warning: ‘Cache_Peek’ defined but not used [-Wunused-function] 3592 | static void* Cache_Peek (Cache *cache, long id) | ^~~~~~~~~~ cdnewlib.c:3569:12: warning: ‘Cache_Touch’ defined but not used [-Wunused-function] 3569 | static int Cache_Touch (Cache *cache, long id) | ^~~~~~~~~~~ cdnewlib.c:3506:12: warning: ‘Cache_Delete’ defined but not used [-Wunused-function] 3506 | static int Cache_Delete (Cache *cache, long id) | ^~~~~~~~~~~~ cdnewlib.c:638:18: warning: ‘_div’ defined but not used [-Wunused-variable] 638 | static DivInfo * _div; | ^~~~ cdnewlib.c:582:15: warning: ‘_empty_string’ defined but not used [-Wunused-variable] 582 | static char * _empty_string = ""; | ^~~~~~~~~~~~~ cdnewlib.c: In function ‘trmncmp’: cdnewlib.c:2375:12: warning: ‘c1’ may be used uninitialized [-Wmaybe-uninitialized] 2375 | if (c1 == '/') | ^ cdnewlib.c:2362:16: note: ‘c1’ was declared here 2362 | int i, c1, c2; | ^~ cdnewlib.c:2377:17: warning: ‘c2’ may be used uninitialized [-Wmaybe-uninitialized] 2377 | else if (c2 == '/') | ^ cdnewlib.c:2362:20: note: ‘c2’ was declared here 2362 | int i, c1, c2; | ^~ cdnewlib.c: In function ‘CdDevice_FileBuildPath.isra.0’: cdnewlib.c:2679:33: warning: ‘__strncat_chk’ specified bound 16 equals destination size [-Wstringop-truncation] 2679 | strncat(volname,cddev->volume->volume_name,sizeof volname); | ^ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘CdDevice_FileBuildPath.isra.0’ at cdnewlib.c:2679:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 16 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ cdnewlib.c: In function ‘UnixFileGets’: cdnewlib.c:1509:6: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized] 1509 | if (ch == '\0') { | ^ cdnewlib.c:1489:8: note: ‘ch’ was declared here 1489 | int ch; | ^~ cdnewlib.c: In function ‘CdDevice_Init’: cdnewlib.c:2751:17: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-truncation] 2751 | strncat(fpath,cddev->inf.root,sizeof fpath); | ^ cdnewlib.c:2769:41: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-truncation] 2769 | strncat(fpath,cddev->inf.root,sizeof fpath); | ^ In function ‘strncat’, inlined from ‘CdDevice_Init’ at cdnewlib.c:2751:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘CdDevice_Init’ at cdnewlib.c:2769:6: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ cdnewlib.c: In function ‘TrmIndex_Lookup’: cdnewlib.c:2166:19: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized] 2166 | for ( ; d <= 0 && mid >0; --mid) | ~~^~~~ cdnewlib.c:2136:31: note: ‘d’ was declared here 2136 | int lo, hi, mid, len, d; | ^ cdnewlib.c:2166:31: warning: ‘mid’ may be used uninitialized [-Wmaybe-uninitialized] 2166 | for ( ; d <= 0 && mid >0; --mid) | ~~~~^~ cdnewlib.c:2136:21: note: ‘mid’ was declared here 2136 | int lo, hi, mid, len, d; | ^~~ cdnewlib.c:2168:41: warning: ‘term’ may be used uninitialized [-Wmaybe-uninitialized] 2168 | if (d==0 && len == (int)strlen(term)) | ^~~~~~~~~~~~ cdnewlib.c:2137:15: note: ‘term’ was declared here 2137 | char *term; | ^~~~ cdnewlib.c: In function ‘UidIndex_Lookup’: cdnewlib.c:1986:27: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 1986 | page_num = (uid < *p && mid >0) ? mid-1 : mid; | ^~ cdnewlib.c:1956:22: note: ‘p’ was declared here 1956 | long *page, *p; | ^ cdnewlib.c:1986:30: warning: ‘mid’ may be used uninitialized [-Wmaybe-uninitialized] 1986 | page_num = (uid < *p && mid >0) ? mid-1 : mid; | ~~~~~~~~~~^~~~~~~~~~ cdnewlib.c:1953:21: note: ‘mid’ was declared here 1953 | int lo, hi, mid; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF casn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from casn.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cdconfig.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cdconfig.c:75: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:58: cdconfig.c: In function ‘ChangeMedia’: ../include/ncbistd.h:247:15: warning: statement with no effect [-Wunused-value] 247 | #define FALSE ((Nlm_Boolean)0) | ^ ../include/ncbifile.h:144:76: note: in expansion of macro ‘FALSE’ 144 | #define EjectCd(sVolume, deviceName, rawDeviceName, mountPoint, mountCmd) FALSE | ^~~~~ cdconfig.c:941:29: note: in expansion of macro ‘EjectCd’ 941 | EjectCd(toBeEjected->entrez_info->volume_label, | ^~~~~~~ ../include/ncbistd.h:247:15: warning: statement with no effect [-Wunused-value] 247 | #define FALSE ((Nlm_Boolean)0) | ^ ../include/ncbifile.h:145:76: note: in expansion of macro ‘FALSE’ 145 | #define MountCd(sVolume, deviceName, mountPoint, mountCmd) FALSE | ^~~~~ cdconfig.c:960:17: note: in expansion of macro ‘MountCd’ 960 | MountCd(newMedia->entrez_info->volume_label, cdm->device_name, | ^~~~~~~ cdconfig.c: At top level: cdconfig.c:191:17: warning: ‘UnMarkLRUineligible’ declared ‘static’ but never defined [-Wunused-function] 191 | static void UnMarkLRUineligible PROTO((void)); | ^~~~~~~~~~~~~~~~~~~ cdconfig.c: In function ‘EntrezInfoMerge’: cdconfig.c:1174:46: warning: ‘InfoWithMaxTypes’ may be used uninitialized [-Wmaybe-uninitialized] 1174 | if (mediaCount <= 1 && ! InfoWithMaxTypes->no_compression) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ cdconfig.c:1140:19: note: ‘InfoWithMaxTypes’ was declared here 1140 | EntrezInfoPtr InfoWithMaxTypes; | ^~~~~~~~~~~~~~~~ cdconfig.c:1248:40: warning: ‘besttype’ may be used uninitialized [-Wmaybe-uninitialized] 1248 | new->types[i].minuid = besttype->minuid; | ~~~~~~~~^~~~~~~~ cdconfig.c:1141:23: note: ‘besttype’ was declared here 1141 | EntrezTypeDataPtr besttype; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/cdrom.h:9, from objentr.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objentr.c: In function ‘CdRomAsnLoad’: objentr.c:170:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 170 | if (loaded) | ^~ objentr.c:172:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 172 | loaded = TRUE; | ^~~~~~ objentr.c: In function ‘DocSumAsnRead’: objentr.c:970:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 970 | AsnReadFunc func; | ^~~~ objentr.c:969:12: warning: unused variable ‘isError’ [-Wunused-variable] 969 | Boolean isError = FALSE; | ^~~~~~~ objentr.c: At top level: objentr.c:806:23: warning: ‘EntrezDivInfo_Destruct’ defined but not used [-Wunused-function] 806 | static EntrezDivInfo* EntrezDivInfo_Destruct (EntrezDivInfo *div) | ^~~~~~~~~~~~~~~~~~~~~~ objentr.c:771:16: warning: ‘EntrezLinkInfo_AsnWrite’ defined but not used [-Wunused-function] 771 | static Boolean EntrezLinkInfo_AsnWrite (const EntrezLinkInfo *link, AsnIo *stream, AsnType *type) | ^~~~~~~~~~~~~~~~~~~~~~~ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:376:25: warning: ‘tinf’ may be used uninitialized [-Wmaybe-uninitialized] 376 | EntrezTypeInfo_AsnRead(tinf++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:238:25: note: ‘tinf’ was declared here 238 | EntrezTypeInfo *tinf; | ^~~~ objentr.c:378:25: warning: ‘fld’ may be used uninitialized [-Wmaybe-uninitialized] 378 | EntrezFieldInfo_AsnRead(fld++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:239:26: note: ‘fld’ was declared here 239 | EntrezFieldInfo *fld; | ^~~ objentr.c:380:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 380 | EntrezLinkInfo_AsnRead(link++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:240:25: note: ‘link’ was declared here 240 | EntrezLinkInfo *link; | ^~~~ In function ‘EntrezDivInfo_AsnRead’, inlined from ‘EntrezInfoAsnRead’ at objentr.c:392:4: objentr.c:818:12: warning: ‘div’ may be used uninitialized [-Wmaybe-uninitialized] 818 | if (div == NULL) | ^ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:241:24: note: ‘div’ was declared here 241 | EntrezDivInfo *div; | ^~~ In function ‘EntrezDivInfo_AsnRead’, inlined from ‘EntrezInfoAsnRead’ at objentr.c:392:4: objentr.c:856:44: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 856 | div->docs[i++] = val.intvalue; | ~^~ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:824:21: note: ‘i’ was declared here 824 | int i; | ^ rm -f libncbicdr.a ar cru libncbicdr.a cdentrez.o cdromlib.o cdnewlib.o casn.o cdconfig.o objentr.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicdr.a ../lib ranlib ../lib/libncbicdr.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibbutns.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibbutns.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibbutns.c: In function ‘Nlm_CheckCallback’: vibbutns.c:354:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 354 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_RadioCallback’: vibbutns.c:373:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 373 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_SetButtonStatus’: vibbutns.c:694:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 694 | Nlm_Int2 val; | ^~~ vibbutns.c: In function ‘Nlm_NewButton.constprop.0’: vibbutns.c:1159:3: warning: ‘call’ may be used uninitialized [-Wmaybe-uninitialized] 1159 | XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vibbutns.c:1021:20: note: ‘call’ was declared here 1021 | String call; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibextra.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibextra.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibextra.c: In function ‘Nlm_RGB2HSL.constprop.0’: vibextra.c:1216:7: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | i = (min + 1); if ( i > 2 ) i=0; | ~~^~~~~~~~~~~ vibextra.c:1191:15: note: ‘min’ was declared here 1191 | int i, min; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibfiles.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibfiles.c: In function ‘Nlm_CardToStr’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_IntToStr’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_LongToStr’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibforms.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibforms.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibgroup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibgroup.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF viblists.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from viblists.c:164: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ viblists.c: In function ‘Nlm_SetListPosition’: viblists.c:1121:15: warning: variable ‘is_realized’ set but not used [-Wunused-but-set-variable] 1121 | Nlm_Boolean is_realized; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibmenus.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmenus.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmenus.c: In function ‘Nlm_IsMenuItemChecked’: vibmenus.c:563:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 563 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CheckMenuItem’: vibmenus.c:591:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 591 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableMenuItem’: vibmenus.c:2006:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2006 | Nlm_Int2 itm; | ^~~ vibmenus.c:2005:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2005 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoice’: vibmenus.c:2072:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2072 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceGroup’: vibmenus.c:2122:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2122 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceItem’: vibmenus.c:2166:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2166 | Nlm_Int2 itm; | ^~~ vibmenus.c:2164:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2164 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableMenuItem’: vibmenus.c:2329:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2329 | Nlm_Int2 itm; | ^~~ vibmenus.c:2328:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2328 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoice’: vibmenus.c:2395:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2395 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoiceItem’: vibmenus.c:2489:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2489 | Nlm_Int2 itm; | ^~~ vibmenus.c:2487:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2487 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_RemoveSubMenu’: vibmenus.c:2627:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2627 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CountMenuItems’: vibmenus.c:3056:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3056 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetMenuItem’: vibmenus.c:3239:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3239 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetPopListTitle’: vibmenus.c:3349:18: warning: variable ‘m’ set but not used [-Wunused-but-set-variable] 3349 | Nlm_MenU m; | ^ vibmenus.c: In function ‘Nlm_AppendItems’: vibmenus.c:3978:17: warning: unused variable ‘accel’ [-Wunused-variable] 3978 | Nlm_Char accel; | ^~~~~ vibmenus.c: In function ‘Nlm_NewPopupList’: vibmenus.c:4969:19: warning: unused variable ‘lbl’ [-Wunused-variable] 4969 | Widget lbl; | ^~~ vibmenus.c:4967:19: warning: unused variable ‘color’ [-Wunused-variable] 4967 | Pixel color; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibprmpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibprmpt.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibsbars.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibsbars.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibslate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibslate.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibslate.c: In function ‘Nlm_EnableSlate’: vibslate.c:1199:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1199 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_DisableSlate’: vibslate.c:1254:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1254 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SelectSlate’: vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=] 1515 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=] 1517 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SelectPanel’: vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=] 1544 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=] 1546 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2026:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2026 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SlateClickCallback’: vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=] 2157 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=] 2159 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateInputCallback’: vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=] 2313 | XtVaGetValues(w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=] 2315 | XtVaGetValues(w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=] 2359 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=] 2361 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_ResetPanel’: vibslate.c:1389:6: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1389 | if (rst != NULL) { | ^ vibslate.c:1378:20: note: ‘pdata.reset’ was declared here 1378 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_RemoveSlate’: vibslate.c:1449:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.click’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.drag’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.hold’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.release’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.draw’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.reset’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_ResetSlate’: vibslate.c:1346:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.click’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.drag’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.hold’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.release’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.draw’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.reset’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.click’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.drag’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.hold’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.release’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.draw’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.reset’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2222:12: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2222 | if (drw != NULL && Nlm_GetVisible ((Nlm_GraphiC) p)) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:560:18: note: ‘pdata.draw’ was declared here 560 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2048:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.click’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.release’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.drag’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.hold’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.reset’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.draw’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2053:12: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2053 | if (clk != NULL && Nlm_GetEnabled ((Nlm_GraphiC) p) | ^ vibslate.c:524:18: note: ‘pdata.click’ was declared here 524 | Nlm_PanelData pdata; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibtexts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibtexts.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibtexts.c: In function ‘Nlm_TextCallback’: vibtexts.c:2982:24: warning: unused variable ‘cbs’ [-Wunused-variable] 2982 | XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data; | ^~~ vibtexts.c: In function ‘Nlm_LoseFocusCallback’: vibtexts.c:2999:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 2999 | XmAnyCallbackStruct *cbs; | ^~~ vibtexts.c: In function ‘Nlm_TabCallback’: vibtexts.c:3109:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3109 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenReturnCallback’: vibtexts.c:3122:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3122 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenActivateCallback’: vibtexts.c:3135:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 3135 | XmAnyCallbackStruct *cbs; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from vibutils.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibutils.c: In function ‘Nlm_VibMessageHook’: vibutils.c:776:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 776 | percent = (Nlm_Int4)Nlm_GetAppProperty( "VibrantMessageWidthMax" ); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibwndws.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibwndws.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibwndws.c: In function ‘Nlm_SetColorMap’: vibwndws.c:1060:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 1060 | int defaultdepth; | ^~~~~~~~~~~~ vibwndws.c: In function ‘Nlm_SetWindowTitle’: vibwndws.c:1567:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1567 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_GetWindowTitle’: vibwndws.c:1610:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1610 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_NewWindow’: vibwndws.c:2155:19: warning: variable ‘screen_num’ set but not used [-Wunused-but-set-variable] 2155 | int screen_num; | ^~~~~~~~~~ vibwndws.c: In function ‘Nlm_HideWindow’: vibwndws.c:2526:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2526 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowNormal’: vibwndws.c:2969:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2969 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowModal’: vibwndws.c:3014:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3014 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowDocument’: vibwndws.c:3060:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3060 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_VibMainPrelude’: vibwndws.c:6800:13: warning: unused variable ‘retval’ [-Wunused-variable] 6800 | Nlm_Int2 retval; | ^~~~~~ vibwndws.c: In function ‘Nlm_RemoveDyingWindows’: vibwndws.c:6922:20: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 6922 | Nlm_WindowTool wptr; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmain.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmain.c:121:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 121 | main (int argc, char *argv[]) | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbidraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidraw.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidraw.c: In function ‘Nlm_CleanUpDrawingTools’: ncbidraw.c:7540:6: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 7540 | if (fdata.handle != NULL) { | ^ ncbidraw.c:7533:17: note: ‘fdata.handle’ was declared here 7533 | Nlm_FontData fdata; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF drawing.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from drawing.c:128: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mapping.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from mapping.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapping.c: In function ‘Nlm_MapRectToWorldBox’: mapping.c:139:8: warning: variable ‘curScale’ set but not used [-Wunused-but-set-variable] 139 | Int4 curScale; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF picture.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from picture.c:100: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF viewer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from viewer.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:12: warning: ‘port.left’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:24: warning: ‘port.right’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:12: warning: ‘port.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:26: warning: ‘port.top’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF document.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from document.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ document.c: In function ‘Nlm_PrintDocument’: document.c:4419:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4419 | system (cmmd); | ^~~~~~~~~~~~~ document.c:4423:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4423 | system (cmmd); | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF table.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from table.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ table.c: In function ‘TableClick’: table.c:1020:14: warning: ‘colRec.click’ may be used uninitialized [-Wmaybe-uninitialized] 1020 | if (actn != NULL) { | ^ table.c:987:14: note: ‘colRec.click’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~^~~~~ table.c:987:14: note: ‘colRec.pos’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:987:14: note: ‘colRec.width’ was declared here 987 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockHilight’, inlined from ‘SetTableBlockHilight’ at table.c:807:13: table.c:843:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~^~~~~ table.c: In function ‘SetTableBlockHilight’: table.c:813:14: note: ‘colRec.pos’ was declared here 813 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockHilight’, inlined from ‘SetTableBlockHilight’ at table.c:807:13: table.c:843:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c: In function ‘SetTableBlockHilight’: table.c:813:14: note: ‘colRec.width’ was declared here 813 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockGray’, inlined from ‘SetTableBlockGray’ at table.c:881:13: table.c:917:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~^~~~~ table.c: In function ‘SetTableBlockGray’: table.c:887:14: note: ‘colRec.pos’ was declared here 887 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockGray’, inlined from ‘SetTableBlockGray’ at table.c:881:13: table.c:917:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c: In function ‘SetTableBlockGray’: table.c:887:14: note: ‘colRec.width’ was declared here 887 | ColRec colRec; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF palette.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from palette.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF diagnost.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from diagnost.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF image.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from image.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ image.c: In function ‘ShiftXMask’: image.c:840:26: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 840 | if(!((mask >> hi + low) & (unsigned long)1)) break; | ~~~^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pictur3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/pictur3d.h:49, from ../include/ppict3d.h:49, from pictur3d.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pictur3d.c: In function ‘Nlm_DeleteFromSeg’: pictur3d.c:114:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 114 | else seg->first = b->next; | ^~~~ pictur3d.c:115:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 115 | if ( seg->last == b ) seg->last = bprev; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d1.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d2.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d3.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d4.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prim3d5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d5.c:66: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF viewer3d.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vibmouse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibmouse.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF netscape.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from netscape.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netscape.c: In function ‘NS_Obtain_lock’: netscape.c:236:10: warning: variable ‘waited’ set but not used [-Wunused-but-set-variable] 236 | Bool waited = False; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF imagelst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/imagelst.h:52, from imagelst.c:61: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF treeview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from treeview.c:91: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ treeview.c: In function ‘getNodeLength’: treeview.c:177:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 177 | length= (Int4)tree_getNode(cursor, TREE_NODE_FMT_DISTANCE, &size); | ^ treeview.c: In function ‘getIconId’: treeview.c:187:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 187 | a= (Int4) tree_getNode(cursor, TREE_NODE_FMT_ICON, &size); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF shim3d.c shim3d.c: In function ‘Nlm_AddHalfWorm3D’: shim3d.c:3470:46: warning: unused variable ‘tmp’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:40: warning: unused variable ‘pCz’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:34: warning: unused variable ‘pCy’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:28: warning: unused variable ‘pCx’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:22: warning: unused variable ‘pNz’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:16: warning: unused variable ‘pNy’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:10: warning: unused variable ‘pNx’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3469:47: warning: unused variable ‘Cz’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:42: warning: unused variable ‘Cy’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:37: warning: unused variable ‘Cx’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:32: warning: unused variable ‘Nz’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:27: warning: unused variable ‘Ny’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:15: warning: unused variable ‘Nx’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3468:21: warning: unused variable ‘pi’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~ shim3d.c:3468:15: warning: unused variable ‘sinj’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~~~ shim3d.c:3468:9: warning: unused variable ‘cosj’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~~~ shim3d.c:3467:33: warning: unused variable ‘prevlen’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~~~~~~ shim3d.c:3467:29: warning: unused variable ‘Vz’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:25: warning: unused variable ‘Vy’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:21: warning: unused variable ‘Vx’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:17: warning: unused variable ‘Hz’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:13: warning: unused variable ‘Hy’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:9: warning: unused variable ‘Hx’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3466:21: warning: unused variable ‘dQtz’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3466:15: warning: unused variable ‘dQty’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3466:9: warning: unused variable ‘dQtx’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3464:14: warning: unused variable ‘len’ [-Wunused-variable] 3464 | GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3], | ^~~ shim3d.c:3463:26: warning: unused variable ‘offset’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^~~~~~ shim3d.c:3463:23: warning: unused variable ‘m’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ shim3d.c:3463:20: warning: unused variable ‘k’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ shim3d.c:3463:17: warning: unused variable ‘j’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF odlbox.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from odlbox.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ odlbox.c: In function ‘LB_onVScroll’: odlbox.c:424:33: warning: variable ‘IsGoUp’ set but not used [-Wunused-but-set-variable] 424 | Boolean IsGoUp=FALSE; | ^~~~~~ rm -f libvibrant.a ar cru libvibrant.a vibbutns.o vibextra.o vibfiles.o vibforms.o vibgroup.o viblists.o vibmenus.o vibprmpt.o vibsbars.o vibslate.o vibtexts.o vibutils.o vibwndws.o vibmain.o ncbidraw.o drawing.o mapping.o picture.o viewer.o document.o table.o palette.o diagnost.o image.o pictur3d.o prim3d1.o prim3d2.o prim3d3.o prim3d4.o prim3d5.o viewer3d.o vibmouse.o netscape.o imagelst.o treeview.o shim3d.o odlbox.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibrant.a ../lib ranlib ../lib/libvibrant.a mv vibbutns.o vibbutns.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibbutns.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibbutns.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibbutns.c: In function ‘Nlm_CheckCallback’: vibbutns.c:354:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 354 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_RadioCallback’: vibbutns.c:373:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 373 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_SetButtonStatus’: vibbutns.c:694:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 694 | Nlm_Int2 val; | ^~~ vibbutns.c: In function ‘Nlm_NewButton.constprop.0’: vibbutns.c:1159:3: warning: ‘call’ may be used uninitialized [-Wmaybe-uninitialized] 1159 | XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vibbutns.c:1021:20: note: ‘call’ was declared here 1021 | String call; | ^~~~ mv vibbutns.o vibbutns.glo mv vibbutns.tmp vibbutns.o mv vibextra.o vibextra.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibextra.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibextra.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibextra.c: In function ‘Nlm_RGB2HSL.constprop.0’: vibextra.c:1216:7: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | i = (min + 1); if ( i > 2 ) i=0; | ~~^~~~~~~~~~~ vibextra.c:1191:15: note: ‘min’ was declared here 1191 | int i, min; | ^~~ mv vibextra.o vibextra.glo mv vibextra.tmp vibextra.o mv vibfiles.o vibfiles.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibfiles.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibfiles.c: In function ‘Nlm_CardToStr’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_IntToStr’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_LongToStr’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mv vibfiles.o vibfiles.glo mv vibfiles.tmp vibfiles.o mv vibforms.o vibforms.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibforms.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibforms.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibforms.o vibforms.glo mv vibforms.tmp vibforms.o mv vibgroup.o vibgroup.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibgroup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibgroup.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibgroup.o vibgroup.glo mv vibgroup.tmp vibgroup.o mv viblists.o viblists.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viblists.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from viblists.c:164: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ viblists.c: In function ‘Nlm_SetListPosition’: viblists.c:1121:15: warning: variable ‘is_realized’ set but not used [-Wunused-but-set-variable] 1121 | Nlm_Boolean is_realized; | ^~~~~~~~~~~ mv viblists.o viblists.glo mv viblists.tmp viblists.o mv vibmenus.o vibmenus.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmenus.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmenus.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmenus.c: In function ‘Nlm_IsMenuItemChecked’: vibmenus.c:563:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 563 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CheckMenuItem’: vibmenus.c:591:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 591 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableMenuItem’: vibmenus.c:2006:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2006 | Nlm_Int2 itm; | ^~~ vibmenus.c:2005:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2005 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoice’: vibmenus.c:2072:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2072 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceGroup’: vibmenus.c:2122:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2122 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceItem’: vibmenus.c:2166:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2166 | Nlm_Int2 itm; | ^~~ vibmenus.c:2164:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2164 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableMenuItem’: vibmenus.c:2329:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2329 | Nlm_Int2 itm; | ^~~ vibmenus.c:2328:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2328 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoice’: vibmenus.c:2395:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2395 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoiceItem’: vibmenus.c:2489:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2489 | Nlm_Int2 itm; | ^~~ vibmenus.c:2487:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2487 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_RemoveSubMenu’: vibmenus.c:2627:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2627 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CountMenuItems’: vibmenus.c:3056:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3056 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetMenuItem’: vibmenus.c:3239:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3239 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetPopListTitle’: vibmenus.c:3349:18: warning: variable ‘m’ set but not used [-Wunused-but-set-variable] 3349 | Nlm_MenU m; | ^ vibmenus.c: In function ‘Nlm_AppendItems’: vibmenus.c:3978:17: warning: unused variable ‘accel’ [-Wunused-variable] 3978 | Nlm_Char accel; | ^~~~~ vibmenus.c: In function ‘Nlm_NewPopupList’: vibmenus.c:4969:19: warning: unused variable ‘lbl’ [-Wunused-variable] 4969 | Widget lbl; | ^~~ vibmenus.c:4967:19: warning: unused variable ‘color’ [-Wunused-variable] 4967 | Pixel color; | ^~~~~ mv vibmenus.o vibmenus.glo mv vibmenus.tmp vibmenus.o mv vibprmpt.o vibprmpt.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibprmpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibprmpt.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibprmpt.o vibprmpt.glo mv vibprmpt.tmp vibprmpt.o mv vibsbars.o vibsbars.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibsbars.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibsbars.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibsbars.o vibsbars.glo mv vibsbars.tmp vibsbars.o mv vibslate.o vibslate.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibslate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibslate.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibslate.c: In function ‘Nlm_EnableSlate’: vibslate.c:1199:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1199 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_DisableSlate’: vibslate.c:1254:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1254 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SelectSlate’: vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=] 1515 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=] 1517 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SelectPanel’: vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=] 1544 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=] 1546 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2026:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2026 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SlateClickCallback’: vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=] 2157 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=] 2159 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateInputCallback’: vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=] 2313 | XtVaGetValues(w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=] 2315 | XtVaGetValues(w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=] 2359 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=] 2361 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_Set3DColorMap’: vibslate.c:2686:17: warning: unused variable ‘testvisual’ [-Wunused-variable] 2686 | Boolean testvisual; | ^~~~~~~~~~ vibslate.c:2685:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 2685 | int defaultdepth; | ^~~~~~~~~~~~ vibslate.c: In function ‘Nlm_ResetPanel’: vibslate.c:1389:6: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1389 | if (rst != NULL) { | ^ vibslate.c:1378:20: note: ‘pdata.reset’ was declared here 1378 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_RemoveSlate’: vibslate.c:1449:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.click’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.drag’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.hold’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.release’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.draw’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.reset’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_ResetSlate’: vibslate.c:1346:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.click’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.drag’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.hold’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.release’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.draw’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.reset’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.click’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.drag’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.hold’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.release’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.draw’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.reset’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2222:12: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2222 | if (drw != NULL && Nlm_GetVisible ((Nlm_GraphiC) p)) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:560:18: note: ‘pdata.draw’ was declared here 560 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2048:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.click’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.release’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.drag’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.hold’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.reset’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.draw’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2053:12: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2053 | if (clk != NULL && Nlm_GetEnabled ((Nlm_GraphiC) p) | ^ vibslate.c:524:18: note: ‘pdata.click’ was declared here 524 | Nlm_PanelData pdata; | ^~~~~ mv vibslate.o vibslate.glo mv vibslate.tmp vibslate.o mv vibtexts.o vibtexts.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibtexts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibtexts.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibtexts.c: In function ‘Nlm_TextCallback’: vibtexts.c:2982:24: warning: unused variable ‘cbs’ [-Wunused-variable] 2982 | XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data; | ^~~ vibtexts.c: In function ‘Nlm_LoseFocusCallback’: vibtexts.c:2999:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 2999 | XmAnyCallbackStruct *cbs; | ^~~ vibtexts.c: In function ‘Nlm_TabCallback’: vibtexts.c:3109:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3109 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenReturnCallback’: vibtexts.c:3122:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3122 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenActivateCallback’: vibtexts.c:3135:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 3135 | XmAnyCallbackStruct *cbs; | ^~~ mv vibtexts.o vibtexts.glo mv vibtexts.tmp vibtexts.o mv vibutils.o vibutils.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from vibutils.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibutils.c: In function ‘Nlm_VibMessageHook’: vibutils.c:776:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 776 | percent = (Nlm_Int4)Nlm_GetAppProperty( "VibrantMessageWidthMax" ); | ^ mv vibutils.o vibutils.glo mv vibutils.tmp vibutils.o mv vibwndws.o vibwndws.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibwndws.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibwndws.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibwndws.c: In function ‘Nlm_SetColorMap’: vibwndws.c:1060:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 1060 | int defaultdepth; | ^~~~~~~~~~~~ vibwndws.c: In function ‘Nlm_SetWindowTitle’: vibwndws.c:1567:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1567 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_GetWindowTitle’: vibwndws.c:1610:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1610 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_NewWindow’: vibwndws.c:2155:19: warning: variable ‘screen_num’ set but not used [-Wunused-but-set-variable] 2155 | int screen_num; | ^~~~~~~~~~ vibwndws.c: In function ‘Nlm_HideWindow’: vibwndws.c:2526:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2526 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowNormal’: vibwndws.c:2969:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2969 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowModal’: vibwndws.c:3014:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3014 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowDocument’: vibwndws.c:3060:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3060 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_VibMainPrelude’: vibwndws.c:6800:13: warning: unused variable ‘retval’ [-Wunused-variable] 6800 | Nlm_Int2 retval; | ^~~~~~ vibwndws.c: In function ‘Nlm_RemoveDyingWindows’: vibwndws.c:6922:20: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 6922 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: At top level: vibwndws.c:1318:16: warning: ‘Nlm_StandardColormap’ defined but not used [-Wunused-function] 1318 | static Boolean Nlm_StandardColormap(Colormap *cMap, | ^~~~~~~~~~~~~~~~~~~~ mv vibwndws.o vibwndws.glo mv vibwndws.tmp vibwndws.o mv vibmain.o vibmain.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmain.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmain.c:121:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 121 | main (int argc, char *argv[]) | ^~~~ mv vibmain.o vibmain.glo mv vibmain.tmp vibmain.o mv ncbidraw.o ncbidraw.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL ncbidraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidraw.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidraw.c: In function ‘Nlm_CleanUpDrawingTools’: ncbidraw.c:7540:6: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 7540 | if (fdata.handle != NULL) { | ^ ncbidraw.c:7533:17: note: ‘fdata.handle’ was declared here 7533 | Nlm_FontData fdata; | ^~~~~ mv ncbidraw.o ncbidraw.glo mv ncbidraw.tmp ncbidraw.o mv drawing.o drawing.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL drawing.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from drawing.c:128: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv drawing.o drawing.glo mv drawing.tmp drawing.o mv mapping.o mapping.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL mapping.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from mapping.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapping.c: In function ‘Nlm_MapRectToWorldBox’: mapping.c:139:8: warning: variable ‘curScale’ set but not used [-Wunused-but-set-variable] 139 | Int4 curScale; | ^~~~~~~~ mv mapping.o mapping.glo mv mapping.tmp mapping.o mv picture.o picture.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL picture.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from picture.c:100: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv picture.o picture.glo mv picture.tmp picture.o mv viewer.o viewer.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from viewer.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:12: warning: ‘port.left’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:24: warning: ‘port.right’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:12: warning: ‘port.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:26: warning: ‘port.top’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ mv viewer.o viewer.glo mv viewer.tmp viewer.o mv document.o document.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL document.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from document.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ document.c: In function ‘Nlm_PrintDocument’: document.c:4419:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4419 | system (cmmd); | ^~~~~~~~~~~~~ document.c:4423:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4423 | system (cmmd); | ^~~~~~~~~~~~~ mv document.o document.glo mv document.tmp document.o mv table.o table.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL table.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from table.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ table.c: In function ‘TableClick’: table.c:1020:14: warning: ‘colRec.click’ may be used uninitialized [-Wmaybe-uninitialized] 1020 | if (actn != NULL) { | ^ table.c:987:14: note: ‘colRec.click’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~^~~~~ table.c:987:14: note: ‘colRec.pos’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:987:14: note: ‘colRec.width’ was declared here 987 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockHilight’, inlined from ‘SetTableBlockHilight’ at table.c:807:13: table.c:843:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~^~~~~ table.c: In function ‘SetTableBlockHilight’: table.c:813:14: note: ‘colRec.pos’ was declared here 813 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockHilight’, inlined from ‘SetTableBlockHilight’ at table.c:807:13: table.c:843:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c: In function ‘SetTableBlockHilight’: table.c:813:14: note: ‘colRec.width’ was declared here 813 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockGray’, inlined from ‘SetTableBlockGray’ at table.c:881:13: table.c:917:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~^~~~~ table.c: In function ‘SetTableBlockGray’: table.c:887:14: note: ‘colRec.pos’ was declared here 887 | ColRec colRec; | ^~~~~~ In function ‘SetTableBlockGray’, inlined from ‘SetTableBlockGray’ at table.c:881:13: table.c:917:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c: In function ‘SetTableBlockGray’: table.c:887:14: note: ‘colRec.width’ was declared here 887 | ColRec colRec; | ^~~~~~ mv table.o table.glo mv table.tmp table.o mv palette.o palette.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL palette.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from palette.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv palette.o palette.glo mv palette.tmp palette.o mv diagnost.o diagnost.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL diagnost.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from diagnost.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv diagnost.o diagnost.glo mv diagnost.tmp diagnost.o mv image.o image.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL image.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from image.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ image.c: In function ‘ShiftXMask’: image.c:840:26: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 840 | if(!((mask >> hi + low) & (unsigned long)1)) break; | ~~~^~~~~ mv image.o image.glo mv image.tmp image.o mv pictur3d.o pictur3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL pictur3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/pictur3d.h:49, from ../include/ppict3d.h:49, from pictur3d.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pictur3d.c: In function ‘Nlm_DeleteFromSeg’: pictur3d.c:114:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 114 | else seg->first = b->next; | ^~~~ pictur3d.c:115:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 115 | if ( seg->last == b ) seg->last = bprev; | ^~ mv pictur3d.o pictur3d.glo mv pictur3d.tmp pictur3d.o mv prim3d1.o prim3d1.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d1.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d1.o prim3d1.glo mv prim3d1.tmp prim3d1.o mv prim3d2.o prim3d2.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d2.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d2.o prim3d2.glo mv prim3d2.tmp prim3d2.o mv prim3d3.o prim3d3.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d3.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d3.o prim3d3.glo mv prim3d3.tmp prim3d3.o mv prim3d4.o prim3d4.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d4.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d4.o prim3d4.glo mv prim3d4.tmp prim3d4.o mv prim3d5.o prim3d5.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d5.c:66: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d5.o prim3d5.glo mv prim3d5.tmp prim3d5.o mv viewer3d.o viewer3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer3d.c mv viewer3d.o viewer3d.glo mv viewer3d.tmp viewer3d.o mv vibmouse.o vibmouse.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmouse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibmouse.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibmouse.o vibmouse.glo mv vibmouse.tmp vibmouse.o mv netscape.o netscape.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL netscape.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from netscape.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netscape.c: In function ‘NS_Obtain_lock’: netscape.c:236:10: warning: variable ‘waited’ set but not used [-Wunused-but-set-variable] 236 | Bool waited = False; | ^~~~~~ mv netscape.o netscape.glo mv netscape.tmp netscape.o mv imagelst.o imagelst.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL imagelst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/imagelst.h:52, from imagelst.c:61: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv imagelst.o imagelst.glo mv imagelst.tmp imagelst.o mv treeview.o treeview.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL treeview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from treeview.c:91: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ treeview.c: In function ‘getNodeLength’: treeview.c:177:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 177 | length= (Int4)tree_getNode(cursor, TREE_NODE_FMT_DISTANCE, &size); | ^ treeview.c: In function ‘getIconId’: treeview.c:187:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 187 | a= (Int4) tree_getNode(cursor, TREE_NODE_FMT_ICON, &size); | ^ mv treeview.o treeview.glo mv treeview.tmp treeview.o mv shim3d.o shim3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c shim3d.c: In function ‘OGL_AddCylinder3D’: shim3d.c:918:14: warning: unused variable ‘iCount’ [-Wunused-variable] 918 | Nlm_Int4 iCount; | ^~~~~~ shim3d.c: In function ‘OGL_AddText3D’: shim3d.c:1210:22: warning: unused variable ‘i’ [-Wunused-variable] 1210 | Nlm_Int4 Length, i; | ^ shim3d.c: In function ‘OGL_Zoom_DragMA’: shim3d.c:1770:16: warning: unused variable ‘OGL_Data’ [-Wunused-variable] 1770 | TOGL_Data *OGL_Data = MAToOGL(ma); | ^~~~~~~~ shim3d.c: In function ‘write_row_callback’: shim3d.c:2923:48: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 2923 | (((float) row) / (-nRows)) * ((end - start) / 15) | ~~~~~^~~~~~~~ shim3d.c:2911:15: note: ‘start’ was declared here 2911 | float start, end; | ^~~~~ shim3d.c:2923:48: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 2923 | (((float) row) / (-nRows)) * ((end - start) / 15) | ~~~~~^~~~~~~~ shim3d.c:2911:22: note: ‘end’ was declared here 2911 | float start, end; | ^~~ shim3d.c: In function ‘Nlm_FindAvailableFonts’: shim3d.c:2234:9: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 2234 | strncpy(fnd_fam,list[i]+1,256); | ^ shim3d.c: In function ‘SetOGLFont’: shim3d.c:2369:21: warning: ‘list’ may be used uninitialized [-Wmaybe-uninitialized] 2369 | pos = list[ii]; | ~~~~^~~~~~~~~~ shim3d.c:2334:28: note: ‘list’ was declared here 2334 | char query[256], **list, *pos; | ^~~~ shim3d.c:2376:37: warning: ‘mindiff’ may be used uninitialized [-Wmaybe-uninitialized] 2376 | if (ii == 0 || diff < mindiff) { | ~~~~~^~~~~~~~~ shim3d.c:2335:41: note: ‘mindiff’ was declared here 2335 | int nFound, ii, ib, size, diff, mindiff, closest; | ^~~~~~~ shim3d.c:2381:64: warning: ‘closest’ may be used uninitialized [-Wmaybe-uninitialized] 2381 | fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]); | ^ shim3d.c:2335:50: note: ‘closest’ was declared here 2335 | int nFound, ii, ib, size, diff, mindiff, closest; | ^~~~~~~ shim3d.c: In function ‘Nlm_AddHalfWorm3D’: shim3d.c:3463:26: warning: ‘offset’ may be used uninitialized [-Wmaybe-uninitialized] 3463 | Nlm_Int4 i, j, k, m, offset; | ^~~~~~ mv shim3d.o shim3d.glo mv shim3d.tmp shim3d.o mv odlbox.o odlbox.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL odlbox.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from odlbox.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ odlbox.c: In function ‘LB_onVScroll’: odlbox.c:424:33: warning: variable ‘IsGoUp’ set but not used [-Wunused-but-set-variable] 424 | Boolean IsGoUp=FALSE; | ^~~~~~ mv odlbox.o odlbox.glo mv odlbox.tmp odlbox.o rm -f libvibrantOGL.a ar cru libvibrantOGL.a vibbutns.glo vibextra.glo vibfiles.glo vibforms.glo vibgroup.glo viblists.glo vibmenus.glo vibprmpt.glo vibsbars.glo vibslate.glo vibtexts.glo vibutils.glo vibwndws.glo vibmain.glo ncbidraw.glo drawing.glo mapping.glo picture.glo viewer.glo document.glo table.glo palette.glo diagnost.glo image.glo pictur3d.glo prim3d1.glo prim3d2.glo prim3d3.glo prim3d4.glo prim3d5.glo viewer3d.glo vibmouse.glo netscape.glo imagelst.glo treeview.glo shim3d.glo odlbox.glo ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibrantOGL.a ../lib ranlib ../lib/libvibrantOGL.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF accentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from accentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ accentr.c: In function ‘EntrezBiostrucGet’: accentr.c:2113:17: warning: unused variable ‘retval’ [-Wunused-variable] 2113 | BiostrucPtr retval = NULL; | ^~~~~~ accentr.c: In function ‘EntrezGIForSeqIdFunc’: accentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ accentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ accentr.c: In function ‘EntrezMedlineEntryGet’: accentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at accentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ accentr.c: In function ‘EntrezSeqEntryGet’: accentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at accentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF accutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from ../include/accutils.h:119, from accutils.c:149: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:62: accutils.c: In function ‘EntrezFieldToString’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 6 [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ rm -f libncbiacc.a ar cru libncbiacc.a accentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiacc.a ../lib ranlib ../lib/libncbiacc.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF drawseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from drawseq.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ drawseq.c: In function ‘AddFlatNodeSymbol’: drawseq.c:811:14: warning: unused variable ‘symbol_height’ [-Wunused-variable] 811 | Int4 symbol_height = 8; | ^~~~~~~~~~~~~ drawseq.c: In function ‘AddAlignBlocks’: drawseq.c:970:14: warning: variable ‘c_num’ set but not used [-Wunused-but-set-variable] 970 | Int2 c_num; | ^~~~~ drawseq.c: In function ‘AddAlignFeature’: drawseq.c:1369:15: warning: unused variable ‘ptype’ [-Wunused-variable] 1369 | Uint1 ptype = 0; | ^~~~~ drawseq.c: In function ‘AddAlignmentMismatch’: drawseq.c:1523:14: warning: variable ‘i_right’ set but not used [-Wunused-but-set-variable] 1523 | Int4 i_right; | ^~~~~~~ drawseq.c: In function ‘DrawRestrictionMap’: drawseq.c:1811:17: warning: unused variable ‘retval’ [-Wunused-variable] 1811 | Boolean retval = FALSE; | ^~~~~~ drawseq.c:1802:22: warning: variable ‘center’ set but not used [-Wunused-but-set-variable] 1802 | Int4 x1, x2, center; | ^~~~~~ drawseq.c: In function ‘DrawFeatures’: drawseq.c:2563:14: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 2563 | Int2 entityID; | ^~~~~~~~ drawseq.c: In function ‘DrawOneSeqLoc’: drawseq.c:3020:17: warning: variable ‘show_seq_label’ set but not used [-Wunused-but-set-variable] 3020 | Boolean show_seq_label = TRUE; /*show the label of a sequence*/ | ^~~~~~~~~~~~~~ drawseq.c:3009:17: warning: variable ‘ends’ set but not used [-Wunused-but-set-variable] 3009 | Boolean ends; | ^~~~ drawseq.c: In function ‘Label_GData’: drawseq.c:3439:17: warning: variable ‘success’ set but not used [-Wunused-but-set-variable] 3439 | Boolean success = FALSE; | ^~~~~~~ drawseq.c: In function ‘DrawEquivAlign’: drawseq.c:3594:15: warning: unused variable ‘my_gray_color’ [-Wunused-variable] 3594 | Uint1 my_gray_color[]={63, 63, 63}; | ^~~~~~~~~~~~~ drawseq.c: In function ‘load_align_label_rectangle’: drawseq.c:4352:17: warning: variable ‘found_it’ set but not used [-Wunused-but-set-variable] 4352 | Boolean found_it; | ^~~~~~~~ drawseq.c: In function ‘PicForAlignNode’: drawseq.c:4558:25: warning: variable ‘min_scale’ set but not used [-Wunused-but-set-variable] 4558 | Int4 max_width, min_scale; | ^~~~~~~~~ drawseq.c: At top level: drawseq.c:3525:22: warning: ‘get_ith_arp’ defined but not used [-Wunused-function] 3525 | static AlignRangePtr get_ith_arp(AlignRangePtr arp, Int2 i) | ^~~~~~~~~~~ drawseq.c:3511:18: warning: ‘get_map_pos’ defined but not used [-Wunused-function] 3511 | static MapPosPtr get_map_pos(MapLayoutPtr mlp, SeqIdPtr sip) | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dotmatrx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dotmatrx.h:47, from dotmatrx.c:32: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF fea2seg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from fea2seg.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF fstyle.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from fstyle.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg1.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg2.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ smdlg2.c: In function ‘Nlm_CreateDlgGroup’: smdlg2.c:631:12: warning: variable ‘toAlign’ set but not used [-Wunused-but-set-variable] 631 | Handle toAlign[3]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF smdlg3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg3.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF smtools.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smtools.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ smtools.c: In function ‘Nlm_CtreateToolsSM’: smtools.c:534:30: warning: ‘%s’ directive writing up to 227 bytes into a region of size 32 [-Wformat-overflow=] 534 | sprintf ( fullFontName, "%s %d", fontNames[i].name, fontNames[i].size ); | ^~ smtools.c:534:29: note: directive argument in the range [-32768, 32767] 534 | sprintf ( fullFontName, "%s %d", fontNames[i].name, fontNames[i].size ); | ^~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CtreateToolsSM’ at smtools.c:534:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 235 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF styleman.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from styleman.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF stylemui.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from stylemui.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF glbpic.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from glbpic.c:22: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ glbpic.c: In function ‘label_linear_mark’: glbpic.c:1295:14: warning: unused variable ‘tick_len’ [-Wunused-variable] 1295 | Int4 tick_len = TICK_LEN; | ^~~~~~~~ glbpic.c: In function ‘add_alignment_to_global’: glbpic.c:1552:15: warning: variable ‘p_val’ set but not used [-Wunused-but-set-variable] 1552 | Uint1 p_val; | ^~~~~ glbpic.c: At top level: glbpic.c:1748:16: warning: ‘get_print_score’ defined but not used [-Wunused-function] 1748 | static Boolean get_print_score(FloatHi min_score, FloatHi max_score, CharPtr label, Uint1 status) | ^~~~~~~~~~~~~~~ glbpic.c:584:19: warning: ‘extract_align_range’ defined but not used [-Wunused-function] 584 | static ValNodePtr extract_align_range(ValNodePtr PNTR arp_list, Uint1 displayOrder) | ^~~~~~~~~~~~~~~~~~~ glbpic.c: In function ‘get_circle_label_align’: glbpic.c:2349:16: warning: ‘align’ may be used uninitialized [-Wmaybe-uninitialized] 2349 | return align; | ^~~~~ glbpic.c:2339:15: note: ‘align’ was declared here 2339 | Uint1 align; | ^~~~~ glbpic.c: In function ‘label_circle_mark.isra.0’: glbpic.c:2417:28: warning: ‘p_align’ may be used uninitialized [-Wmaybe-uninitialized] 2417 | Uint1 label_align, p_align, first_align; | ^~~~~~~ glbpic.c:2469:56: warning: ‘first_width’ may be used uninitialized [-Wmaybe-uninitialized] 2469 | t_width = (first_width + width)/2; | ~~~~~~~~~~~~~^~~~~~~~ glbpic.c:2412:25: note: ‘first_width’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~~~ glbpic.c:2470:35: warning: ‘first_align’ may be used uninitialized [-Wmaybe-uninitialized] 2470 | if(label_align != first_align) | ^ glbpic.c:2417:37: note: ‘first_align’ was declared here 2417 | Uint1 label_align, p_align, first_align; | ^~~~~~~~~~~ In file included from ../include/ncbi.h:58: glbpic.c:2488:74: warning: ‘first_top’ may be used uninitialized [-Wmaybe-uninitialized] 2488 | if(ABS(first_top - top )< (font_height+3)) glbpic.c:2412:14: note: ‘first_top’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~ glbpic.c:2483:75: warning: ‘first_left’ may be used uninitialized [-Wmaybe-uninitialized] 2483 | if(ABS(first_left - left) < (t_width +3)) glbpic.c:2412:38: note: ‘first_left’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~~ In file included from ../include/glbpic.h:7, from glbpic.c:23: glbpic.c: In function ‘add_alignment_to_global’: ../include/picture.h:511:22: warning: ‘g_top’ may be used uninitialized [-Wmaybe-uninitialized] 511 | #define AddRectangle Nlm_AddRectangle glbpic.c:1560:14: note: ‘g_top’ was declared here 1560 | Int4 g_top, g_bottom; | ^~~~~ In function ‘Draw_Global_Linear’, inlined from ‘Draw_Global’ at glbpic.c:2840:4: glbpic.c:2177:40: warning: ‘seglen’ may be used uninitialized [-Wmaybe-uninitialized] 2177 | m_stop += seglen; | ~~~~~~~^~~~~~~~~ glbpic.c: In function ‘Draw_Global’: glbpic.c:1943:8: note: ‘seglen’ was declared here 1943 | Int4 seglen; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF layout.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from ../include/layout.h:3, from layout.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ layout.c: In function ‘LayoutNodeFlat’: layout.c:326:31: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 326 | ValNodePtr vnp, next, prev; | ^~~~ layout.c: In function ‘layout_uncompressed_group’: layout.c:1244:27: warning: variable ‘group_stop’ set but not used [-Wunused-but-set-variable] 1244 | Int2 group_start, group_stop; | ^~~~~~~~~~ layout.c: In function ‘LayoutFeatNode’: layout.c:1365:24: warning: variable ‘y_next’ set but not used [-Wunused-but-set-variable] 1365 | Int4 cur_line, y_next; | ^~~~~~ layout.c:1364:24: warning: variable ‘labelstyle’ set but not used [-Wunused-but-set-variable] 1364 | Int4 segstyle, labelstyle; | ^~~~~~~~~~ layout.c:1363:17: warning: variable ‘show_trunc’ set but not used [-Wunused-but-set-variable] 1363 | Boolean show_trunc = FALSE; | ^~~~~~~~~~ layout.c:1350:17: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 1350 | Int2 i, k; | ^ layout.c: In function ‘LayoutAlignNode’: layout.c:2208:14: warning: unused variable ‘num’ [-Wunused-variable] 2208 | Int4 num = 0; | ^~~ layout.c: At top level: layout.c:1779:16: warning: ‘modify_master_line’ defined but not used [-Wunused-function] 1779 | static Boolean modify_master_line(ValNodePtr vnp, Int4Ptr m_left, Int4Ptr m_right, Int4 maxScale, Uint1 label_align) | ^~~~~~~~~~~~~~~~~~ In function ‘link_to_group’, inlined from ‘make_prev_group’ at layout.c:761:4, inlined from ‘GroupFeatNode’ at layout.c:810:2: layout.c:635:22: warning: ‘prev’ may be used uninitialized [-Wmaybe-uninitialized] 635 | next = prev->next; | ~~~~~^~~~~~~~~~~~ layout.c: In function ‘GroupFeatNode’: layout.c:594:42: note: ‘prev’ was declared here 594 | ValNodePtr my_node = NULL, curr, prev, next; | ^~~~ layout.c: In function ‘LayoutFeatNode’: layout.c:1435:35: warning: ‘p_left’ may be used uninitialized [-Wmaybe-uninitialized] 1435 | if(left < p_left) | ^ layout.c:1351:27: note: ‘p_left’ was declared here 1351 | Int4 left, right, p_left, p_right; | ^~~~~~ layout.c:1447:35: warning: ‘p_right’ may be used uninitialized [-Wmaybe-uninitialized] 1447 | if(right > p_right) | ^ layout.c:1351:35: note: ‘p_right’ was declared here 1351 | Int4 left, right, p_left, p_right; | ^~~~~~~ layout.c:1461:29: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 1461 | fnp->bottom = height; | ~~~~~~~~~~~~^~~~~~~~ layout.c:1348:14: note: ‘height’ was declared here 1348 | Int4 height; | ^~~~~~ layout.c: In function ‘LayoutAlignNode’: layout.c:2352:16: warning: ‘next_line’ may be used uninitialized [-Wmaybe-uninitialized] 2352 | return next_line; | ^~~~~~~~~ layout.c:2215:24: note: ‘next_line’ was declared here 2215 | Int4 cur_line, next_line; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF saldist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/saldist.h:48, from saldist.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ saldist.c: In function ‘AAcode’: saldist.c:1003:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1003 | if (car=='A') return(1); if (car=='B') return(2); | ^~ saldist.c:1003:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1003 | if (car=='A') return(1); if (car=='B') return(2); | ^~ saldist.c:1004:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1004 | if (car=='C') return(3); if (car=='D') return(4); | ^~ saldist.c:1004:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1004 | if (car=='C') return(3); if (car=='D') return(4); | ^~ saldist.c:1005:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1005 | if (car=='E') return(5); if (car=='F') return(6); | ^~ saldist.c:1005:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1005 | if (car=='E') return(5); if (car=='F') return(6); | ^~ saldist.c:1006:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1006 | if (car=='G') return(7); if (car=='H') return(8); | ^~ saldist.c:1006:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1006 | if (car=='G') return(7); if (car=='H') return(8); | ^~ saldist.c:1007:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1007 | if (car=='I') return(9); if (car=='K') return(10); | ^~ saldist.c:1007:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1007 | if (car=='I') return(9); if (car=='K') return(10); | ^~ saldist.c:1008:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1008 | if (car=='L') return(11); if (car=='M') return(12); | ^~ saldist.c:1008:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1008 | if (car=='L') return(11); if (car=='M') return(12); | ^~ saldist.c:1009:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1009 | if (car=='N') return(13); if (car=='P') return(14); | ^~ saldist.c:1009:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1009 | if (car=='N') return(13); if (car=='P') return(14); | ^~ saldist.c:1010:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1010 | if (car=='Q') return(15); if (car=='R') return(16); | ^~ saldist.c:1010:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1010 | if (car=='Q') return(15); if (car=='R') return(16); | ^~ saldist.c:1011:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1011 | if (car=='S') return(17); if (car=='T') return(18); | ^~ saldist.c:1011:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1011 | if (car=='S') return(17); if (car=='T') return(18); | ^~ saldist.c:1012:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1012 | if (car=='V') return(19); if (car=='W') return(20); | ^~ saldist.c:1012:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1012 | if (car=='V') return(19); if (car=='W') return(20); | ^~ saldist.c:1013:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1013 | if (car=='X') return(21); if (car=='Y') return(22); | ^~ saldist.c:1013:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1013 | if (car=='X') return(21); if (car=='Y') return(22); | ^~ saldist.c:1014:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1014 | if (car=='Z') return(23); if (car=='U') return(24); | ^~ saldist.c:1014:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1014 | if (car=='Z') return(23); if (car=='U') return(24); | ^~ saldist.c: In function ‘copy_string’: saldist.c:1289:12: warning: value computed is not used [-Wunused-value] 1289 | *from++; | ^~~~~~~ saldist.c:1302:11: warning: value computed is not used [-Wunused-value] 1302 | *from++; | ^~~~~~~ saldist.c: In function ‘nss_ref_complength’: saldist.c:1479:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1479 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1455:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1455 | c1, c2; | ^~ saldist.c:1455:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1455 | c1, c2; | ^~ saldist.c: In function ‘nss_pw_complength’: saldist.c:1572:18: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1572 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1547:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1547 | c1, c2; | ^~ saldist.c:1547:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1547 | c1, c2; | ^~ saldist.c: In function ‘nss_gp_complength’: saldist.c:1675:21: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1675 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1640:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1640 | c1, c2; | ^~ saldist.c:1640:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1640 | c1, c2; | ^~ saldist.c: In function ‘SortbySimProc’: saldist.c:2139:31: warning: variable ‘newsalpd’ set but not used [-Wunused-but-set-variable] 2139 | SeqAlignPtr newsalp, newsalpd; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from saldist.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ saldist.c:1853:22: warning: ‘scangp_calcul’ defined but not used [-Wunused-function] 1853 | static Int4Ptr PNTR scangp_calcul (EditAlignDataPtr adp, Int2 seq1, Int2 seq2, Int4 from, Int4 to, Int2 group, Int2 choice, Int2 win_width) | ^~~~~~~~~~~~~ saldist.c:1080:24: warning: ‘FloatLomatrix’ defined but not used [-Wunused-function] 1080 | static FloatLoPtr PNTR FloatLomatrix (Int2 nrows, Int2 ncol) | ^~~~~~~~~~~~~ saldist.c:999:13: warning: ‘AAcode’ defined but not used [-Wunused-function] 999 | static Int2 AAcode(Char car) | ^~~~~~ saldist.c:928:16: warning: ‘new_matrice’ defined but not used [-Wunused-function] 928 | static Boolean new_matrice (Int2 simmatrix, CharPtr path) | ^~~~~~~~~~~ saldist.c:910:14: warning: ‘matrixlst’ defined but not used [-Wunused-variable] 910 | static Char *matrixlst [] = {"", "idmat", | ^~~~~~~~~ saldist.c: In function ‘writematrixhalf.constprop.0’: saldist.c:1225:18: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1225 | vnp=vnp->next; | ~~~^~~~~~~~~~ saldist.c:1174:19: note: ‘vnp’ was declared here 1174 | ValNodePtr vnp, | ^~~ In function ‘writematrix’, inlined from ‘PwDistProc’ at saldist.c:2019:9: saldist.c:1151:18: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1151 | vnp=vnp->next; | ~~~^~~~~~~~~~ saldist.c: In function ‘PwDistProc’: saldist.c:1104:19: note: ‘vnp’ was declared here 1104 | ValNodePtr vnp, | ^~~ In function ‘SortbyLenProc’, inlined from ‘SortbyLenItem’ at saldist.c:2323:3: saldist.c:2191:14: warning: ‘mink’ may be used uninitialized [-Wmaybe-uninitialized] 2191 | sortlst [mink] = j + 1; | ^ saldist.c: In function ‘SortbyLenItem’: saldist.c:2172:28: note: ‘mink’ was declared here 2172 | Int2 j, k, mink; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF saled.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from saled.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ saled.c: In function ‘ReadAlignmentForSeqEntry’: saled.c:3310:21: warning: unused variable ‘dirty’ [-Wunused-variable] 3310 | dirty = FALSE; | ^~~~~ saled.c:3306:21: warning: unused variable ‘salp’ [-Wunused-variable] 3306 | SeqAlignPtr salp=NULL, | ^~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from saled.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from saled.c:55: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from ../include/salfiles.h:48, from salfiles.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salfiles.c: In function ‘NewFastaRead’: salfiles.c:315:30: warning: variable ‘lastsegsip’ set but not used [-Wunused-but-set-variable] 315 | SeqIdPtr segsip=NULL, lastsegsip=NULL; | ^~~~~~~~~~ salfiles.c: In function ‘ReadAlignmentToStrings’: salfiles.c:664:16: warning: unused variable ‘nseq’ [-Wunused-variable] 664 | Int2 nseq = 0; | ^~~~ salfiles.c: In function ‘MacawRead’: salfiles.c:1257:15: warning: unused variable ‘vnp’ [-Wunused-variable] 1257 | vnp = NULL; | ^~~ salfiles.c: In function ‘ReadLocalAlign’: salfiles.c:1444:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1444 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1444:22: note: did you mean to dereference the pointer? 1444 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1446:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1446 | if (tmp!='\0') | ^~ salfiles.c:1446:19: note: did you mean to dereference the pointer? 1446 | if (tmp!='\0') | ^ salfiles.c:1455:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1455 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1455:22: note: did you mean to dereference the pointer? 1455 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1457:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1457 | if (tmp!='\0') | ^~ salfiles.c:1457:19: note: did you mean to dereference the pointer? 1457 | if (tmp!='\0') | ^ salfiles.c:1536:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1536 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1536:22: note: did you mean to dereference the pointer? 1536 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1538:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1538 | if (tmp!='\0') | ^~ salfiles.c:1538:19: note: did you mean to dereference the pointer? 1538 | if (tmp!='\0') | ^ salfiles.c:1547:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1547 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1547:22: note: did you mean to dereference the pointer? 1547 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1549:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1549 | if (tmp!='\0') | ^~ salfiles.c:1549:19: note: did you mean to dereference the pointer? 1549 | if (tmp!='\0') | ^ salfiles.c:1370:14: warning: variable ‘tmp1’ set but not used [-Wunused-but-set-variable] 1370 | tmp1; | ^~~~ salfiles.c: In function ‘ImportFromFile’: salfiles.c:2072:20: warning: unused variable ‘sep’ [-Wunused-variable] 2072 | SeqEntryPtr sep = NULL; | ^~~ salfiles.c:2071:20: warning: unused variable ‘sap’ [-Wunused-variable] 2071 | SeqAnnotPtr sap = NULL; | ^~~ salfiles.c: In function ‘FindSeqEntryForSeqIdCallback’: salfiles.c:2672:12: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2672 | if (SeqIdForSameBioseq(cip->sip, sip)) | ^~ salfiles.c:2674:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2674 | cip->bsp = bsp; | ^~~ salfiles.c: In function ‘sesp_to_pept’: salfiles.c:2713:18: warning: unused variable ‘bufferPtr’ [-Wunused-variable] 2713 | bufferPtr = NULL; | ^~~~~~~~~ salfiles.c: In function ‘SaveFeatProc’: salfiles.c:3387:22: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 3387 | Int2 handled; | ^~~~~~~ salfiles.c: In function ‘CCReadAnythingLoop’: salfiles.c:3685:16: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 3685 | Uint2 entityID; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salfiles.c:48: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salfiles.c:501:19: warning: ‘get_lens_fromseqalign’ defined but not used [-Wunused-function] 501 | static ValNodePtr get_lens_fromseqalign (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~~ salfiles.c: In function ‘NewFastaRead.constprop.0’: salfiles.c:460:6: warning: ‘sip’ may be used uninitialized [-Wmaybe-uninitialized] 460 | if (sip!=NULL) | ^ salfiles.c:312:17: note: ‘sip’ was declared here 312 | SeqIdPtr sip; | ^~~ In function ‘ReadAlignmentToStrings’, inlined from ‘GapFastaRead’ at salfiles.c:811:12: salfiles.c:724:15: warning: ‘startp’ may be used uninitialized [-Wmaybe-uninitialized] 724 | if (!startp) { | ^ salfiles.c: In function ‘GapFastaRead’: salfiles.c:660:16: note: ‘startp’ was declared here 660 | Boolean startp; | ^~~~~~ In function ‘ReadAlignmentToStrings’, inlined from ‘GapFastaRead’ at salfiles.c:811:12: salfiles.c:747:25: warning: ‘seqstr’ may be used uninitialized [-Wmaybe-uninitialized] 747 | seqstr [lgseq] = strp[j]; | ^ salfiles.c: In function ‘GapFastaRead’: salfiles.c:654:16: note: ‘seqstr’ was declared here 654 | seqstr; | ^~~~~~ In file included from ../include/sequtil.h:43, from ../include/gather.h:169, from ../include/saledit.h:52: In function ‘align_this’, inlined from ‘CCDownloadProc’ at salfiles.c:2364:9: ../include/objsset.h:230:26: warning: ‘new_sep’ may be used uninitialized [-Wmaybe-uninitialized] 230 | #define IS_Bioseq(a) ((a)->choice == 1) | ~~~^~~~~~~~ salfiles.c: In function ‘CCDownloadProc’: salfiles.c:2286:15: note: ‘new_sep’ was declared here 2286 | SeqEntryPtr new_sep; | ^~~~~~~ In function ‘MacawRead’, inlined from ‘ReadLocalAlignment’ at salfiles.c:2045:19: salfiles.c:1278:6: warning: ‘seqvnp’ may be used uninitialized [-Wmaybe-uninitialized] 1278 | if (seqvnp == NULL) | ^ salfiles.c: In function ‘ReadLocalAlignment’: salfiles.c:1113:19: note: ‘seqvnp’ was declared here 1113 | ValNodePtr vnp, seqvnp; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from salpanel.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpanel.c: In function ‘go_to_next_to_draw’: salpanel.c:331:17: warning: statement with no effect [-Wunused-value] 331 | offsettmp; | ^~~~~~~~~ salpanel.c: In function ‘next_to_draw’: salpanel.c:471:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 471 | if ( curstr != NULL ) | ^ salpanel.c: In function ‘AssociatePropagatedSubloc’: salpanel.c:3131:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 3131 | ValNodePtr vnp; | ^~~ salpanel.c: In function ‘FeaturePropagateForm’: salpanel.c:4674:15: warning: variable ‘ppt’ set but not used [-Wunused-but-set-variable] 4674 | PrompT ppt; | ^~~ salpanel.c:4669:15: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 4669 | ButtoN b; | ^ salpanel.c: In function ‘OkToContinueWithFeatureApply’: salpanel.c:6103:14: warning: unused variable ‘num_missing’ [-Wunused-variable] 6103 | Int4 num_missing = 0, seq_num, start_num; | ^~~~~~~~~~~ salpanel.c: In function ‘DoApplyFeatureToAlignment’: salpanel.c:6219:31: warning: unused variable ‘found_null’ [-Wunused-variable] 6219 | Boolean found_null = FALSE; | ^~~~~~~~~~ salpanel.c: In function ‘ApplyFeatureToAlignment’: salpanel.c:6421:31: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 6421 | ButtoN b; | ^ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salpanel.c:45: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salpanel.c:52: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salpanel.c:5059:13: warning: ‘BatchApplyFeatureDetailsMessage’ defined but not used [-Wunused-function] 5059 | static void BatchApplyFeatureDetailsMessage (DialoG d, Int2 mssg) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpanel.c:224:13: warning: ‘get_client_rectxy’ defined but not used [-Wunused-function] 224 | static void get_client_rectxy (PaneL p, RectPtr prc, Int2 x, Int2 y) | ^~~~~~~~~~~~~~~~~ salpanel.c:113:14: warning: ‘leftOvalFillSym’ defined but not used [-Wunused-variable] 113 | static Uint1 leftOvalFillSym [] = { | ^~~~~~~~~~~~~~~ salpanel.c:110:14: warning: ‘rightOvalFillSym’ defined but not used [-Wunused-variable] 110 | static Uint1 rightOvalFillSym [] = { | ^~~~~~~~~~~~~~~~ salpanel.c:107:14: warning: ‘leftOvalSym’ defined but not used [-Wunused-variable] 107 | static Uint1 leftOvalSym [] = { | ^~~~~~~~~~~ salpanel.c:104:14: warning: ‘rightOvalSym’ defined but not used [-Wunused-variable] 104 | static Uint1 rightOvalSym [] = { | ^~~~~~~~~~~~ salpanel.c:101:14: warning: ‘downTriFillSym’ defined but not used [-Wunused-variable] 101 | static Uint1 downTriFillSym [] = { | ^~~~~~~~~~~~~~ salpanel.c:98:14: warning: ‘upTriFillSym’ defined but not used [-Wunused-variable] 98 | static Uint1 upTriFillSym [] = { | ^~~~~~~~~~~~ salpanel.c:89:14: warning: ‘ovalFillSym’ defined but not used [-Wunused-variable] 89 | static Uint1 ovalFillSym [] = { | ^~~~~~~~~~~ salpanel.c:86:14: warning: ‘diamondFillSym’ defined but not used [-Wunused-variable] 86 | static Uint1 diamondFillSym [] = { | ^~~~~~~~~~~~~~ salpanel.c:80:14: warning: ‘downTriSym’ defined but not used [-Wunused-variable] 80 | static Uint1 downTriSym [] = { | ^~~~~~~~~~ salpanel.c:77:14: warning: ‘upTriSym’ defined but not used [-Wunused-variable] 77 | static Uint1 upTriSym [] = { | ^~~~~~~~ salpanel.c:68:14: warning: ‘ovalSym’ defined but not used [-Wunused-variable] 68 | static Uint1 ovalSym [] = { | ^~~~~~~ salpanel.c:65:14: warning: ‘diamondSym’ defined but not used [-Wunused-variable] 65 | static Uint1 diamondSym [] = { | ^~~~~~~~~~ In function ‘draw_line’, inlined from ‘draw_feat.isra.0’ at salpanel.c:2208:3: salpanel.c:1988:30: warning: ‘col1’ may be used uninitialized [-Wmaybe-uninitialized] 1988 | for (j=0, gap=gapline; jitemtype, FALSE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpanel.c:2348:28: note: ‘draw_diff’ was declared here 2348 | Boolean is_master, draw_diff; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salparam.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salparam.h:48, from salparam.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salparam.c: In function ‘mergelst’: salparam.c:1325:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 1325 | Boolean val; | ^~~ salparam.c: In function ‘unmergelst’: salparam.c:1340:20: warning: variable ‘dbdp’ set but not used [-Wunused-but-set-variable] 1340 | DialogBoxDataPtr dbdp; | ^~~~ salparam.c: In function ‘FormulaDialog’: salparam.c:1398:36: warning: variable ‘b5’ set but not used [-Wunused-but-set-variable] 1398 | ButtoN b1, b2, b3, b4, b5; | ^~ salparam.c: In function ‘JK_NTPattern2Ex’: salparam.c:1596:19: warning: variable ‘debug_str’ set but not used [-Wunused-but-set-variable] 1596 | CharPtr debug_str; | ^~~~~~~~~ salparam.c: In function ‘get_string_fromtext’: salparam.c:1721:11: warning: the comparison will always evaluate as ‘false’ for the address of ‘str’ will never be NULL [-Waddress] 1721 | if (str == NULL) | ^~ salparam.c:1715:22: note: ‘str’ declared here 1715 | Char str [128]; | ^~~ salparam.c: In function ‘DotPlotBtn’: salparam.c:1936:22: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1936 | Int2 status; | ^~~~~~ salparam.c: In function ‘DotPlotDialog’: salparam.c:1973:20: warning: variable ‘bt1’ set but not used [-Wunused-but-set-variable] 1973 | ButtoN bt1, bt2; | ^~~ salparam.c: In function ‘DotPlotItem’: salparam.c:2004:22: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 2004 | Int2 status; | ^~~~~~ salparam.c: In function ‘SelectSeqFunc’: salparam.c:2308:20: warning: variable ‘str’ set but not used [-Wunused-but-set-variable] 2308 | CharPtr str; | ^~~ salparam.c: In function ‘HighlightSelectionFunc’: salparam.c:2344:22: warning: variable ‘wdp’ set but not used [-Wunused-but-set-variable] 2344 | SeqEditViewFormPtr wdp; | ^~~ salparam.c: In function ‘PropagateFeatureProc’: salparam.c:2623:25: warning: variable ‘iID’ set but not used [-Wunused-but-set-variable] 2623 | Uint2 eID, iID, | ^~~ salparam.c:2614:20: warning: variable ‘salp’ set but not used [-Wunused-but-set-variable] 2614 | SeqAlignPtr salp; | ^~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2959:22: warning: the comparison will always evaluate as ‘true’ for the address of ‘label’ will never be NULL [-Waddress] 2959 | if (feat->label != NULL) | ^~ ../include/salsa.h:171:20: note: ‘label’ declared here 171 | Char label[101]; | ^~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salparam.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from salparam.c:58: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salparam.c: In function ‘FileInProc’: salparam.c:782:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 782 | fscanf(fp, "%d %ld", &n, &lens); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salparam.c: In function ‘DotPlotBtn’: salparam.c:1950:9: warning: ‘sep’ may be used uninitialized [-Wmaybe-uninitialized] 1950 | if (sep != NULL && IS_Bioseq (sep)) { | ^ salparam.c:1931:22: note: ‘sep’ was declared here 1931 | SeqEntryPtr sep; | ^~~ salparam.c: In function ‘SalsaExportDialog’: salparam.c:2258:19: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size 10 [-Wformat-overflow=] 2258 | sprintf (str2, "%ld", (long) adp->int4value); | ^~~ salparam.c:2258:18: note: directive argument in the range [-2147483648, 2147483647] 2258 | sprintf (str2, "%ld", (long) adp->int4value); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SalsaExportDialog’ at salparam.c:2258:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘SalsaExportDialog’: salparam.c:2261:19: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size 10 [-Wformat-overflow=] 2261 | sprintf (str2, "%ld", (long) adp->int4value2); | ^~~ salparam.c:2261:18: note: directive argument in the range [-2147483648, 2147483647] 2261 | sprintf (str2, "%ld", (long) adp->int4value2); | ^~~~~ In function ‘sprintf’, inlined from ‘SalsaExportDialog’ at salparam.c:2261:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2964:32: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 9 and 19 [-Wformat-overflow=] 2964 | sprintf (str2, " (%ld..%ld)", (long)start, (long)stop); | ^~~ salparam.c:2964:24: note: directive argument in the range [-2147483647, 2147483647] 2964 | sprintf (str2, " (%ld..%ld)", (long)start, (long)stop); | ^~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PropagateFeatDialog’ at salparam.c:2964:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 28 bytes into a destination of size 24 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2962:32: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 9 and 19 [-Wformat-overflow=] 2962 | sprintf (str2, " (%ld..%ld) minus strand", (long)start, (long)stop); | ^~~ salparam.c:2962:24: note: directive argument in the range [-2147483647, 2147483647] 2962 | sprintf (str2, " (%ld..%ld) minus strand", (long)start, (long)stop); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PropagateFeatDialog’ at salparam.c:2962:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 21 and 41 bytes into a destination of size 24 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salsa.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from salsa.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salsa.c: In function ‘UndoProc’: salsa.c:1799:20: warning: the comparison will always evaluate as ‘true’ for the address of ‘tmpfile’ will never be NULL [-Waddress] 1799 | if (adp->tmpfile != NULL && adp->tmpfile[0] != '\0') | ^~ ../include/salsa.h:364:19: note: ‘tmpfile’ declared here 364 | Char tmpfile [PATH_MAX]; /* path + filename */ | ^~~~~~~ salsa.c: In function ‘SelectSubsProc’: salsa.c:2140:23: warning: variable ‘svpp’ set but not used [-Wunused-but-set-variable] 2140 | SeqEditViewProcsPtr svpp=NULL; | ^~~~ salsa.c: In function ‘SetSeqInfo’: salsa.c:3195:17: warning: unused variable ‘vnp’ [-Wunused-variable] 3195 | ValNodePtr vnp = NULL; | ^~~ salsa.c: In function ‘SetupAlignDataSap’: salsa.c:3410:16: warning: variable ‘entityID_sap’ set but not used [-Wunused-but-set-variable] 3410 | Uint2 entityID_sap; | ^~~~~~~~~~~~ salsa.c: In function ‘get_bestpos_formerge’: salsa.c:4304:17: warning: variable ‘insert_after’ set but not used [-Wunused-but-set-variable] 4304 | insert_after=FALSE; | ^~~~~~~~~~~~ salsa.c:4303:17: warning: variable ‘insert_before’ set but not used [-Wunused-but-set-variable] 4303 | Boolean insert_before=FALSE, | ^~~~~~~~~~~~~ salsa.c: In function ‘CreateSeqAlignViewForm’: salsa.c:4689:22: warning: variable ‘mergebtn’ set but not used [-Wunused-but-set-variable] 4689 | ButtoN mergebtn; | ^~~~~~~~ salsa.c: In function ‘AlgEditFunc’: salsa.c:4976:23: warning: unused variable ‘wdp’ [-Wunused-variable] 4976 | SeqEditViewFormPtr wdp = NULL; | ^~~ salsa.c:4974:23: warning: unused variable ‘w’ [-Wunused-variable] 4974 | WindoW w = NULL; | ^ salsa.c: In function ‘OldAlignmentEditor’: salsa.c:5106:16: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 5106 | Int2 rval; | ^~~~ salsa.c: In function ‘LaunchAnnotAlignEditor’: salsa.c:5293:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5293 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignEditor’: salsa.c:5310:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5310 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignViewer’: salsa.c:5327:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5327 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignEditorFromDesktop’: salsa.c:5342:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 5342 | OMProcControlPtr ompcp; | ^~~~~ salsa.c: In function ‘LaunchAlignEditorFromDesktop2’: salsa.c:5359:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 5359 | OMProcControlPtr ompcp; | ^~~~~ salsa.c: In function ‘InsertSeqProc’: salsa.c:5538:17: warning: variable ‘cnclbt’ set but not used [-Wunused-but-set-variable] 5538 | ButtoN insbt, cnclbt; | ^~~~~~ salsa.c:5536:10: warning: variable ‘insprt’ set but not used [-Wunused-but-set-variable] 5536 | PrompT insprt; | ^~~~~~ salsa.c: In function ‘SeqAlignBestHit’: salsa.c:5605:22: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 5605 | Int4 last; | ^~~~ salsa.c: In function ‘SeqAlignStartUpdate’: salsa.c:5791:22: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 5791 | Int2 index, k, j; | ^ salsa.c:5790:15: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5790 | start; | ^~~~~ salsa.c:5789:15: warning: variable ‘len_sum’ set but not used [-Wunused-but-set-variable] 5789 | Int4 len_sum, | ^~~~~~~ salsa.c:5786:15: warning: variable ‘lenp’ set but not used [-Wunused-but-set-variable] 5786 | Int4Ptr lenp, | ^~~~ salsa.c:5785:15: warning: variable ‘pre’ set but not used [-Wunused-but-set-variable] 5785 | SeqIdPtr pre, sip, next; | ^~~ salsa.c: In function ‘CCNormalizeSeqAlignId’: salsa.c:6746:23: warning: unused variable ‘gi’ [-Wunused-variable] 6746 | Int4 gi = 0; | ^~ salsa.c:6745:17: warning: unused variable ‘missing_fmt’ [-Wunused-variable] 6745 | CharPtr missing_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\n"; | ^~~~~~~~~~~ salsa.c:6744:17: warning: unused variable ‘missing_cont_fmt’ [-Wunused-variable] 6744 | CharPtr missing_cont_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\nContinue anyway?\n"; | ^~~~~~~~~~~~~~~~ salsa.c: In function ‘ValidateSeqAlignandACCEx’: salsa.c:7106:16: warning: variable ‘ans’ set but not used [-Wunused-but-set-variable] 7106 | MsgAnswer ans; | ^~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salsa.c:48: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salsa.c:68: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salsa.c:87:13: warning: ‘InsertSequenceDlg’ declared ‘static’ but never defined [-Wunused-function] 87 | static void InsertSequenceDlg (ButtoN b); | ^~~~~~~~~~~~~~~~~ salsa.c:5973:13: warning: ‘SWPrintFarpointerAln’ defined but not used [-Wunused-function] 5973 | static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp) | ^~~~~~~~~~~~~~~~~~~~ salsa.c:2360:13: warning: ‘MakeCdRgnrProc’ defined but not used [-Wunused-function] 2360 | static void MakeCdRgnrProc (IteM i) { | ^~~~~~~~~~~~~~ salsa.c:2356:13: warning: ‘MakeCdRgnProc’ defined but not used [-Wunused-function] 2356 | static void MakeCdRgnProc (IteM i) { | ^~~~~~~~~~~~~ salsa.c:1760:13: warning: ‘AcceptCloseWindowButton’ defined but not used [-Wunused-function] 1760 | static void AcceptCloseWindowButton (ButtoN b) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from salsa.c:52: ../include/salprop.h:50:16: warning: ‘GBFeat’ defined but not used [-Wunused-variable] 50 | static CharPtr GBFeat[number_GBFeat] = { | ^~~~~~ In file included from ../include/ncbi.h:65: salsa.c: In function ‘ExportFASTAForUnselectedUpdates’: ../include/ncbifile.h:113:19: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized] 113 | #define FileClose Nlm_FileClose salsa.c:6350:23: note: ‘fp’ was declared here 6350 | FILE *fp; | ^~ salsa.c: In function ‘ExportBadAlignments’: ../include/ncbifile.h:113:19: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized] 113 | #define FileClose Nlm_FileClose salsa.c:6318:23: note: ‘fp’ was declared here 6318 | FILE *fp; | ^~ salsa.c: In function ‘SeqAlignBestHit.constprop.0’: salsa.c:5748:24: warning: ‘beg’ may be used uninitialized [-Wmaybe-uninitialized] 5748 | *nonly = -(beg+end); | ~~~~^~~~~ salsa.c:5598:22: note: ‘beg’ was declared here 5598 | Int4 beg; | ^~~ salsa.c:5748:24: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 5748 | *nonly = -(beg+end); | ~~~~^~~~~ salsa.c:5600:22: note: ‘end’ was declared here 5600 | Int4 end; | ^~~ salsa.c:5745:10: warning: ‘nctr’ may be used uninitialized [-Wmaybe-uninitialized] 5745 | if (nctr > 0) | ^ salsa.c:5608:22: note: ‘nctr’ was declared here 5608 | Int4 nctr; | ^~~~ In function ‘update_length’, inlined from ‘BioseqEditMsgFunc’ at salsa.c:1165:14: salsa.c:912:32: warning: ‘anp’ may be used uninitialized [-Wmaybe-uninitialized] 912 | ssp = SelStructNew (anp->seq_entityID, anp->bsp_itemID, OBJ_BIOSEQ, from, to, anp->sip, Seq_strand_plus, FALSE); | ~~~^~~~~~~~~~~~~~ salsa.c: In function ‘BioseqEditMsgFunc’: salsa.c:890:20: note: ‘anp’ was declared here 890 | AlignNodePtr anp; | ^~~ salsa.c: In function ‘DeleteProc’: salsa.c:1945:14: warning: ‘sap’ may be used uninitialized [-Wmaybe-uninitialized] 1945 | newsalp = (SeqAlignPtr)sap->data; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ salsa.c:1921:22: note: ‘sap’ was declared here 1921 | SeqAnnotPtr sap; | ^~~ salsa.c: In function ‘SkipThisWindowProc’: salsa.c:4590:6: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 4590 | if (salp) | ^ salsa.c:4574:22: note: ‘salp’ was declared here 4574 | SeqAlignPtr salp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqfltr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqfltr.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqfltr.c: In function ‘FilterSeq’: seqfltr.c:253:10: warning: ‘fptr’ may be used uninitialized [-Wmaybe-uninitialized] 253 | if (fptr == NULL) | ^ seqfltr.c:213:17: note: ‘fptr’ was declared here 213 | FloatHiPtr fptr; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqgraph.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqgraph.c: In function ‘EndPointDialogToEndPointValNode’: seqgraph.c:140:10: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 140 | return (Pointer) eplist; | ^~~~~~~~~~~~~~~~ seqgraph.c:133:22: note: ‘eplist’ was declared here 133 | ValNodePtr eplist; | ^~~~~~ seqgraph.c: In function ‘SeqLocGraphViewProc’: seqgraph.c:1136:17: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 1136 | while (eplist != NULL) | ^ seqgraph.c:1120:31: note: ‘eplist’ was declared here 1120 | ValNodePtr ephead, eplist; | ^~~~~~ seqgraph.c: In function ‘MarkPrims’: seqgraph.c:911:11: warning: ‘fval’ may be used uninitialized [-Wmaybe-uninitialized] 911 | val = fval/2; | ~~~~^~~~~~~~ seqgraph.c:841:14: note: ‘fval’ was declared here 841 | FloatHi fval; | ^~~~ seqgraph.c: In function ‘CutOffProc’: seqgraph.c:1018:17: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 1018 | while (eplist != NULL) | ^ seqgraph.c:1005:23: note: ‘eplist’ was declared here 1005 | ValNodePtr eplist, ephead, epprev, epnext; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqgrphx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqgrphx.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqgrphx.c:301:13: warning: ‘CleanupGCFilterForm’ defined but not used [-Wunused-function] 301 | static void CleanupGCFilterForm (GraphiC g, VoidPtr data) | ^~~~~~~~~~~~~~~~~~~ seqgrphx.c:152:25: warning: ‘FilterMsgFunc’ defined but not used [-Wunused-function] 152 | static Int2 LIBCALLBACK FilterMsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~~~ seqgrphx.c:28:25: warning: ‘MatrixMsgFunc’ defined but not used [-Wunused-function] 28 | static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqmtrx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqmtrx.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqmtrx.c:387:20: warning: ‘MatrixSearch’ defined but not used [-Wunused-function] 387 | static SeqGraphPtr MatrixSearch (BioseqPtr bsp, Int2 matrixtype) | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqpcc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqpcc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqpcc.c: In function ‘PCCProc’: seqpcc.c:229:14: warning: ‘pbsp’ may be used uninitialized [-Wmaybe-uninitialized] 229 | if ((spp = SeqPortNew (pbsp, start, end, 0, Seq_code_iupacaa)) != NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpcc.c:196:16: note: ‘pbsp’ was declared here 196 | BioseqPtr pbsp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqanal.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqanal.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF aacomp.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from aacomp.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ aacomp.c:86:20: warning: ‘AACGraph’ defined but not used [-Wunused-function] 86 | static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window, | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqscrl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from ../include/seqscrl.h:4, from seqscrl.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF valdlg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vibforms.h:46, from valdlg.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valdlg.c: In function ‘ClickRulesDoc’: valdlg.c:373:22: warning: unused variable ‘scroll_pos’ [-Wunused-variable] 373 | Int2 scroll_pos = 0; | ^~~~~~~~~~ valdlg.c:372:22: warning: unused variable ‘sb_vert’ [-Wunused-variable] 372 | BaR sb_vert = NULL; | ^~~~~~~ valdlg.c: In function ‘UpdateRuleList’: valdlg.c:479:26: warning: unused variable ‘last_cr’ [-Wunused-variable] 479 | CommentRulePtr new_cr, last_cr = NULL; | ^~~~~~~ valdlg.c: In function ‘SaveRuleChanges’: valdlg.c:540:23: warning: variable ‘dlg’ set but not used [-Wunused-but-set-variable] 540 | CommentSetDlgPtr dlg; | ^~~ valdlg.c: In function ‘LaunchCommentRulesEditor’: valdlg.c:553:23: warning: unused variable ‘m’ [-Wunused-variable] 553 | MenU m; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vsm.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vsmpriv.h:48, from vsm.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsm.c: In function ‘VSMDrawAbout’: vsm.c:1436:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1436 | if (vsmp->title != NULL) | ^~ vsm.c:1438:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1438 | if (vsmp->aboutinfo != NULL) | ^~ vsm.c: In function ‘VSMAboutProc’: vsm.c:1466:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 1466 | PaneL p; | ^ vsm.c: In function ‘VSeqMgrCreateMainWindow’: vsm.c:1569:19: warning: variable ‘omp’ set but not used [-Wunused-but-set-variable] 1569 | ObjMgrPtr omp; | ^~~ vsm.c: In function ‘VSeqMgrPopulateMain’: vsm.c:1710:20: warning: variable ‘atp’ set but not used [-Wunused-but-set-variable] 1710 | AsnTypePtr atp; | ^~~ vsm.c: In function ‘VSMGatherPictProc’: vsm.c:2193:22: warning: variable ‘bssp’ set but not used [-Wunused-but-set-variable] 2193 | BioseqSetPtr bssp; | ^~~~ vsm.c:2188:37: warning: variable ‘bottom’ set but not used [-Wunused-but-set-variable] 2188 | Int4 top, lineheight, left, bottom, width, maxwidth; | ^~~~~~ vsm.c: In function ‘VSMAddPictureToEntity’: vsm.c:2821:17: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 2821 | Pointer ptr; | ^~~ vsm.c:2820:20: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2820 | ValNodePtr vnp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vsmfile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vsmpriv.h:48, from vsmfile.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsmfile.c: In function ‘VSMGenericBinAsnOpen’: vsmfile.c:259:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 259 | ButtoN b; | ^ vsmfile.c: In function ‘VSMGenericFastaSave’: vsmfile.c:395:11: warning: variable ‘code’ set but not used [-Wunused-but-set-variable] 395 | Uint1 code; | ^~~~ vsmfile.c: In function ‘VSMFastaProtSaveWithProduct’: vsmfile.c:527:11: warning: variable ‘code’ set but not used [-Wunused-but-set-variable] 527 | Uint1 code; | ^~~~ vsmfile.c: In function ‘VSMSaveSetsAsFiles’: vsmfile.c:1368:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 1368 | OMProcControlPtr ompcp; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vsmutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vsmutil.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsmutil.c: In function ‘GetDocPosForError’: vsmutil.c:1743:18: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 1743 | Int2 val; | ^~~ vsmutil.c: At top level: vsmutil.c:1628:16: warning: ‘MakeFieldReports’ defined but not used [-Wunused-function] 1628 | static Boolean MakeFieldReports (ValNodePtr report_list, ValNodePtr field_list, FILE *fp) | ^~~~~~~~~~~~~~~~ vsmutil.c:387:20: warning: ‘GetSeqDescGivenIDs’ defined but not used [-Wunused-function] 387 | static SeqDescrPtr GetSeqDescGivenIDs (Uint2 entityID, Uint4 itemID, Uint2 itemtype) | ^~~~~~~~~~~~~~~~~~ vsmutil.c: In function ‘ContinueProc’: vsmutil.c:2256:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2256 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2255:26: note: within this loop 2255 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘RevalidateProc’: vsmutil.c:2223:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2223 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2222:26: note: within this loop 2222 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘SetVerbosityAndRepopulate’: vsmutil.c:2297:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2297 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2296:26: note: within this loop 2296 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘ClearValidateWindow’: vsmutil.c:613:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 613 | vep->counts [sev] = 0; | ~~~~~~~~~~~~~~~~~~^~~ vsmutil.c:612:32: note: within this loop 612 | for (sev = SEV_NONE; sev <= SEV_MAX; sev++) { | ~~~~^~~~~~~~~~ vsmutil.c: In function ‘CreateValidateWindowExExEx’: vsmutil.c:2620:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2620 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2619:30: note: within this loop 2619 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘ContinueProc’: vsmutil.c:2256:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2256 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘RevalidateProc’: vsmutil.c:2223:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2223 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘SetVerbosityAndRepopulate’: vsmutil.c:2297:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2297 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘ClearValidateWindow’: vsmutil.c:613:21: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 613 | vep->counts [sev] = 0; | ~~~~~~~~~~~~^~~~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘CreateValidateWindowExExEx’: vsmutil.c:2620:23: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2620 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘ShowValidateDoc’: vsmutil.c:2758:61: warning: ‘ REJECT: ’ directive writing 14 bytes into a region of size between 13 and 43 [-Wformat-overflow=] 2758 | sprintf (str, "INFO: %ld WARNING: %ld ERROR: %ld REJECT: %ld", | ^~~~~~~~~~~~~~ vsmutil.c:2758:17: note: directive argument in the range [-2147483648, 2147483647] 2758 | sprintf (str, "INFO: %ld WARNING: %ld ERROR: %ld REJECT: %ld", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ShowValidateDoc’ at vsmutil.c:2758:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 53 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF udvgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvgraph.c:177: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvgraph.c: In function ‘UDV_click_item’: udvgraph.c:877:9: warning: unused variable ‘IsTransNeeded’ [-Wunused-variable] 877 | Boolean IsTransNeeded=FALSE; | ^~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_SendBSPSelectMsg’: udvgraph.c:1230:13: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 1230 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ udvgraph.c:1226:30: warning: variable ‘bsp_coord_old’ set but not used [-Wunused-but-set-variable] 1226 | Int4 first_bsp_coord, bsp_coord_old,old_pos; | ^~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_draw_helixDNA’: udvgraph.c:1827:15: warning: variable ‘cyChar_2’ set but not used [-Wunused-but-set-variable] 1827 | Int2 cxChar_2,cyChar_2; | ^~~~~~~~ udvgraph.c: In function ‘draw_logo’: udvgraph.c:1940:38: warning: variable ‘cyGlobal’ set but not used [-Wunused-but-set-variable] 1940 | Int2 pos,cxChar=7,cyChar=13,cxGlobal,cyGlobal; | ^~~~~~~~ udvgraph.c: In function ‘UDV_draw_CDS_minus’: udvgraph.c:2337:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 2337 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ udvgraph.c:2332:33: warning: variable ‘numivals2’ set but not used [-Wunused-but-set-variable] 2332 | numivals2=0, | ^~~~~~~~~ udvgraph.c: In function ‘UDV_draw_CDS_plus’: udvgraph.c:2461:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 2461 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_draw_panel’: udvgraph.c:4111:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4111 | if(vdp->vgp->MasterViewer == SAMVIEWDDV) | ^~ udvgraph.c:4113:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4113 | Row = ViewMgr_GetRow(svpp, vdp->userkey); | ^~~ udvgraph.c:4041:21: warning: unused variable ‘vnp_seqinfo’ [-Wunused-variable] 4041 | ValNodePtr vnp_seqinfo=NULL; | ^~~~~~~~~~~ udvgraph.c:4035:68: warning: variable ‘nLinesDraw’ set but not used [-Wunused-but-set-variable] 4035 | Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw; | ^~~~~~~~~~ udvgraph.c:4035:60: warning: variable ‘nTotRow’ set but not used [-Wunused-but-set-variable] 4035 | Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw; | ^~~~~~~ udvgraph.c: At top level: udvgraph.c:3921:14: warning: ‘UDV_calc_decalRC’ defined but not used [-Wunused-function] 3921 | static Int4 UDV_calc_decalRC(ValNodePtr ParaG,Int4 ScrollPos, | ^~~~~~~~~~~~~~~~ udvgraph.c:3433:14: warning: ‘UDV_Draw_features_label’ defined but not used [-Wunused-function] 3433 | static void UDV_Draw_features_label(UnDViewerGraphDataPtr GrData, | ^~~~~~~~~~~~~~~~~~~~~~~ udvgraph.c:1298:13: warning: ‘UDV_AutoSelectAllSeq’ defined but not used [-Wunused-function] 1298 | static void UDV_AutoSelectAllSeq(ViewerDialogDataPtr vdp,Boolean bSelect) | ^~~~~~~~~~~~~~~~~~~~ udvgraph.c:971:17: warning: ‘UDV_draw_horz_cursor’ defined but not used [-Wunused-function] 971 | static void UDV_draw_horz_cursor(UnDViewerGraphDataPtr GrData, | ^~~~~~~~~~~~~~~~~~~~ udvgraph.c:948:13: warning: ‘UDV_draw_vert_cursor’ defined but not used [-Wunused-function] 948 | static void UDV_draw_vert_cursor(RecT rcClip,PoinT pos) | ^~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from udvgraph.c:180: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ udvgraph.c: In function ‘UDV_GetCurrentDispRange’: udvgraph.c:638:22: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 638 | *from_bsp=pgp->StartLetter; | ~~~^~~~~~~~~~~~~ udvgraph.c:610:12: note: ‘pgp’ was declared here 610 | ParaGPtr pgp; | ^~~ In file included from ../include/udviewer.h:225: udvgraph.c: In function ‘UDV_Draw_features’: udvgraph.c:3182:77: warning: ‘idx1’ may be used uninitialized [-Wmaybe-uninitialized] 3182 | start2=_max_(pgp->StartLetter,context->ivals[idx1]); | ^ udvgraph.c:2809:6: note: ‘idx1’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3189:66: warning: ‘idx2’ may be used uninitialized [-Wmaybe-uninitialized] 3189 | UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y, | ~~~~~~~~^~~~~~ udvgraph.c:2809:11: note: ‘idx2’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3189:86: warning: ‘idx3’ may be used uninitialized [-Wmaybe-uninitialized] 3189 | UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y, | ~~~~~~~^~~~~~ udvgraph.c:2809:16: note: ‘idx3’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3196:75: warning: ‘idx4’ may be used uninitialized [-Wmaybe-uninitialized] 3196 | stop2=_min_(pgp->StopLetter,context->ivals[idx4]); | ^ udvgraph.c:2809:21: note: ‘idx4’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3203:66: warning: ‘idx5’ may be used uninitialized [-Wmaybe-uninitialized] 3203 | UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y, | ~~~~~~~~^~~~~~ udvgraph.c:2809:26: note: ‘idx5’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3203:86: warning: ‘idx6’ may be used uninitialized [-Wmaybe-uninitialized] 3203 | UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y, | ~~~~~~~^~~~~~ udvgraph.c:2809:31: note: ‘idx6’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ ../include/udvdef.h:187:40: warning: ‘stop_x2’ may be used uninitialized [-Wmaybe-uninitialized] 187 | #define _max_(a,b) ((a)>=(b)?(a):(b)) | ~~~~~~~~~~~~~^~~~~ udvgraph.c:2803:21: note: ‘stop_x2’ was declared here 2803 | Int2 start_x,stop_x,stop_x2, /*id. but in pixels*/ | ^~~~~~~ udvgraph.c: In function ‘UDV_ClickProc’: udvgraph.c:1458:52: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 1458 | if (vmp && vmp->hFeatDlg){/*update Features List Dlg if needed; | ^ udvgraph.c:1382:25: note: ‘vmp’ was declared here 1382 | ViewerMainPtr vmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF udvopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvopen.c:101: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvopen.c: In function ‘UDV_FileOpen’: udvopen.c:875:38: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 875 | ButtoN b,b1,b2; | ^~ udvopen.c:875:33: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 875 | ButtoN b,b1,b2; | ^ udvopen.c: In function ‘UDV_CreateListBioseqDlg’: udvopen.c:1180:37: warning: the address of ‘szName’ will always evaluate as ‘true’ [-Waddress] 1180 | if (szName){ | ^~~~~~ udvopen.c: In function ‘UDV_FOpenCancelProc’: udvopen.c:792:23: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 792 | UDV_set_PullMenus(&vmp->MainMenu,TRUE); | ^~~~~~~~~~~~~~ udvopen.c:779:25: note: ‘vmp’ was declared here 779 | ViewerMainPtr vmp; | ^~~ udvopen.c: In function ‘UDV_analyze_SEP_for_open’: udvopen.c:327:21: warning: ‘dataptr’ may be used uninitialized [-Wmaybe-uninitialized] 327 | vmp->dataptr=dataptr; | ~~~~~~~~~~~~^~~~~~~~ udvopen.c:241:13: note: ‘dataptr’ was declared here 241 | Pointer dataptr; | ^~~~~~~ udvopen.c:242:22: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 242 | Uint2 datatype,entityID,eID; | ^~~~~~~~ udvopen.c: In function ‘UDV_FOpenAcceptProc’: udvopen.c:855:23: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 855 | UDV_set_PullMenus(&vmp->MainMenu,TRUE); | ^~~~~~~~~~~~~~ udvopen.c:811:25: note: ‘vmp’ was declared here 811 | ViewerMainPtr vmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF udvpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvpanel.c:197: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvpanel.c: In function ‘UDV_GotoBtnProc’: udvpanel.c:2080:22: warning: variable ‘old_ivalue’ set but not used [-Wunused-but-set-variable] 2080 | Int4 iValue,old_ivalue,line_num,from_bsp,to_bsp, | ^~~~~~~~~~ udvpanel.c:2079:15: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2079 | ValNodePtr vnp; | ^~~ udvpanel.c: In function ‘CreateMainControls’: udvpanel.c:2165:8: warning: variable ‘cxChar’ set but not used [-Wunused-but-set-variable] 2165 | Int2 cxChar,cyChar,Margins; | ^~~~~~ udvpanel.c: In function ‘UDV_SearchFeatForKey’: udvpanel.c:3478:36: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3478 | ButtoN b1,b2; | ^~ udvpanel.c: At top level: udvpanel.c:2773:28: warning: ‘FeaturesListBoxScan’ defined but not used [-Wunused-function] 2773 | static Boolean LIBCALLBACK FeaturesListBoxScan (SeqFeatPtr sfp, | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dotvibrant.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/dotviewer.h:15, from dotvibrant.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dotvibrant.c: In function ‘DOT_DisplayHits’: dotvibrant.c:564:18: warning: variable ‘ycomp’ set but not used [-Wunused-but-set-variable] 564 | Int4 ycomp, xcomp; | ^~~~~ dotvibrant.c: In function ‘DOT_VscrlProc’: dotvibrant.c:918:16: warning: variable ‘visLines’ set but not used [-Wunused-but-set-variable] 918 | Int2 visLines, vmargin, hmargin; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_HscrlProc’: dotvibrant.c:972:20: warning: variable ‘visLines’ set but not used [-Wunused-but-set-variable] 972 | Int2 dx, visLines, offset, hmargin, vmargin; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_VCrossHairs’: dotvibrant.c:1402:10: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1402 | Int4 cursor_size =15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_HCrossHairs’: dotvibrant.c:1427:9: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1427 | Int4 cursor_size = 15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MoveCrossHairs’: dotvibrant.c:1453:18: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 1453 | DOTSelDataPtr data; | ^~~~ dotvibrant.c:1452:10: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1452 | Int4 cursor_size = 15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_DrawXAxis’: dotvibrant.c:1532:38: warning: unused variable ‘title’ [-Wunused-variable] 1532 | Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/ | ^~~~~ dotvibrant.c: In function ‘DOT_DrawYAxis’: dotvibrant.c:1642:38: warning: unused variable ‘title’ [-Wunused-variable] 1642 | Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/ | ^~~~~ dotvibrant.c:1641:55: warning: variable ‘Fh_4’ set but not used [-Wunused-but-set-variable] 1641 | Int4 pos, ylen, x, y, scale_pos, i, j, Fh_2,Fh_4; | ^~~~ dotvibrant.c: In function ‘DOT_SVDisplayDiags’: dotvibrant.c:1770:28: warning: variable ‘aln_diag’ set but not used [-Wunused-but-set-variable] 1770 | Int4 diag, aln_diag; | ^~~~~~~~ dotvibrant.c:1770:22: warning: variable ‘diag’ set but not used [-Wunused-but-set-variable] 1770 | Int4 diag, aln_diag; | ^~~~ dotvibrant.c:1766:22: warning: variable ‘width’ set but not used [-Wunused-but-set-variable] 1766 | Int4 width, height; | ^~~~~ dotvibrant.c:1765:31: warning: variable ‘p_HFrom’ set but not used [-Wunused-but-set-variable] 1765 | Int4 p_VFrom, p_HFrom; | ^~~~~~~ dotvibrant.c:1765:22: warning: variable ‘p_VFrom’ set but not used [-Wunused-but-set-variable] 1765 | Int4 p_VFrom, p_HFrom; | ^~~~~~~ dotvibrant.c:1762:28: warning: unused variable ‘cutoff’ [-Wunused-variable] 1762 | Int4 stop, cutoff=0, q_start, s_start, length; | ^~~~~~ dotvibrant.c:1760:34: warning: variable ‘seg3’ set but not used [-Wunused-but-set-variable] 1760 | SegmenT seg1, seg2, seg3, seg4; | ^~~~ dotvibrant.c: In function ‘DOT_FillNewSeqBufs’: dotvibrant.c:2197:19: warning: unused variable ‘alp’ [-Wunused-variable] 2197 | DOTAlignInfoPtr alp=NULL; | ^~~ dotvibrant.c: In function ‘DOT_InitCInfo’: dotvibrant.c:2258:14: warning: unused variable ‘colBuf’ [-Wunused-variable] 2258 | Char colBuf[12]={""}; | ^~~~~~ dotvibrant.c: In function ‘DOT_SVDisplaySequence’: dotvibrant.c:2379:16: warning: variable ‘matrix’ set but not used [-Wunused-but-set-variable] 2379 | Int4Ptr PNTR matrix; | ^~~~~~ dotvibrant.c:2367:14: warning: variable ‘vis_2’ set but not used [-Wunused-but-set-variable] 2367 | Int4 vis_2, buf_len; | ^~~~~ dotvibrant.c:2364:14: warning: unused variable ‘prot_threshold’ [-Wunused-variable] 2364 | Int4 prot_threshold=0, bloc_cntr; | ^~~~~~~~~~~~~~ dotvibrant.c:2350:24: warning: variable ‘mip2’ set but not used [-Wunused-but-set-variable] 2350 | DOTMainDataPtr mip1, mip2; | ^~~~ dotvibrant.c: In function ‘DOT_SVClickProc’: dotvibrant.c:2807:17: warning: unused variable ‘handled’ [-Wunused-variable] 2807 | Int2 handled=0; | ^~~~~~~ dotvibrant.c: In function ‘DOT_ResizeFeatWindow’: dotvibrant.c:3016:63: warning: variable ‘SubjectHeight’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~~~~~~~~~~~ dotvibrant.c:3016:51: warning: variable ‘QueryHeight’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~~~~~~~~~ dotvibrant.c:3016:37: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~ dotvibrant.c: In function ‘DOT_ResizeSequenceWindow’: dotvibrant.c:3098:25: warning: variable ‘is_visible2’ set but not used [-Wunused-but-set-variable] 3098 | Boolean is_visible1, is_visible2; | ^~~~~~~~~~~ dotvibrant.c:3098:12: warning: variable ‘is_visible1’ set but not used [-Wunused-but-set-variable] 3098 | Boolean is_visible1, is_visible2; | ^~~~~~~~~~~ dotvibrant.c:3095:51: warning: variable ‘V1Height’ set but not used [-Wunused-but-set-variable] 3095 | Int2 height,width,gap,vsbWidth,in,hsbHeight,V1Height,V2Height, goHeight; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_HideFeatDlg’: dotvibrant.c:3745:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 3745 | ButtoN b; | ^ dotvibrant.c: In function ‘DOT_SVBuildDiagViewer’: dotvibrant.c:4031:18: warning: variable ‘mip’ set but not used [-Wunused-but-set-variable] 4031 | DOTMainDataPtr mip; | ^~~ dotvibrant.c:4029:28: warning: unused variable ‘str2’ [-Wunused-variable] 4029 | Char str1[41]={""}, str2[41]={""}; | ^~~~ dotvibrant.c:4029:13: warning: unused variable ‘str1’ [-Wunused-variable] 4029 | Char str1[41]={""}, str2[41]={""}; | ^~~~ dotvibrant.c:4022:18: warning: variable ‘pr2’ set but not used [-Wunused-but-set-variable] 4022 | PrompT pr1, pr2; | ^~~ dotvibrant.c:4022:13: warning: variable ‘pr1’ set but not used [-Wunused-but-set-variable] 4022 | PrompT pr1, pr2; | ^~~ dotvibrant.c: In function ‘DOT_UpdateDataRects’: dotvibrant.c:4166:19: warning: variable ‘dy’ set but not used [-Wunused-but-set-variable] 4166 | Int4 comp, dx, dy, xstart, ystart; | ^~ dotvibrant.c:4166:15: warning: variable ‘dx’ set but not used [-Wunused-but-set-variable] 4166 | Int4 comp, dx, dy, xstart, ystart; | ^~ dotvibrant.c: In function ‘DOT_MsgFunc’: dotvibrant.c:4215:17: warning: variable ‘vdp2’ set but not used [-Wunused-but-set-variable] 4215 | DOTVibDataPtr vdp2 = NULL; | ^~~~ dotvibrant.c: In function ‘DOT_ReleaseProc’: dotvibrant.c:4373:32: warning: unused variable ‘yaxis_incr’ [-Wunused-variable] 4373 | Boolean xaxis_incr=TRUE, yaxis_incr=TRUE; | ^~~~~~~~~~ dotvibrant.c:4373:15: warning: unused variable ‘xaxis_incr’ [-Wunused-variable] 4373 | Boolean xaxis_incr=TRUE, yaxis_incr=TRUE; | ^~~~~~~~~~ dotvibrant.c:4371:19: warning: variable ‘alp’ set but not used [-Wunused-but-set-variable] 4371 | DOTAlignInfoPtr alp=NULL; | ^~~ dotvibrant.c:4370:18: warning: variable ‘mip1’ set but not used [-Wunused-but-set-variable] 4370 | DOTMainDataPtr mip1=NULL; | ^~~~ dotvibrant.c: In function ‘DOT_StartDOTPLOT’: dotvibrant.c:4891:23: warning: variable ‘vdp’ set but not used [-Wunused-but-set-variable] 4891 | DOTVibDataPtr vdp; | ^~~ dotvibrant.c: In function ‘DOT_DoZoom’: dotvibrant.c:5106:18: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 5106 | DOTSelDataPtr data; | ^~~~ dotvibrant.c: In function ‘DOT_ZoomProc’: dotvibrant.c:5204:23: warning: variable ‘temport’ set but not used [-Wunused-but-set-variable] 5204 | WindoW temport, w; | ^~~~~~~ dotvibrant.c: In function ‘AlnMgr2GetNextLine’: dotvibrant.c:5315:3: warning: value computed is not used [-Wunused-value] 5315 | *n++; | ^~~~ dotvibrant.c: In function ‘DOT_GetAlign’: dotvibrant.c:5332:44: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 5332 | Int4 x1, y1, x2, y2, numlines=0, n=0, i=0; | ^ dotvibrant.c: In function ‘DOT_FillAlignInfoPointer’: dotvibrant.c:5565:16: warning: unused variable ‘i’ [-Wunused-variable] 5565 | Int4 i=0, n=0; | ^ dotvibrant.c: In function ‘DOT_Prob_FillAlignInfoPointer’: dotvibrant.c:5681:16: warning: unused variable ‘i’ [-Wunused-variable] 5681 | Int4 i=0, n=0; | ^ dotvibrant.c:5680:16: warning: unused variable ‘numsaps’ [-Wunused-variable] 5680 | Int4 numsaps = 0, numlines = 0; | ^~~~~~~ dotvibrant.c:5678:37: warning: unused variable ‘sap_tmp’ [-Wunused-variable] 5678 | SeqAlignPtr sap=NULL, salp=NULL, sap_tmp=NULL; | ^~~~~~~ dotvibrant.c: In function ‘DOT_DoBlast’: dotvibrant.c:5918:23: warning: unused variable ‘eval’ [-Wunused-variable] 5918 | Char eval[11]={""}; | ^~~~ dotvibrant.c:5917:23: warning: variable ‘is_local’ set but not used [-Wunused-but-set-variable] 5917 | Boolean is_local; | ^~~~~~~~ dotvibrant.c:5915:23: warning: unused variable ‘entityID’ [-Wunused-variable] 5915 | Uint2 entityID=0; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_CreateWindowDetails’: dotvibrant.c:6214:27: warning: variable ‘pr2’ set but not used [-Wunused-but-set-variable] 6214 | PrompT pr1, pr2; | ^~~ dotvibrant.c:6214:22: warning: variable ‘pr1’ set but not used [-Wunused-but-set-variable] 6214 | PrompT pr1, pr2; | ^~~ dotvibrant.c:6207:21: warning: variable ‘g1’ set but not used [-Wunused-but-set-variable] 6207 | GrouP g, g1, g2; | ^~ dotvibrant.c: In function ‘DOT_ResizeMainWindow’: dotvibrant.c:6273:35: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 6273 | Int2 height, width, in , gap; | ^~~ dotvibrant.c: In function ‘DOT_OpenSeqAnnotFile’: dotvibrant.c:6451:16: warning: the comparison will always evaluate as ‘true’ for the address of ‘path’ will never be NULL [-Waddress] 6451 | if (path != NULL) | ^~ dotvibrant.c:6439:13: note: ‘path’ declared here 6439 | Char path [PATH_MAX]; | ^~~~ dotvibrant.c: In function ‘DOT_FindAlignment’: dotvibrant.c:6662:29: warning: unused variable ‘rb_fixed’ [-Wunused-variable] 6662 | Boolean lt_fixed=FALSE, rb_fixed=FALSE; | ^~~~~~~~ dotvibrant.c:6662:13: warning: unused variable ‘lt_fixed’ [-Wunused-variable] 6662 | Boolean lt_fixed=FALSE, rb_fixed=FALSE; | ^~~~~~~~ dotvibrant.c:6661:17: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 6661 | DOTSelDataPtr data; | ^~~~ dotvibrant.c: In function ‘SCP_CompareOrderOrganizeBioseqs’: dotvibrant.c:6792:25: warning: variable ‘itemID’ set but not used [-Wunused-but-set-variable] 6792 | Uint4 itemID=0; | ^~~~~~ dotvibrant.c: In function ‘SCP_OrganizeAlnsInSet’: dotvibrant.c:6873:21: warning: variable ‘indextype’ set but not used [-Wunused-but-set-variable] 6873 | Int4 indextype; | ^~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from ../include/dotviewer.h:32: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dotvibrant.c:6642:16: warning: ‘DOT_DeselectPrim’ defined but not used [-Wunused-function] 6642 | static Boolean DOT_DeselectPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata) | ^~~~~~~~~~~~~~~~ dotvibrant.c:6346:13: warning: ‘DOT_NewAnalysis’ defined but not used [-Wunused-function] 6346 | static void DOT_NewAnalysis (ButtoN b) | ^~~~~~~~~~~~~~~ dotvibrant.c:5894:16: warning: ‘DOT_get_eval’ defined but not used [-Wunused-function] 5894 | static FloatHi DOT_get_eval(Int4 exp) | ^~~~~~~~~~~~ dotvibrant.c:5325:16: warning: ‘DOT_GetAlign’ defined but not used [-Wunused-function] 5325 | static Boolean DOT_GetAlign (DOTAlignInfoPtr alp) | ^~~~~~~~~~~~ dotvibrant.c:5281:16: warning: ‘AlnMgr2GetNextLine’ defined but not used [-Wunused-function] 5281 | static Boolean AlnMgr2GetNextLine(SeqAlignPtr sap, AlnMsg2Ptr amp1, AlnMsg2Ptr amp2, Int4Ptr x1, Int4Ptr y1, Int4Ptr x2, Int4Ptr y2, Int4Ptr n) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:4767:13: warning: ‘DOT_FeatAnalysisProc’ defined but not used [-Wunused-function] 4767 | static void DOT_FeatAnalysisProc(ButtoN b) | ^~~~~~~~~~~~~~~~~~~~ dotvibrant.c:4749:13: warning: ‘DOT_GetInfoProc’ defined but not used [-Wunused-function] 4749 | static void DOT_GetInfoProc (IteM i) | ^~~~~~~~~~~~~~~ dotvibrant.c:4213:25: warning: ‘DOT_MsgFunc’ defined but not used [-Wunused-function] 4213 | static Int2 LIBCALLBACK DOT_MsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~ dotvibrant.c:3688:13: warning: ‘DOT_HideAcceptProc’ defined but not used [-Wunused-function] 3688 | static void DOT_HideAcceptProc(ButtoN b) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:3318:13: warning: ‘DOT_AddFeatureToSegment’ defined but not used [-Wunused-function] 3318 | static void DOT_AddFeatureToSegment(SeqMgrFeatContextPtr context, | ^~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c:2954:13: warning: ‘DOT_SVChangeLabels’ defined but not used [-Wunused-function] 2954 | static void DOT_SVChangeLabels (GrouP g) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:2760:16: warning: ‘DOT_SVGetDiag’ defined but not used [-Wunused-function] 2760 | static Boolean DOT_SVGetDiag (Uint2 segID, Uint2 primID, VoidPtr userdata) | ^~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_GetNthSeqFromAlign’: dotvibrant.c:5064:6: warning: ‘spp’ may be used uninitialized [-Wmaybe-uninitialized] 5064 | if (spp == NULL) | ^ dotvibrant.c:5038:20: note: ‘spp’ was declared here 5038 | SeqPortPtr spp; | ^~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2503:6: warning: ‘s’ may be used uninitialized [-Wmaybe-uninitialized] 2503 | end=s+buf_len-1; | ~~~^~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2357:14: note: ‘s’ was declared here 2357 | Uint1Ptr s; | ^ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2545:18: warning: ‘is_na’ may be used uninitialized [-Wmaybe-uninitialized] 2545 | if (is_na) | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2361:27: note: ‘is_na’ was declared here 2361 | Boolean ambig=FALSE, is_na; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2503:16: warning: ‘buf_len’ may be used uninitialized [-Wmaybe-uninitialized] 2503 | end=s+buf_len-1; | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2367:21: note: ‘buf_len’ was declared here 2367 | Int4 vis_2, buf_len; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2570:26: warning: ‘hit_start’ may be used uninitialized [-Wmaybe-uninitialized] 2570 | if (hit_start<=i && i<=(hit_stop+bloc_size)) | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:14: note: ‘hit_start’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2504:21: warning: ‘hit_stop’ may be used uninitialized [-Wmaybe-uninitialized] 2504 | hit_stop+=hit_stop/10; | ~~~~~~~~^~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:25: note: ‘hit_stop’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘q_pos’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:35: note: ‘q_pos’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘s_pos’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:42: note: ‘s_pos’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2583:37: warning: ‘residue_names’ may be used uninitialized [-Wmaybe-uninitialized] 2583 | sBuf[c]=*residue_names[(int)*s]; | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2378:16: note: ‘residue_names’ was declared here 2378 | CharPtr PNTR residue_names; | ^~~~~~~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘strand1’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2380:14: note: ‘strand1’ was declared here 2380 | Uint1 strand1, strand2; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘strand2’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2380:23: note: ‘strand2’ was declared here 2380 | Uint1 strand1, strand2; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2547:23: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized] 2547 | if (*q > 3 || *s > 3) | ^~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2356:14: note: ‘q’ was declared here 2356 | Uint1Ptr q; | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘qname’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6208:23: note: ‘qname’ was declared here 6208 | Char PNTR qname, PNTR sname; | ^~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘sname’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6208:35: note: ‘sname’ was declared here 6208 | Char PNTR qname, PNTR sname; | ^~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘q_start’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:18: note: ‘q_start’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘q_stop’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:27: note: ‘q_stop’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘s_start’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:35: note: ‘s_start’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘s_stop’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:44: note: ‘s_stop’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dlgutil1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from dlgutil1.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dlgutil1.c: In function ‘IsAuthList’: dlgutil1.c:2962:8: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 2962 | Int4 len; | ^~~ dlgutil1.c: In function ‘TestIntervalEditor’: dlgutil1.c:5324:20: warning: variable ‘fuzz_to’ set but not used [-Wunused-but-set-variable] 5324 | Int2 fuzz_to; | ^~~~~~~ dlgutil1.c:5323:20: warning: variable ‘fuzz_from’ set but not used [-Wunused-but-set-variable] 5323 | Int2 fuzz_from; | ^~~~~~~~~ dlgutil1.c:5322:41: warning: variable ‘fuzz_before’ set but not used [-Wunused-but-set-variable] 5322 | Boolean isInterval, isPoint, fuzz_before, fuzz_after; | ^~~~~~~~~~~ dlgutil1.c: In function ‘DbtagDialogToDbtagPtr’: dlgutil1.c:7254:16: warning: unused variable ‘val’ [-Wunused-variable] 7254 | long int val; | ^~~ dlgutil1.c:7250:16: warning: unused variable ‘ptr’ [-Wunused-variable] 7250 | CharPtr ptr; | ^~~ dlgutil1.c:7247:16: warning: unused variable ‘num_digits’ [-Wunused-variable] 7247 | Int2 num_digits; | ^~~~~~~~~~ dlgutil1.c:7246:16: warning: unused variable ‘notallzero’ [-Wunused-variable] 7246 | Boolean notallzero; | ^~~~~~~~~~ dlgutil1.c:7243:16: warning: unused variable ‘leadingzero’ [-Wunused-variable] 7243 | Boolean leadingzero; | ^~~~~~~~~~~ dlgutil1.c:7238:16: warning: unused variable ‘alldigits’ [-Wunused-variable] 7238 | Boolean alldigits; | ^~~~~~~~~ dlgutil1.c: In function ‘CreateStandardEditMenu’: dlgutil1.c:9427:8: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 9427 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from dlgutil1.c:55: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dlgutil1.c:8603:25: warning: ‘GetNthNameValuePair’ defined but not used [-Wunused-function] 8603 | static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list) | ^~~~~~~~~~~~~~~~~~~ dlgutil1.c:8051:16: warning: ‘ParseSpecimenVoucherOk’ defined but not used [-Wunused-function] 8051 | static Boolean ParseSpecimenVoucherOk (CharPtr str) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil1.c:1293:13: warning: ‘GbqualsToVisStringDialog’ defined but not used [-Wunused-function] 1293 | static void GbqualsToVisStringDialog (SeqFeatPtr sfp, DialoG d, CharPtr qual) | ^~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dlgutil2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from dlgutil2.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dlgutil2.c: In function ‘CitListToDialog’: dlgutil2.c:945:18: warning: the comparison will always evaluate as ‘false’ for the address of ‘last’ will never be NULL [-Waddress] 945 | if (last == NULL || StringCmp (cldp->label, last) != 0) { | ^~ dlgutil2.c:897:19: note: ‘last’ declared here 897 | Char last [128]; | ^~~~ dlgutil2.c: In function ‘CreateImportFields’: dlgutil2.c:1401:19: warning: variable ‘is_gap’ set but not used [-Wunused-but-set-variable] 1401 | Boolean is_gap = FALSE; | ^~~~~~ dlgutil2.c: In function ‘UpdateTableDisplayDialogScrollBars’: dlgutil2.c:3552:11: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] 3552 | Int4 x, y; | ^ dlgutil2.c:3552:8: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] 3552 | Int4 x, y; | ^ dlgutil2.c: In function ‘GetTableDisplayCell’: dlgutil2.c:3951:8: warning: variable ‘start_row’ set but not used [-Wunused-but-set-variable] 3951 | Int4 start_row, start_col; | ^~~~~~~~~ dlgutil2.c: In function ‘NewCreateInferenceDialog’: dlgutil2.c:7633:19: warning: variable ‘fnt’ set but not used [-Wunused-but-set-variable] 7633 | FonT fnt; | ^~~ dlgutil2.c: In function ‘ClickableListOnKey’: dlgutil2.c:10479:20: warning: variable ‘clp’ set but not used [-Wunused-but-set-variable] 10479 | ClickableListPtr clp; | ^~~ dlgutil2.c: In function ‘GetSelectedClickableListText’: dlgutil2.c:11151:36: warning: variable ‘char_offset’ set but not used [-Wunused-but-set-variable] 11151 | Int2 item, row, col, char_offset; | ^~~~~~~~~~~ dlgutil2.c: In function ‘AutomatchFeatures’: dlgutil2.c:14210:36: warning: variable ‘s3’ set but not used [-Wunused-but-set-variable] 14210 | SeqIntPtr s1, s2, s3; | ^~ dlgutil2.c: At top level: dlgutil2.c:12342:16: warning: ‘ParseMultiListQualOk’ defined but not used [-Wunused-function] 12342 | static Boolean ParseMultiListQualOk (CharPtr val) | ^~~~~~~~~~~~~~~~~~~~ dlgutil2.c:10336:13: warning: ‘ClickClickableListItem’ defined but not used [-Wunused-function] 10336 | static void ClickClickableListItem (DoC d, PoinT pt) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:10316:13: warning: ‘DrawClickableListItem’ defined but not used [-Wunused-function] 10316 | static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine) | ^~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:8854:13: warning: ‘GetCategoryNumFromName’ defined but not used [-Wunused-function] 8854 | static Int4 GetCategoryNumFromName (CharPtr category) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:1676:16: warning: ‘GetNameForFeature’ defined but not used [-Wunused-function] 1676 | static CharPtr GetNameForFeature (SeqFeatPtr sfp) | ^~~~~~~~~~~~~~~~~ dlgutil2.c: In function ‘PopulateDayPopup’: dlgutil2.c:11438:24: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 11438 | sprintf (day, "%d", i); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PopulateDayPopup’ at dlgutil2.c:11438:7, inlined from ‘PopulateDayPopup’ at dlgutil2.c:11428:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF e2trmlst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from e2trmlst.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ e2trmlst.c: In function ‘ReadAFew’: e2trmlst.c:2230:61: warning: left-hand operand of comma expression has no effect [-Wunused-value] 2230 | for (row = 1, termPtr = e2TermListPtr->list; row <= *count, termPtr != NULL; row++, termPtr = termPtr->next) { | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF e2docsum.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from e2docsum.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ e2docsum.c: In function ‘FormatCdsSeq’: e2docsum.c:1523:22: warning: variable ‘gene’ set but not used [-Wunused-but-set-variable] 1523 | SeqFeatPtr gene = NULL; | ^~~~ e2docsum.c: In function ‘FetchSequence’: e2docsum.c:1591:16: warning: variable ‘currDbName’ set but not used [-Wunused-but-set-variable] 1591 | CharPtr currDbName; | ^~~~~~~~~~ e2docsum.c:1580:16: warning: variable ‘group_segs’ set but not used [-Wunused-but-set-variable] 1580 | Uint1 group_segs = 0; | ^~~~~~~~~~ e2docsum.c: In function ‘ReleaseDocSum’: e2docsum.c:3305:27: warning: the comparison will always evaluate as ‘true’ for the address of ‘launchPopups’ will never be NULL [-Waddress] 3305 | if (sfp->launchPopups != NULL) { | ^~ e2docsum.c:490:25: note: ‘launchPopups’ declared here 490 | PopuP launchPopups [MAX_DBS + 1]; | ^~~~~~~~~~~~ e2docsum.c: In function ‘SaveDocsumProject’: e2docsum.c:3606:16: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 3606 | SummFormPtr sfp; | ^~~ e2docsum.c: In function ‘RetrieveGeneration’: e2docsum.c:4135:19: warning: variable ‘e2ip’ set but not used [-Wunused-but-set-variable] 4135 | Entrez2InfoPtr e2ip; | ^~~~ e2docsum.c: In function ‘SetupMenus’: e2docsum.c:4849:16: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 4849 | ChoicE c; | ^ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/bspview.h:48, from e2docsum.c:53: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strucapi.h:52, from e2docsum.c:62: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchStructureViewer’: e2docsum.c:2981:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2981 | system (cmmd); | ^~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchSequin’: e2docsum.c:2838:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2838 | system (cmmd); | ^~~~~~~~~~~~~ e2docsum.c: At top level: e2docsum.c:2883:13: warning: ‘GetBiostrucMaxModels’ defined but not used [-Wunused-function] 2883 | static Int4 GetBiostrucMaxModels (void) | ^~~~~~~~~~~~~~~~~~~~ e2docsum.c:2850:13: warning: ‘GetBiostrucComplexity’ defined but not used [-Wunused-function] 2850 | static Int4 GetBiostrucComplexity (void) | ^~~~~~~~~~~~~~~~~~~~~ e2docsum.c:2154:20: warning: ‘cddDocProcs’ defined but not used [-Wunused-variable] 2154 | static DocPrntProc cddDocProcs [] = { Query_FetchDocSum, Query_FetchFields, FetchUid, NULL }; | ^~~~~~~~~~~ e2docsum.c: In function ‘LaunchStructureViewer’: e2docsum.c:2980:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4091 [-Wformat-overflow=] 2980 | sprintf (cmmd, "Cn3D %s &", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘LaunchStructureViewer’ at e2docsum.c:2980:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 4103 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchSequin.isra.0’: e2docsum.c:2837:31: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4084 [-Wformat-overflow=] 2837 | sprintf (cmmd, "sequin -x < %s &", path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘LaunchSequin.isra.0’ at e2docsum.c:2837:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 15 and 4110 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF asn2graphic.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2graphic.h:45, from ../include/asn2graphicp.h:45, from asn2graphic.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2graphic.c: In function ‘ParseBioseqAppearanceItem’: asn2graphic.c:779:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 779 | if (buf != NULL) { | ^~ asn2graphic.c:740:28: note: ‘buf’ declared here 740 | Char buf [128]; | ^~~ asn2graphic.c:789:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 789 | if (buf != NULL) { | ^~ asn2graphic.c:740:28: note: ‘buf’ declared here 740 | Char buf [128]; | ^~~ asn2graphic.c: In function ‘ParseFeatureAppearanceItem’: asn2graphic.c:894:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 894 | if (buf != NULL) { | ^~ asn2graphic.c:827:22: note: ‘buf’ declared here 827 | Char buf [128]; | ^~~ asn2graphic.c: In function ‘ParseFilterItem’: asn2graphic.c:1191:21: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 1191 | Int2 i, j; | ^ asn2graphic.c: In function ‘GeneProductsLayoutInternal’: asn2graphic.c:3730:36: warning: variable ‘featureStart’ set but not used [-Wunused-but-set-variable] 3730 | Int4 newLeft, featureStart, rowMaxRight; | ^~~~~~~~~~~~ asn2graphic.c: In function ‘ScaleSntDrawProc’: asn2graphic.c:4402:28: warning: variable ‘r’ set but not used [-Wunused-but-set-variable] 4402 | RecT r; | ^ asn2graphic.c: In function ‘GphSentProc’: asn2graphic.c:4997:16: warning: variable ‘scaleY’ set but not used [-Wunused-but-set-variable] 4997 | Int4 scaleY; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2graphic.c:46: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In function ‘BuildClippedRFIP’, inlined from ‘BuildRenderInputFromRFIP’ at asn2graphic.c:2659:15: asn2graphic.c:2487:17: warning: ‘lastClippedRight’ may be used uninitialized [-Wmaybe-uninitialized] 2487 | } else if (lastClippedRight && useThis) { | ^ asn2graphic.c: In function ‘BuildRenderInputFromRFIP’: asn2graphic.c:2421:28: note: ‘lastClippedRight’ was declared here 2421 | Boolean lastClippedLeft, lastClippedRight; | ^~~~~~~~~~~~~~~~ In file included from ../include/asn2graphic.h:46: asn2graphic.c: In function ‘ProcessRows’: ../include/picture.h:499:23: warning: ‘SegmentTreeTop’ may be used uninitialized [-Wmaybe-uninitialized] 499 | #define CreateSegment Nlm_CreateSegment asn2graphic.c:4277:27: note: ‘SegmentTreeTop’ was declared here 4277 | SegmenT SegmentTreeTop; | ^~~~~~~~~~~~~~ ../include/picture.h:499:23: warning: ‘SegmentTreeMid’ may be used uninitialized [-Wmaybe-uninitialized] 499 | #define CreateSegment Nlm_CreateSegment asn2graphic.c:4278:27: note: ‘SegmentTreeMid’ was declared here 4278 | SegmenT SegmentTreeMid; | ^~~~~~~~~~~~~~ asn2graphic.c:4362:13: warning: ‘SegmentTreeBot’ may be used uninitialized [-Wmaybe-uninitialized] 4362 | if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2graphic.c:4279:27: note: ‘SegmentTreeBot’ was declared here 4279 | SegmenT SegmentTreeBot; | ^~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1198:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size 120 [-Wformat-overflow=] 1198 | sprintf (sect, "filters.%s", filterItemName); | ^~ ...... 1500 | FIP = ParseFilterItem (buf, defaultRowPadding, defaultGroupPadding, defaultLayout, VCP); | ~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ParseFilterItem’ at asn2graphic.c:1198:3, inlined from ‘ParseFilter’ at asn2graphic.c:1500:13, inlined from ‘ParseConfigFile’ at asn2graphic.c:1695:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 136 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:946:21: warning: ‘.master’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 946 | sprintf (sect, "%s.master", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:946:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1006:29: warning: ‘.bioseq’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1006 | sprintf (outputBuffer, "%s.bioseq", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1006:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1008:29: warning: ‘.imp’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1008 | sprintf (outputBuffer, "%s.imp", appearanceNameInFile); | ^~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1008:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 132 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1011:31: warning: ‘.import’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1011 | sprintf (outputBuffer, "%s.import", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1011:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 129) into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:32: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 127 [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 134 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:32: warning: ‘%s’ directive writing between 5 and 7 bytes into a region of size between 0 and 127 [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 136 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF medview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/medview.h:48, from medview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medview.c: In function ‘PrintMedlineViewForm’: medview.c:588:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 588 | system (cmmd); | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bspview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from bspview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from bspview.c:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gbfview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from gbfview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gbfview.c: In function ‘RelModeFailText’: gbfview.c:1004:22: warning: variable ‘hasPubs’ set but not used [-Wunused-but-set-variable] 1004 | Boolean hasPubs; | ^~~~~~~ gbfview.c: In function ‘PopulateFlatFile’: gbfview.c:1292:22: warning: variable ‘doColors’ set but not used [-Wunused-but-set-variable] 1292 | Boolean doColors; | ^~~~~~~~ gbfview.c: In function ‘PopulateFasta’: gbfview.c:1717:33: warning: left-hand operand of comma expression has no effect [-Wunused-value] 1717 | if (ISA_na (bsp->mol)) {TRUE, | ^ gbfview.c:1649:20: warning: variable ‘group_segs’ set but not used [-Wunused-but-set-variable] 1649 | Uint1 group_segs; | ^~~~~~~~~~ gbfview.c: In function ‘PopulateAsnOrXML’: gbfview.c:1972:16: warning: variable ‘lookupFar’ set but not used [-Wunused-but-set-variable] 1972 | Boolean lookupFar = FALSE; | ^~~~~~~~~ gbfview.c:1971:16: warning: variable ‘lockFar’ set but not used [-Wunused-but-set-variable] 1971 | Boolean lockFar = FALSE; | ^~~~~~~ gbfview.c: In function ‘PrintFlatFileFastaOrAsn’: gbfview.c:2494:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2494 | system (cmmd); | ^~~~~~~~~~~~~ gbfview.c: In function ‘ReleaseIcon’: gbfview.c:667:21: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 667 | system (cmmd); | ^~~~~~~~~~~~~ gbfview.c: At top level: gbfview.c:1234:13: warning: ‘LookForFarProds’ defined but not used [-Wunused-function] 1234 | static void LookForFarProds ( | ^~~~~~~~~~~~~~~ gbfview.c:1215:13: warning: ‘LookForFarBsp’ defined but not used [-Wunused-function] 1215 | static void LookForFarBsp ( | ^~~~~~~~~~~~~ gbfview.c:944:13: warning: ‘LookForPubs’ defined but not used [-Wunused-function] 944 | static void LookForPubs (BioseqPtr bsp, Pointer userdata) | ^~~~~~~~~~~ gbfview.c:289:16: warning: ‘ColorIcon’ defined but not used [-Wunused-function] 289 | static Boolean ColorIcon ( | ^~~~~~~~~ gbfview.c: In function ‘ReleaseIcon’: gbfview.c:666:42: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 666 | sprintf (cmmd, "open %s", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ReleaseIcon’ at gbfview.c:666:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 4101 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gphview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from gphview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gphview.c: In function ‘ReleaseAlignment’: gphview.c:1306:18: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 1306 | SeqLocPtr slp; | ^~~ gphview.c: In function ‘DrawAlignOnAllSequences’: gphview.c:1391:17: warning: variable ‘vn’ set but not used [-Wunused-but-set-variable] 1391 | ValNode vn; | ^~ gphview.c: In function ‘ReleaseDesktop’: gphview.c:1836:18: warning: variable ‘seg’ set but not used [-Wunused-but-set-variable] 1836 | SegmenT seg; | ^~~ gphview.c: In function ‘AutoScrollGeneName’: gphview.c:2100:21: warning: variable ‘num’ set but not used [-Wunused-but-set-variable] 2100 | Int2 num; | ^~~ gphview.c: In function ‘DisplayGeneChoiceWindow’: gphview.c:2426:22: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 2426 | PrompT p; | ^ gphview.c: In function ‘PrintGraphical’: gphview.c:3268:14: warning: unused variable ‘ans’ [-Wunused-variable] 3268 | MsgAnswer ans; | ^~~ gphview.c: In function ‘PopulateAsn2GphGraphic’: gphview.c:3868:16: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 3868 | Int4 min; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gphdraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gphdraw.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gphdraw.c: In function ‘GraphSentProc’: gphdraw.c:195:18: warning: variable ‘scaleY’ set but not used [-Wunused-but-set-variable] 195 | Int4 scaleY; | ^~~~~~ gphdraw.c: In function ‘DrawGraphToPanel’: gphdraw.c:453:27: warning: variable ‘xp’ set but not used [-Wunused-but-set-variable] 453 | Int4Ptr xpoints, xp; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gxydraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gxydraw.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gxydraw.c: In function ‘DotXYPlot’: gxydraw.c:182:19: warning: ‘xaxiscount’ may be used uninitialized [-Wmaybe-uninitialized] 182 | Int4 xaxiscount, yaxiscount; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gtrdraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gtrdraw.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/vibrant.h:130: In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curB’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:23: note: ‘curB’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curG’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:17: note: ‘curG’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curR’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:11: note: ‘curR’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:685:20: warning: ‘f’ may be used uninitialized [-Wmaybe-uninitialized] 685 | #define DeleteFont Nlm_DeleteFont gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:82:11: note: ‘f’ was declared here 82 | FonT f, fx; | ^ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:673:20: warning: ‘fx’ may be used uninitialized [-Wmaybe-uninitialized] 673 | #define SelectFont Nlm_SelectFont gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:82:14: note: ‘fx’ was declared here 82 | FonT f, fx; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from seqpanel.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqpanel.c: In function ‘FillFeatureInfo’: seqpanel.c:427:18: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 427 | Int4 j, start, stop; | ^~~~ seqpanel.c:427:11: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 427 | Int4 j, start, stop; | ^~~~~ seqpanel.c: In function ‘DrawFeatureCodonLines’: seqpanel.c:1897:21: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 1897 | Char tmp[2]; | ^~~ seqpanel.c: In function ‘DrawFeature’: seqpanel.c:2127:21: warning: variable ‘prot_len’ set but not used [-Wunused-but-set-variable] 2127 | Int4 prot_len; | ^~~~~~~~ seqpanel.c: In function ‘GetSeqChapterFeatureInfo’: seqpanel.c:3136:18: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 3136 | Int4 j, start, stop; | ^~~~ seqpanel.c:3136:11: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 3136 | Int4 j, start, stop; | ^~~~~ seqpanel.c: In function ‘onSeqEdVScrollBarSeqPanel’: seqpanel.c:3406:17: warning: variable ‘totallines’ set but not used [-Wunused-but-set-variable] 3406 | Int4 totallines; | ^~~~~~~~~~ seqpanel.c: In function ‘PrintFeature’: seqpanel.c:3812:28: warning: variable ‘fRight’ set but not used [-Wunused-but-set-variable] 3812 | Int4 fLeft, fRight, swap; | ^~~~~~ seqpanel.c:3812:21: warning: variable ‘fLeft’ set but not used [-Wunused-but-set-variable] 3812 | Int4 fLeft, fRight, swap; | ^~~~~ seqpanel.c: In function ‘PrintTranslatedFrame’: seqpanel.c:3966:17: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 3966 | Char tmp[2]; | ^~~ seqpanel.c: In function ‘ExportSequenceText’: seqpanel.c:4372:44: warning: pointer targets in passing argument 1 of ‘complement_string’ differ in signedness [-Wpointer-sign] 4372 | complement_string (file_line + SEQ_ED_PRINT_SEQ_OFFSET); | ^ | | | Nlm_Uint1Ptr {aka unsigned char *} In file included from ../include/alignmgr2.h:112, from seqpanel.c:39: ../include/salutil.h:78:47: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘Nlm_Uint1Ptr’ {aka ‘unsigned char *’} 78 | NLM_EXTERN CharPtr complement_string (CharPtr str); seqpanel.c:4236:17: warning: variable ‘curr_para_strings’ set but not used [-Wunused-but-set-variable] 4236 | ValNodePtr curr_para_strings = NULL; | ^~~~~~~~~~~~~~~~~ seqpanel.c:4229:17: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 4229 | Uint1Ptr buf; | ^~~ seqpanel.c: In function ‘SeqEdOnClick’: seqpanel.c:4946:21: warning: variable ‘direction’ set but not used [-Wunused-but-set-variable] 4946 | Int4 direction; | ^~~~~~~~~ seqpanel.c: In function ‘SeqAlnOnDrag’: seqpanel.c:5685:34: warning: variable ‘is_ctrl’ set but not used [-Wunused-but-set-variable] 5685 | Boolean is_double_click, is_ctrl; | ^~~~~~~ seqpanel.c:5685:17: warning: variable ‘is_double_click’ set but not used [-Wunused-but-set-variable] 5685 | Boolean is_double_click, is_ctrl; | ^~~~~~~~~~~~~~~ seqpanel.c: In function ‘ResizeSeqEdView’: seqpanel.c:5760:8: warning: variable ‘sequence_pos’ set but not used [-Wunused-but-set-variable] 5760 | Int4 sequence_pos = 0; | ^~~~~~~~~~~~ seqpanel.c:5755:8: warning: variable ‘height’ set but not used [-Wunused-but-set-variable] 5755 | Int4 height, width; | ^~~~~~ seqpanel.c: In function ‘WriteAlignmentInterleaveToFileEx’: seqpanel.c:8665:22: warning: passing argument 1 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8665 | fputs (fp, printed_line); | ^~ | | | FILE * In file included from ../include/ncbilcl.h:154: /usr/include/stdio.h:717:42: note: expected ‘const char * restrict’ but argument is of type ‘FILE *’ 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~~~~~~~^~~ seqpanel.c:8665:26: warning: passing argument 2 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8665 | fputs (fp, printed_line); | ^~~~~~~~~~~~ | | | Nlm_CharPtr {aka char *} /usr/include/stdio.h:717:64: note: expected ‘FILE * restrict’ but argument is of type ‘Nlm_CharPtr’ {aka ‘char *’} 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~^~~~~~~~ seqpanel.c: In function ‘WriteAlignmentContiguousToFile’: seqpanel.c:8761:20: warning: passing argument 1 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8761 | fputs (fp, printed_line); | ^~ | | | FILE * /usr/include/stdio.h:717:42: note: expected ‘const char * restrict’ but argument is of type ‘FILE *’ 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~~~~~~~^~~ seqpanel.c:8761:24: warning: passing argument 2 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8761 | fputs (fp, printed_line); | ^~~~~~~~~~~~ | | | Nlm_CharPtr {aka char *} /usr/include/stdio.h:717:64: note: expected ‘FILE * restrict’ but argument is of type ‘Nlm_CharPtr’ {aka ‘char *’} 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~^~~~~~~~ seqpanel.c: In function ‘ReverseSequenceStrandsInAlignment’: seqpanel.c:9008:17: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 9008 | SeqEntryPtr sep; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ seqpanel.c:1171:16: warning: ‘GetAlignmentColumnPercentIDsForAlignmentSection’ defined but not used [-Wunused-function] 1171 | static double *GetAlignmentColumnPercentIDsForAlignmentSection (BioseqViewPtr bvp, Int4 line, Int4 aln_idx) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: seqpanel.c: In function ‘SeqEdFindPatternDialog’: ../include/vibdefns.h:535:22: warning: ‘g1’ may be used uninitialized [-Wmaybe-uninitialized] 535 | #define AlignObjects Nlm_AlignObjects seqpanel.c:7632:25: note: ‘g1’ was declared here 7632 | GrouP h, g1, g2; | ^~ In file included from ../include/ncbi.h:62: In function ‘PrintPlusProtein’, inlined from ‘PrintFeature’ at seqpanel.c:3923:9: ../include/ncbistr.h:331:25: warning: ‘str_prot’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen seqpanel.c: In function ‘PrintFeature’: seqpanel.c:3810:21: note: ‘str_prot’ was declared here 3810 | CharPtr str_prot; | ^~~~~~~~ seqpanel.c: In function ‘SeqEdOnClick’: seqpanel.c:5026:10: warning: ‘is_left_end’ may be used uninitialized [-Wmaybe-uninitialized] 5026 | if (is_left_end) | ^ seqpanel.c:4952:21: note: ‘is_left_end’ was declared here 4952 | Boolean is_left_end, is_right_end; | ^~~~~~~~~~~ seqpanel.c:5030:15: warning: ‘is_right_end’ may be used uninitialized [-Wmaybe-uninitialized] 5030 | else if (is_right_end) | ^ seqpanel.c:4952:34: note: ‘is_right_end’ was declared here 4952 | Boolean is_left_end, is_right_end; | ^~~~~~~~~~~~ In function ‘ExportSequenceText’, inlined from ‘SeqEdExportProc’ at seqpanel.c:6972:7: seqpanel.c:4353:13: warning: ‘seq_pos’ may be used uninitialized [-Wmaybe-uninitialized] 4353 | SeqEdPrintTextLineToFile ((CharPtr)file_line, from, to, seq_pos, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘SeqEdExportProc’: seqpanel.c:4233:17: note: ‘seq_pos’ was declared here 4233 | Int4 seq_pos; | ^~~~~~~ In function ‘DrawAlignment’, inlined from ‘DrawSeqPanel’ at seqpanel.c:2551:11, inlined from ‘onDrawSeqPanel’ at seqpanel.c:2624:3: seqpanel.c:1252:3: warning: ‘seqbuf’ may be used uninitialized [-Wmaybe-uninitialized] 1252 | AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 | bvp->showAlnSubstitutions); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘onDrawSeqPanel’: seqpanel.c:2466:25: note: ‘seqbuf’ was declared here 2466 | Uint1Ptr buf, seqbuf, alnbuf; | ^~~~~~ In function ‘DrawAlignment’, inlined from ‘DrawSeqPanel’ at seqpanel.c:2551:11, inlined from ‘onDrawSeqPanel’ at seqpanel.c:2624:3: seqpanel.c:1252:3: warning: ‘alnbuf’ may be used uninitialized [-Wmaybe-uninitialized] 1252 | AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 | bvp->showAlnSubstitutions); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘onDrawSeqPanel’: seqpanel.c:2466:33: note: ‘alnbuf’ was declared here 2466 | Uint1Ptr buf, seqbuf, alnbuf; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ingengraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from ../include/ingengraph.h:52, from ingengraph.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingengraph.c: In function ‘Ing_BigEncodeIdxFeat’: ingengraph.c:262:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 262 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ ingengraph.c: In function ‘Ing_AddOneAlignToOverviewPage’: ingengraph.c:355:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 355 | else | ^~~~ ingengraph.c:357:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 357 | prim = AddRectangle(seg, start, (row)*(-20), stop, (row)*(-20)+j, NO_ARROW, FALSE,0); | ^~~~ ingengraph.c:347:13: warning: unused variable ‘bsp’ [-Wunused-variable] 347 | BioseqPtr bsp=NULL; | ^~~ ingengraph.c: In function ‘Ing_AddAlignsToOverviewPage’: ingengraph.c:372:18: warning: unused variable ‘buf’ [-Wunused-variable] 372 | Char buf[41]={""}; | ^~~ ingengraph.c:367:18: warning: variable ‘NewLine’ set but not used [-Wunused-but-set-variable] 367 | Boolean NewLine=FALSE; | ^~~~~~~ ingengraph.c: In function ‘Ing_DrawOverviewPage’: ingengraph.c:492:14: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 492 | Int4 offset; | ^~~~~~ In file included from ../include/vibrant.h:130, from ../include/ingengraph.h:54: ../include/vibdefns.h:468:17: warning: unused variable ‘Nlm_Visible’ [-Wunused-variable] 468 | #define Visible Nlm_Visible | ^~~~~~~~~~~ ingengraph.c:488:14: note: in expansion of macro ‘Visible’ 488 | Boolean Visible=FALSE; | ^~~~~~~ ingengraph.c: In function ‘Ing_PopOverviewPage’: ingengraph.c:715:16: warning: variable ‘margin’ set but not used [-Wunused-but-set-variable] 715 | Int4 margin, len; | ^~~~~~ ingengraph.c:714:16: warning: unused variable ‘buf’ [-Wunused-variable] 714 | Char buf[50]={""}; | ^~~ ingengraph.c:708:16: warning: unused variable ‘sanp’ [-Wunused-variable] 708 | SeqAnnotPtr sanp=NULL; | ^~~~ ingengraph.c: In function ‘Ing_AddAlignsToDetailedPage’: ingengraph.c:1097:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1097 | if ((start - offset - (label_len - feat_len)/2)<0) | ^~ ingengraph.c:1099:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1099 | if (bOver_the_edge) | ^~ ingengraph.c: In function ‘Ing_PopDetailedPage’: ingengraph.c:1437:16: warning: variable ‘CurrentSeg’ set but not used [-Wunused-but-set-variable] 1437 | SegmenT CurrentSeg=NULL; | ^~~~~~~~~~ ingengraph.c: In function ‘Ing_ExploreSegments’: ingengraph.c:1829:22: warning: unused variable ‘isDraft’ [-Wunused-variable] 1829 | Boolean isDraft = FALSE; | ^~~~~~~ ingengraph.c:1827:22: warning: unused variable ‘vnp’ [-Wunused-variable] 1827 | ValNodePtr vnp = NULL; | ^~~ ingengraph.c:1826:22: warning: unused variable ‘gbp’ [-Wunused-variable] 1826 | GBBlockPtr gbp = NULL; | ^~~ ingengraph.c:1824:33: warning: variable ‘black’ set but not used [-Wunused-but-set-variable] 1824 | Uint1 orange[3], black[3]; | ^~~~~ ingengraph.c:1823:33: warning: variable ‘lime’ set but not used [-Wunused-but-set-variable] 1823 | Uint1 indigo[3], lime[3]; | ^~~~ ingengraph.c:1823:22: warning: variable ‘indigo’ set but not used [-Wunused-but-set-variable] 1823 | Uint1 indigo[3], lime[3]; | ^~~~~~ ingengraph.c: In function ‘Ing_AddGCRect’: ingengraph.c:1933:17: warning: variable ‘comp2’ set but not used [-Wunused-but-set-variable] 1933 | FloatHi comp2, comp_prev; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/ingengraph.h:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ ingengraph.c:71:13: warning: ‘Ing_GetNamesZoomedVal’ declared ‘static’ but never defined [-Wunused-function] 71 | static void Ing_GetNamesZoomedVal(VieweR vNames,Int4Ptr from, Int4Ptr to, | ^~~~~~~~~~~~~~~~~~~~~ ingengraph.c:602:28: warning: ‘Ing_CollectFeatures1’ defined but not used [-Wunused-function] 602 | static Boolean LIBCALLBACK Ing_CollectFeatures1(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) | ^~~~~~~~~~~~~~~~~~~~ ingengraph.c:583:24: warning: ‘Ing_SortByChoice’ defined but not used [-Wunused-function] 583 | static int LIBCALLBACK Ing_SortByChoice (VoidPtr ptr1, VoidPtr ptr2) | ^~~~~~~~~~~~~~~~ ingengraph.c: In function ‘Ing_BigEncodeIdxFeat’: ingengraph.c:262:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 262 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ ingengraph.c:257:7: note: ‘index_g’ declared here 257 | Uint4 index_g[2]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ingenext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2ff.h:113, from ../include/ingenwin.h:58, from ../include/ingenext.h:53, from ingenext.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingenext.c: In function ‘Ing_KeepTheBestAlignments’: ingenext.c:167:20: warning: variable ‘amaip’ set but not used [-Wunused-but-set-variable] 167 | AMAlignIndex2Ptr amaip = NULL; | ^~~~~ ingenext.c: In function ‘Ing_HandleQBlastResults’: ingenext.c:272:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 272 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){ | ^~~~~~~ ingenext.c: In function ‘Ing_HandleResults’: ingenext.c:535:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 535 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){ | ^~~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:739:18: warning: unused variable ‘paramlist’ [-Wunused-variable] 739 | ValNodePtr paramlist = NULL; | ^~~~~~~~~ ingenext.c: In function ‘Ing_tRNAscanProc’: ingenext.c:915:22: warning: unused variable ‘moveMe’ [-Wunused-variable] 915 | ValNodePtr moveMe = NULL; | ^~~~~~ ingenext.c:906:22: warning: unused variable ‘first’ [-Wunused-variable] 906 | TexT first = NULL; | ^~~~~ ingenext.c:902:22: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 902 | ButtoN b; | ^ ingenext.c:896:17: warning: unused variable ‘args’ [-Wunused-variable] 896 | CharPtr args = NULL; | ^~~~ ingenext.c: In function ‘Ing_ReadtRNAConfigFile’: ingenext.c:1125:15: warning: variable ‘demomode’ set but not used [-Wunused-but-set-variable] 1125 | Boolean demomode = FALSE; | ^~~~~~~~ ingenext.c: In function ‘Ing_DoBlast2Seqs’: ingenext.c:1369:12: warning: the comparison will always evaluate as ‘true’ for the address of ‘eval’ will never be NULL [-Waddress] 1369 | if (eval != NULL) | ^~ ingenext.c:1313:23: note: ‘eval’ declared here 1313 | Char eval[8]; | ^~~~ ingenext.c:1376:12: warning: the comparison will always evaluate as ‘true’ for the address of ‘eval’ will never be NULL [-Waddress] 1376 | if (eval != NULL) | ^~ ingenext.c:1313:23: note: ‘eval’ declared here 1313 | Char eval[8]; | ^~~~ ingenext.c:1312:23: warning: variable ‘is_local’ set but not used [-Wunused-but-set-variable] 1312 | Boolean is_local, first_bsp=TRUE; | ^~~~~~~~ ingenext.c: In function ‘Ing_CreateDotMatrixForm’: ingenext.c:1834:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1834 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) | ^~~~~~~ ingenext.c: In function ‘Ing_RunSpidey’: ingenext.c:1994:20: warning: unused variable ‘sanp’ [-Wunused-variable] 1994 | SeqAnnotPtr sanp = NULL; | ^~~~ ingenext.c:1993:20: warning: unused variable ‘spidp_next’ [-Wunused-variable] 1993 | SPI_mRNAPtr spidp_next = NULL; | ^~~~~~~~~~ ingenext.c:1992:20: warning: unused variable ‘spidp_head’ [-Wunused-variable] 1992 | SPI_mRNAPtr spidp_head = NULL; | ^~~~~~~~~~ ingenext.c: In function ‘Ing_ReadmRNAs_ext’: ingenext.c:2025:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) | ^~~~~~~ ingenext.c: In function ‘Ing_DeleteInsertInGenomic’: ingenext.c:2522:16: warning: unused variable ‘newsegs’ [-Wunused-variable] 2522 | Int2 newsegs = 0, offset = 0; | ^~~~~~~ ingenext.c: In function ‘Ing_ReplaceAllMismatchedInLocation’: ingenext.c:2777:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2777 | if (!All) | ^~ ingenext.c:2781:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2781 | SeqLocReplace(msip, mmis, mmis, mstrand, gsip, gmis, gmis, gstrand); | ^~~~~~~~~~~~~ ingenext.c:2615:21: warning: unused variable ‘str’ [-Wunused-variable] 2615 | Char str[200] = {""}; | ^~~ ingenext.c:2612:22: warning: unused variable ‘amaip’ [-Wunused-variable] 2612 | AMAlignIndex2Ptr amaip = NULL; | ^~~~~ ingenext.c: In function ‘Ing_MismatchProc’: ingenext.c:3025:15: warning: unused variable ‘sip’ [-Wunused-variable] 3025 | SeqIdPtr sip = NULL; | ^~~ ingenext.c: In function ‘Ing_PrintSpideyReport’: ingenext.c:3471:27: warning: variable ‘gmis’ set but not used [-Wunused-but-set-variable] 3471 | Int4 mmis, gmis, miscount = 0; | ^~~~ ingenext.c: In function ‘Ing_PrintBlastReport’: ingenext.c:3853:18: warning: unused variable ‘more’ [-Wunused-variable] 3853 | Boolean more = FALSE; | ^~~~ In file included from ../include/vibrant.h:130, from ../include/dlogutil.h:48, from ../include/import.h:48, from ../include/ingenwin.h:64: ../include/vibdefns.h:652:16: warning: variable ‘Nlm_DkGray’ set but not used [-Wunused-but-set-variable] 652 | #define DkGray Nlm_DkGray | ^~~~~~~~~~ ingenext.c:3850:18: note: in expansion of macro ‘DkGray’ 3850 | Uint1 DkGray[3]; | ^~~~~~ ingenext.c: In function ‘Ing_PopulateReport’: ingenext.c:4328:20: warning: unused variable ‘sip’ [-Wunused-variable] 4328 | SeqIdPtr sip=NULL; | ^~~ ingenext.c:4324:20: warning: unused variable ‘temp’ [-Wunused-variable] 4324 | CharPtr temp = NULL; | ^~~~ ingenext.c: In function ‘Ing_ResizeReportWindow’: ingenext.c:4484:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 4484 | BaR hsb; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/ingenwin.h:60: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ingenwin.h:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:135, from ../include/ingenwin.h:62: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ingenext.c:130:13: warning: ‘querytimercount’ defined but not used [-Wunused-variable] 130 | static Int4 querytimercount = 0; | ^~~~~~~~~~~~~~~ ingenext.c:129:13: warning: ‘querytimerlimit’ defined but not used [-Wunused-variable] 129 | static Int4 querytimerlimit = 100; | ^~~~~~~~~~~~~~~ ingenext.c:59:28: warning: ‘Ing_BlastCallback’ defined but not used [-Wunused-function] 59 | static Boolean LIBCALLBACK Ing_BlastCallback (BlastResponse *brp, | ^~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ ingenext.c: In function ‘Ing_SpideyCallback’: ingenext.c:2097:54: warning: ‘%%’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 2097 | sprintf(igvp->progress_counter, "Completed %d%%", progress->percentdone); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Ing_SpideyCallback’ at ingenext.c:2097:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 22 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_DoBlast2Seqs’: ingenext.c:1457:17: warning: ‘e_head’ may be used uninitialized [-Wmaybe-uninitialized] 1457 | e_tmp->next=e_head; | ~~~~~~~~~~~^~~~~~~ ingenext.c:1317:39: note: ‘e_head’ was declared here 1317 | IngEntityPtr e_list, e_next, e_head, e_tmp; | ^~~~~~ ingenext.c: In function ‘Ing_MismatchProc’: ingenext.c:3181:7: warning: ‘mstart’ may be used uninitialized [-Wmaybe-uninitialized] 3181 | SeqPortSeek(spp_mrna, mstart-start, SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenext.c:3020:15: note: ‘mstart’ was declared here 3020 | Int4 mstart, gstart; | ^~~~~~ ingenext.c:3170:32: warning: ‘gstart’ may be used uninitialized [-Wmaybe-uninitialized] 3170 | gstart = start + (stop - gstart); | ~~~~~~^~~~~~~~~ ingenext.c:3020:23: note: ‘gstart’ was declared here 3020 | Int4 mstart, gstart; | ^~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:780:32: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 780 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘Ing_AccepttRNAargsProc’ at ingenext.c:780:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:794:30: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 794 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘Ing_AccepttRNAargsProc’ at ingenext.c:794:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_ReplaceAllMismatchedInLocation’: ingenext.c:2648:8: warning: ‘nmismatches’ may be used uninitialized [-Wmaybe-uninitialized] 2648 | if (nmismatches > 0){ | ^ ingenext.c:2617:33: note: ‘nmismatches’ was declared here 2617 | Int4 gmis, mmis, nmismatches, nkeep = 0; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ingenwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2ff.h:113, from ../include/ingenwin.h:58, from ingenwin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingenwin.c: In function ‘Ing_PopulateDetailedPage’: ingenwin.c:134:22: warning: unused variable ‘bSelected’ [-Wunused-variable] 134 | Boolean bSelected = FALSE; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_DoRange’: ingenwin.c:394:22: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 394 | BioseqPtr bsp; | ^~~ ingenwin.c: In function ‘Ing_PopulateCpG’: ingenwin.c:576:19: warning: variable ‘nchars’ set but not used [-Wunused-but-set-variable] 576 | Int2 cxChar, nchars; | ^~~~~~ ingenwin.c: In function ‘Ing_ResizeCpGWindow’: ingenwin.c:642:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 642 | BaR hsb; | ^~~ ingenwin.c: In function ‘Ing_PopulateMotif’: ingenwin.c:718:26: warning: variable ‘nchars’ set but not used [-Wunused-but-set-variable] 718 | Int2 cxChar, nchars; | ^~~~~~ ingenwin.c:717:24: warning: variable ‘swidth’ set but not used [-Wunused-but-set-variable] 717 | Int4 slen, swidth; | ^~~~~~ ingenwin.c:717:18: warning: variable ‘slen’ set but not used [-Wunused-but-set-variable] 717 | Int4 slen, swidth; | ^~~~ ingenwin.c: In function ‘Ing_ResizeMotifWindow’: ingenwin.c:785:12: warning: unused variable ‘name’ [-Wunused-variable] 785 | CharPtr name = NULL; | ^~~~ ingenwin.c:783:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 783 | BaR hsb; | ^~~ ingenwin.c: In function ‘Ing_ShowComplexity’: ingenwin.c:1270:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1270 | while ((Boolean)(slp_feat=SeqLocFindNext(slp_dust,slp_feat))){ | ^ ingenwin.c: In function ‘Ing_CreateNewFeature’: ingenwin.c:1301:22: warning: unused variable ‘rnatype’ [-Wunused-variable] 1301 | Uint1 rnatype=0; | ^~~~~~~ ingenwin.c: In function ‘Ing_GetAlignmentIntervals’: ingenwin.c:1418:20: warning: unused variable ‘master’ [-Wunused-variable] 1418 | SeqIdPtr master = NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_OldGetAlignmentIntervals’: ingenwin.c:1494:20: warning: unused variable ‘master’ [-Wunused-variable] 1494 | SeqIdPtr master = NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_OldMakeLocListFromSAP’: ingenwin.c:1613:26: warning: unused variable ‘slp2’ [-Wunused-variable] 1613 | SeqLocPtr slp1 = NULL, slp2 = NULL; | ^~~~ ingenwin.c:1613:13: warning: unused variable ‘slp1’ [-Wunused-variable] 1613 | SeqLocPtr slp1 = NULL, slp2 = NULL; | ^~~~ ingenwin.c: In function ‘Ing_OM_MsgFunc’: ingenwin.c:2380:15: warning: the address of ‘sfc’ will always evaluate as ‘true’ [-Waddress] 2380 | if (&sfc) | ^ ingenwin.c:2284:22: warning: unused variable ‘segID’ [-Wunused-variable] 2284 | Uint2 segID=0; | ^~~~~ ingenwin.c:2280:22: warning: unused variable ‘sep’ [-Wunused-variable] 2280 | SeqEntryPtr sep=NULL; | ^~~ ingenwin.c:2271:31: warning: unused variable ‘number’ [-Wunused-variable] 2271 | Int4 score=0, number=0; | ^~~~~~ ingenwin.c:2271:22: warning: unused variable ‘score’ [-Wunused-variable] 2271 | Int4 score=0, number=0; | ^~~~~ ingenwin.c:2270:34: warning: unused variable ‘n’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^ ingenwin.c:2270:28: warning: unused variable ‘s2’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^~ ingenwin.c:2270:22: warning: unused variable ‘s1’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^~ ingenwin.c: In function ‘Ing_MoveCursor’: ingenwin.c:2631:9: warning: variable ‘grayClr2’ set but not used [-Wunused-but-set-variable] 2631 | Uint1 grayClr2[3]; | ^~~~~~~~ ingenwin.c: In function ‘Ing_FeatViewerClickProc’: ingenwin.c:2814:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2814 | if (subSeg=FindSegPrim(v, pt, NULL, NULL, &prim)){ | ^~~~~~ ingenwin.c:2804:14: warning: unused variable ‘slp’ [-Wunused-variable] 2804 | SeqLocPtr slp=NULL; | ^~~ ingenwin.c: In function ‘Ing_SequenceClickProc’: ingenwin.c:2908:22: warning: variable ‘ssp’ set but not used [-Wunused-but-set-variable] 2908 | SelStructPtr ssp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInBlastAsn’: ingenwin.c:3077:19: warning: unused variable ‘Report’ [-Wunused-variable] 3077 | IngReportPtr Report=NULL; | ^~~~~~ ingenwin.c:3075:19: warning: unused variable ‘sip’ [-Wunused-variable] 3075 | SeqIdPtr sip=NULL; | ^~~ ingenwin.c:3074:19: warning: unused variable ‘salp’ [-Wunused-variable] 3074 | SeqAlignPtr salp=NULL; | ^~~~ ingenwin.c:3073:19: warning: unused variable ‘n_sap’ [-Wunused-variable] 3073 | SeqAlignPtr n_sap=NULL; | ^~~~~ ingenwin.c: In function ‘Ing_ParseSeqIdFile’: ingenwin.c:3142:20: warning: unused variable ‘bsp’ [-Wunused-variable] 3142 | BioseqPtr bsp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInFeatureTable’: ingenwin.c:3194:20: warning: variable ‘sanp’ set but not used [-Wunused-but-set-variable] 3194 | SeqAnnotPtr sanp; | ^~~~ ingenwin.c: In function ‘Ing_AssembleGenscanInfo’: ingenwin.c:3258:17: warning: unused variable ‘slp’ [-Wunused-variable] 3258 | SeqLocPtr slp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInGenscan’: ingenwin.c:3300:33: warning: unused variable ‘str’ [-Wunused-variable] 3300 | CharPtr letter=NULL, str=NULL; | ^~~ ingenwin.c:3300:20: warning: unused variable ‘letter’ [-Wunused-variable] 3300 | CharPtr letter=NULL, str=NULL; | ^~~~~~ ingenwin.c:3298:33: warning: unused variable ‘first_pass’ [-Wunused-variable] 3298 | Boolean found=FALSE, first_pass=FALSE; | ^~~~~~~~~~ ingenwin.c: In function ‘Ing_AssembleTabDelimited’: ingenwin.c:3519:17: warning: variable ‘score’ set but not used [-Wunused-but-set-variable] 3519 | Int4 score; | ^~~~~ ingenwin.c:3516:17: warning: unused variable ‘tmp’ [-Wunused-variable] 3516 | CharPtr tmp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInTabDelimited’: ingenwin.c:3659:40: warning: variable ‘label_str’ set but not used [-Wunused-but-set-variable] 3659 | CharPtr tmp=NULL, str=NULL, label_str=NULL; | ^~~~~~~~~ ingenwin.c:3659:20: warning: unused variable ‘tmp’ [-Wunused-variable] 3659 | CharPtr tmp=NULL, str=NULL, label_str=NULL; | ^~~ ingenwin.c:3653:20: warning: unused variable ‘lip_tmp’ [-Wunused-variable] 3653 | IngInfoPtr lip_tmp=NULL; | ^~~~~~~ ingenwin.c:3650:20: warning: unused variable ‘letter’ [-Wunused-variable] 3650 | CharPtr letter=NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_FileOpenSpecial’: ingenwin.c:3984:16: warning: unused variable ‘Report’ [-Wunused-variable] 3984 | IngReportPtr Report=NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_FileOpenMain’: ingenwin.c:4078:21: warning: unused variable ‘sep_orig’ [-Wunused-variable] 4078 | SeqEntryPtr sep_orig=NULL, sep=NULL; | ^~~~~~~~ ingenwin.c: In function ‘Ing_ResizeMainWindow’: ingenwin.c:4187:25: warning: variable ‘InfoHeight’ set but not used [-Wunused-but-set-variable] 4187 | Int2 RulerHeight, InfoHeight; | ^~~~~~~~~~ ingenwin.c: In function ‘Ing_OpenFromFileORNetwork’: ingenwin.c:4491:25: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 4491 | ButtoN b,b2; | ^~ ingenwin.c: In function ‘Ing_EditFeature’: ingenwin.c:4640:22: warning: variable ‘igvp’ set but not used [-Wunused-but-set-variable] 4640 | IngGenomeViewerPtr igvp=NULL; | ^~~~ ingenwin.c: In function ‘Ing_MarkSeqAnnot’: ingenwin.c:4713:16: warning: unused variable ‘bNoParent’ [-Wunused-variable] 4713 | Boolean bNoParent = FALSE; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_PropagateClickProc’: ingenwin.c:5064:22: warning: unused variable ‘primID’ [-Wunused-variable] 5064 | Uint2 primID=0; | ^~~~~~ ingenwin.c:5063:22: warning: unused variable ‘itemtype’ [-Wunused-variable] 5063 | Uint2 itemtype=0; | ^~~~~~~~ ingenwin.c:5062:22: warning: unused variable ‘itemID’ [-Wunused-variable] 5062 | Uint4 itemID=0; | ^~~~~~ ingenwin.c:5061:22: warning: unused variable ‘entityID’ [-Wunused-variable] 5061 | Uint2 entityID=0; | ^~~~~~~~ ingenwin.c:5060:22: warning: unused variable ‘ssp’ [-Wunused-variable] 5060 | SelStructPtr ssp=NULL; | ^~~ ingenwin.c:5059:22: warning: unused variable ‘igvp’ [-Wunused-variable] 5059 | IngGenomeViewerPtr igvp=NULL; | ^~~~ ingenwin.c: In function ‘Ing_PrintCompProteins’: ingenwin.c:5146:32: warning: unused variable ‘str2’ [-Wunused-variable] 5146 | Char str1[200] = {""}, str2[10] = {""}; | ^~~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5282:14: warning: variable ‘ARROW’ set but not used [-Wunused-but-set-variable] 5282 | Uint1 ARROW=NO_ARROW; | ^~~~~ ingenwin.c:5279:14: warning: unused variable ‘stringwidth’ [-Wunused-variable] 5279 | Int4 stringwidth = 0; | ^~~~~~~~~~~ ingenwin.c:5277:14: warning: unused variable ‘left’ [-Wunused-variable] 5277 | Int4 left = 10; | ^~~~ ingenwin.c:5276:14: warning: variable ‘prim’ set but not used [-Wunused-but-set-variable] 5276 | PrimitivE prim; | ^~~~ ingenwin.c: In function ‘Ing_DoPropagate’: ingenwin.c:5596:14: warning: unused variable ‘strErr’ [-Wunused-variable] 5596 | Char strErr[50]={""}; | ^~~~~~ ingenwin.c: In function ‘Ing_GetFromNetwork’: ingenwin.c:7518:11: warning: unused variable ‘szAppName’ [-Wunused-variable] 7518 | Char szAppName [10]={"Ingenue"}; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_SetupMainWindow’: ingenwin.c:7761:16: warning: unused variable ‘szAppName’ [-Wunused-variable] 7761 | Char szAppName [10]={"Ingenue"}; | ^~~~~~~~~ ingenwin.c:7760:48: warning: unused variable ‘str2’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~ ingenwin.c:7760:33: warning: unused variable ‘str1’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~ ingenwin.c:7760:16: warning: unused variable ‘title’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/ingenwin.h:60: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ingenwin.h:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:135, from ../include/ingenwin.h:62: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ingenwin.c:7552:13: warning: ‘Ing_ItemtoNetwork’ defined but not used [-Wunused-function] 7552 | static void Ing_ItemtoNetwork(IteM i){ | ^~~~~~~~~~~~~~~~~ ingenwin.c:6717:13: warning: ‘Ing_BspListProc’ defined but not used [-Wunused-function] 6717 | static void Ing_BspListProc(IteM i) | ^~~~~~~~~~~~~~~ ingenwin.c:5535:16: warning: ‘Ing_KeywordAlreadyInList’ defined but not used [-Wunused-function] 5535 | static Boolean Ing_KeywordAlreadyInList (ValNodePtr head, CharPtr kwd) | ^~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:1869:16: warning: ‘Ing_DeSelectPrim’ defined but not used [-Wunused-function] 1869 | static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) | ^~~~~~~~~~~~~~~~ ingenwin.c:1610:18: warning: ‘Ing_OldMakeLocListFromSAP’ defined but not used [-Wunused-function] 1610 | static SeqLocPtr Ing_OldMakeLocListFromSAP(SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:1487:23: warning: ‘Ing_OldGetAlignmentIntervals’ defined but not used [-Wunused-function] 1487 | static IngIvalInfoPtr Ing_OldGetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ ingenwin.c: In function ‘Ing_ReplaceMismatchedProc’: ingenwin.c:4902:3: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 4902 | Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:4882:23: note: ‘start’ was declared here 4882 | Int4 start, stop; | ^~~~~ ingenwin.c:4902:3: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 4902 | Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:4882:30: note: ‘stop’ was declared here 4882 | Int4 start, stop; | ^~~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5353:17: warning: ‘%s’ directive writing up to 299 bytes into a region of size 255 [-Wformat-overflow=] 5353 | sprintf(str, "%s", pfp->name); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Ing_PropagateReport’ at ingenwin.c:5353:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 1 and 300 bytes into a destination of size 255 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘Ing_PrintCompProteins’, inlined from ‘Ing_PropagateReport’ at ingenwin.c:5365:5: ingenwin.c:5224:12: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 5224 | last_pos = j; | ~~~~~~~~~^~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5137:17: note: ‘j’ was declared here 5137 | Int4 i, j, k, row; | ^ ingenwin.c: In function ‘Ing_DoPropagate’: ingenwin.c:5625:26: warning: ‘ already exists. Do you stil...’ directive writing 51 bytes into a region of size between 1 and 300 [-Wformat-overflow=] 5625 | sprintf (str_buf, "%s already exists. Do you still want to propagate it?", pfp->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘Ing_DoPropagate’ at ingenwin.c:5625:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 52 and 351 bytes into a destination of size 300 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘Ing_AssembleGenscanInfo’, inlined from ‘Ing_ReadInGenscan’ at ingenwin.c:3345:12, inlined from ‘Ing_FileOpenSpecial’ at ingenwin.c:4021:9: ingenwin.c:3290:13: warning: ‘strand’ may be used uninitialized [-Wmaybe-uninitialized] 3290 | slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c: In function ‘Ing_FileOpenSpecial’: ingenwin.c:3255:17: note: ‘strand’ was declared here 3255 | Uint1 strand; | ^~~~~~ In file included from ../include/vibrant.h:130, from ../include/dlogutil.h:48, from ../include/import.h:48, from ../include/ingenwin.h:64: ingenwin.c: In function ‘Ing_KozakProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:1006:22: note: ‘ReportW’ was declared here 1006 | WindoW ReportW; | ^~~~~~~ ingenwin.c:1048:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | if (ans == ANS_NO) | ^ ingenwin.c:1010:22: note: ‘ans’ was declared here 1010 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_SignalPeptideProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:1057:22: note: ‘ReportW’ was declared here 1057 | WindoW ReportW; | ^~~~~~~ ingenwin.c:1099:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 1099 | if (ans == ANS_NO) | ^ ingenwin.c:1061:22: note: ‘ans’ was declared here 1061 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_RepeatsProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:955:22: note: ‘ReportW’ was declared here 955 | WindoW ReportW; | ^~~~~~~ ingenwin.c:997:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 997 | if (ans == ANS_NO) | ^ ingenwin.c:959:22: note: ‘ans’ was declared here 959 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_PolyAProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:904:22: note: ‘ReportW’ was declared here 904 | WindoW ReportW; | ^~~~~~~ ingenwin.c:946:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 946 | if (ans == ANS_NO) | ^ ingenwin.c:908:22: note: ‘ans’ was declared here 908 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_CpGProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:857:22: note: ‘ReportW’ was declared here 857 | WindoW ReportW; | ^~~~~~~ ingenwin.c:895:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 895 | if (ans == ANS_NO) | ^ ingenwin.c:860:22: note: ‘ans’ was declared here 860 | MsgAnswer ans; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF macrodlg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from macrodlg.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ macrodlg.c: In function ‘ExistingTextDialog’: macrodlg.c:1959:22: warning: variable ‘ppt’ set but not used [-Wunused-but-set-variable] 1959 | PrompT ppt; | ^~~ macrodlg.c: In function ‘EndDistanceToDialog’: macrodlg.c:3076:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3076 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:3082:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3082 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:3088:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3088 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘SourceQualChoiceDialog’: macrodlg.c:3757:48: warning: variable ‘b4’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c: In function ‘SourceConstraintDialog’: macrodlg.c:3995:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c:3995:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c:3995:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c: In function ‘CDSGeneProtQualConstraintDialog’: macrodlg.c:4309:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c:4309:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c:4309:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c: In function ‘QuantityConstraintToDialog’: macrodlg.c:7368:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7368 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:7373:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7373 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:7378:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7378 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘TestApplyActionDialog’: macrodlg.c:12965:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 12965 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘TestEditActionDialog’: macrodlg.c:13170:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 13170 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘TestRemoveOutsideActionDialog’: macrodlg.c:13328:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 13328 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘ApplyFeatureActionToDialog’: macrodlg.c:15186:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15186 | sprintf (num, "%d^", action->location->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:15188:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15188 | sprintf (num, "%d", action->location->data.intvalue + 1); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘AddMacroActions’: macrodlg.c:20523:25: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 20523 | Boolean rval = FALSE; | ^~~~ macrodlg.c: In function ‘PointerToSampleDialog’: macrodlg.c:20659:19: warning: variable ‘max_char_per_line’ set but not used [-Wunused-but-set-variable] 20659 | Int4 max_char_per_line; | ^~~~~~~~~~~~~~~~~ macrodlg.c: In function ‘SampleDialogCopy’: macrodlg.c:20779:53: warning: variable ‘last_col’ set but not used [-Wunused-but-set-variable] 20779 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~ macrodlg.c:20779:42: warning: variable ‘first_col’ set but not used [-Wunused-but-set-variable] 20779 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~~ macrodlg.c: In function ‘SingleMacroAcceptButton’: macrodlg.c:22071:33: warning: variable ‘num_features’ set but not used [-Wunused-but-set-variable] 22071 | Int4 num_fields, num_features; | ^~~~~~~~~~~~ macrodlg.c:22071:21: warning: variable ‘num_fields’ set but not used [-Wunused-but-set-variable] 22071 | Int4 num_fields, num_features; | ^~~~~~~~~~ macrodlg.c: In function ‘LaunchMacroTemplateEditor’: macrodlg.c:23785:23: warning: variable ‘bfp’ set but not used [-Wunused-but-set-variable] 23785 | BaseFormPtr bfp; | ^~~ macrodlg.c: In function ‘SearchFuncToDialog’: macrodlg.c:25755:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 25755 | sprintf (buf, "%d", func->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:25776:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 25776 | sprintf (buf, "%d", func->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: At top level: macrodlg.c:20095:13: warning: ‘ChangeMacroActionPopup’ defined but not used [-Wunused-function] 20095 | static void ChangeMacroActionPopup (LisT t) | ^~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:20038:13: warning: ‘GetPopupChoiceForActionChoice’ defined but not used [-Wunused-function] 20038 | static Int2 GetPopupChoiceForActionChoice (Uint1 action_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:19715:13: warning: ‘GetCategoryForActionChoice’ defined but not used [-Wunused-function] 19715 | static Int2 GetCategoryForActionChoice (Uint1 action_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:19698:14: warning: ‘GetActionChoiceForCategoryPopupChoice’ defined but not used [-Wunused-function] 19698 | static Uint1 GetActionChoiceForCategoryPopupChoice (Int2 category, Int2 popup_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c: In function ‘ActionToSingleMacroActionForm’: macrodlg.c:22273:30: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 22273 | Show (frm->action_dlgs[val - 1]); | ~~~~^~~ macrodlg.c:22216:25: note: ‘val’ was declared here 22216 | Int2 val, i; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF biosrc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/biosrc.h:48, from biosrc.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ biosrc.c: In function ‘CreateSimpleBioSourceDialog’: biosrc.c:2455:18: warning: variable ‘indexerVersion’ set but not used [-Wunused-but-set-variable] 2455 | Boolean indexerVersion; | ^~~~~~~~~~~~~~ biosrc.c: In function ‘CreateBioSourceDialog’: biosrc.c:3615:18: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] 3615 | PrompT y; | ^ biosrc.c: At top level: biosrc.c:3291:26: warning: ‘EnumListFromQualNameAssoc’ defined but not used [-Wunused-function] 3291 | static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:3100:16: warning: ‘SubsourceDialogToSubSourcePtr’ defined but not used [-Wunused-function] 3100 | static Pointer SubsourceDialogToSubSourcePtr (DialoG d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2677:13: warning: ‘SubSourcePtrToSubsourceDialog’ defined but not used [-Wunused-function] 2677 | static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2617:16: warning: ‘OrgmodDialogToOrgModPtr’ defined but not used [-Wunused-function] 2617 | static Pointer OrgmodDialogToOrgModPtr (DialoG d) | ^~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2568:13: warning: ‘OrgModPtrToOrgmodDialog’ defined but not used [-Wunused-function] 2568 | static void OrgModPtrToOrgmodDialog (DialoG d, Pointer data) | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cdrgn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/cdrgn.h:89, from cdrgn.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdrgn.c: In function ‘SetBestProteinFeature’: cdrgn.c:1003:21: warning: unused variable ‘prp’ [-Wunused-variable] 1003 | ProtRefPtr prp; | ^~~ cdrgn.c: In function ‘CdRegionPtrToForm’: cdrgn.c:1050:19: warning: unused variable ‘vnp’ [-Wunused-variable] 1050 | ValNodePtr vnp; | ^~~ cdrgn.c: In function ‘ProductToSeqLocPtr’: cdrgn.c:1293:19: warning: variable ‘rfp’ set but not used [-Wunused-but-set-variable] 1293 | RnaFormPtr rfp = NULL; | ^~~ cdrgn.c: In function ‘CreateCodeBreakAlist’: cdrgn.c:1926:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 1926 | Uint1 first; | ^~~~~ cdrgn.c: In function ‘CodeBreakPtrToCodeBreakDialog’: cdrgn.c:1977:19: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 1977 | Uint1 aa; | ^~ cdrgn.c: In function ‘PopulateAAPopup’: cdrgn.c:7041:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 7041 | Uint1 first; | ^~~~~ cdrgn.c: In function ‘RnaRefPtrToForm’: cdrgn.c:7557:17: warning: unused variable ‘is_iMet’ [-Wunused-variable] 7557 | Boolean is_iMet = FALSE; | ^~~~~~~ cdrgn.c:7556:17: warning: unused variable ‘is_fMet’ [-Wunused-variable] 7556 | Boolean is_fMet = FALSE; | ^~~~~~~ cdrgn.c: At top level: cdrgn.c:6851:13: warning: ‘ConvertRnaRefNameToProductQual’ defined but not used [-Wunused-function] 6851 | static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cdrgn.c:6789:13: warning: ‘RemoveQualByName’ defined but not used [-Wunused-function] 6789 | static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name) | ^~~~~~~~~~~~~~~~ cdrgn.c:6770:18: warning: ‘FindOrAddQual’ defined but not used [-Wunused-function] 6770 | static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name) | ^~~~~~~~~~~~~ cdrgn.c:6323:15: warning: ‘CreateMrnaUserObjectDialog’ defined but not used [-Wunused-function] 6323 | static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cdrgn.c:6246:14: warning: ‘check_rna_type’ defined but not used [-Wunused-function] 6246 | static Uint1 check_rna_type (Uint1 type) | ^~~~~~~~~~~~~~ cdrgn.c:3183:13: warning: ‘SetComment’ defined but not used [-Wunused-function] 3183 | static void SetComment (CharPtr new_comment, WindoW w) | ^~~~~~~~~~ cdrgn.c:2149:13: warning: ‘AccessionToGi’ defined but not used [-Wunused-function] 2149 | static Int4 AccessionToGi (CharPtr string) | ^~~~~~~~~~~~~ cdrgn.c:961:13: warning: ‘FormToProtRef’ defined but not used [-Wunused-function] 961 | static void FormToProtRef(CdRgnFormPtr cfp, ProtRefPtr prp) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF import.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/import.h:48, from import.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ import.c:3776:22: warning: ‘kDoNotEditTitle’ initialized and declared ‘extern’ 3776 | extern const CharPtr kDoNotEditTitle = "You are manually editing a title. If you continue, the title will not be automatically updated if the taxonomy information changes. Are you sure you want to do this? It is a very bad idea."; | ^~~~~~~~~~~~~~~ import.c: In function ‘ExpandSecondaries’: import.c:3394:30: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 3394 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ import.c:3394:29: note: directive argument in the range [-2147483648, 2147483647] 3394 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ExpandSecondaries’ at import.c:3394:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pubdesc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/pubdesc.h:48, from pubdesc.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pubdesc.c: In function ‘MakeReplaceAuthorsForm’: pubdesc.c:4303:24: warning: variable ‘pepp’ set but not used [-Wunused-but-set-variable] 4303 | PubdescEditProcsPtr pepp; | ^~~~ pubdesc.c: In function ‘DisplayDocSum’: pubdesc.c:4865:9: warning: variable ‘lineheight’ set but not used [-Wunused-but-set-variable] 4865 | Int2 lineheight; | ^~~~~~~~~~ pubdesc.c: In function ‘GetLastNameFromPersonId’: pubdesc.c:5592:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘names’ will never be NULL [-Waddress] 5592 | if (nsp->names != NULL) { | ^~ In file included from ../include/objsset.h:51, from ../include/sequtil.h:43, from ../include/sqnutils.h:49, from ../include/dlogutil.h:50: ../include/objgen.h:212:17: note: ‘names’ declared here 212 | CharPtr names[7]; | ^~~~~ pubdesc.c: At top level: pubdesc.c:5377:13: warning: ‘Quit’ defined but not used [-Wunused-function] 5377 | static void Quit (ButtoN b) | ^~~~ pubdesc.c:5113:14: warning: ‘AddAll’ defined but not used [-Wunused-function] 5113 | static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st) | ^~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5096:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5096 | sprintf (year_buf, "%d", year - 1); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5096:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5099:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5099 | sprintf (year_buf, "%d", year); | ^ In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5099:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5102:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5102 | sprintf (year_buf, "%d", year + 1); | ^ In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5102:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqsub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/seqsub.h:58, from seqsub.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqsub.c: In function ‘SeqSubmitFromTemplateEditor’: seqsub.c:3250:20: warning: variable ‘omdp’ set but not used [-Wunused-but-set-variable] 3250 | ObjMgrDataPtr omdp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mapgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from mapgene.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapgene.c: In function ‘load_new_align’: mapgene.c:79:24: warning: variable ‘match_slp’ set but not used [-Wunused-but-set-variable] 79 | SeqLocPtr slp, match_slp, t_slp; | ^~~~~~~~~ mapgene.c: In function ‘figure_loc_by_position’: mapgene.c:1039:27: warning: variable ‘center’ set but not used [-Wunused-but-set-variable] 1039 | Int4 start, stop, center; | ^~~~~~ mapgene.c: In function ‘cvt_loc_for_single_gene’: mapgene.c:1958:36: warning: variable ‘p_align_offset’ set but not used [-Wunused-but-set-variable] 1958 | Int4 offset, align_offset, p_align_offset; | ^~~~~~~~~~~~~~ mapgene.c:1957:14: warning: unused variable ‘shift’ [-Wunused-variable] 1957 | Int4 shift = 0; | ^~~~~ mapgene.c: In function ‘print_header_for_center’: mapgene.c:2693:17: warning: variable ‘link’ set but not used [-Wunused-but-set-variable] 2693 | CharPtr link; | ^~~~ mapgene.c: In function ‘PrintGeneticMarkerForOneMap’: mapgene.c:3635:17: warning: variable ‘link’ set but not used [-Wunused-but-set-variable] 3635 | CharPtr link; | ^~~~ mapgene.c: At top level: mapgene.c:3207:16: warning: ‘convert_center_name_to_gifname’ defined but not used [-Wunused-function] 3207 | static Boolean convert_center_name_to_gifname (CharPtr center_name, CharPtr gif_name) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mapgene.c:1788:13: warning: ‘adjust_slp_list’ defined but not used [-Wunused-function] 1788 | static void adjust_slp_list(ValNodePtr slp_list) | ^~~~~~~~~~~~~~~ mapgene.c:1748:16: warning: ‘merge_slp_list’ defined but not used [-Wunused-function] 1748 | static Boolean merge_slp_list(ValNodePtr PNTR gene_slp_list, ValNodePtr slp_list) | ^~~~~~~~~~~~~~ mapgene.c:1280:13: warning: ‘change_anchor_to_front’ defined but not used [-Wunused-function] 1280 | static void change_anchor_to_front(ValNodePtr msp_list, SeqIdPtr anchor_id) | ^~~~~~~~~~~~~~~~~~~~~~ mapgene.c:200:13: warning: ‘get_center_pointer’ defined but not used [-Wunused-function] 200 | static Int4 get_center_pointer(SeqLocPtr slp) | ^~~~~~~~~~~~~~~~~~ mapgene.c:27:13: warning: ‘print_this_id’ defined but not used [-Wunused-function] 27 | static void print_this_id (SeqIdPtr sip) | ^~~~~~~~~~~~~ mapgene.c: In function ‘PrintHTMLContigAlign.isra.0’: mapgene.c:2798:51: warning: ‘%s’ directive writing up to 30 bytes into a region of size 25 [-Wformat-overflow=] 2798 | sprintf(link_name, "CONTIG%s", alpha_name); | ^~ ~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FindEricContigMap’ at mapgene.c:2798:4, inlined from ‘create_CONTIG_link’ at mapgene.c:2817:10, inlined from ‘PrintHTMLContigAlign.isra.0’ at mapgene.c:3050:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 37 bytes into a destination of size 31 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘print_contig_info’, inlined from ‘PrintContigForOneMap’ at mapgene.c:3410:9, inlined from ‘PrintContigForOneMap’ at mapgene.c:3396:9: mapgene.c:3181:25: warning: ‘yac_num’ may be used uninitialized [-Wmaybe-uninitialized] 3181 | PrintHTMLContigAlign(band_name, contig_name, anp_list, fp, db, fish_list, yac_list, yac_num); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mapgene.c: In function ‘PrintContigForOneMap’: mapgene.c:3152:14: note: ‘yac_num’ was declared here 3152 | Int4 yac_num; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prtgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/tofile.h:66, from ../include/prtgene.h:3, from prtgene.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prtgene.c: In function ‘print_sfp_ext’: prtgene.c:108:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 108 | if(ufp->choice == 2) /*integer */ | ^~ prtgene.c:110:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 110 | print_store_buf(temp, buf, buf_size, &len, fp); | ^~~~~~~~~~~~~~~ prtgene.c: In function ‘print_store_for_html’: prtgene.c:749:14: warning: variable ‘white_sp’ set but not used [-Wunused-but-set-variable] 749 | Char white_sp; | ^~~~~~~~ prtgene.c: In function ‘PrintSequenceToFile.isra.0’: prtgene.c:950:49: warning: ‘ (bp) on the genome’ directive writing 19 bytes into a region of size between 16 and 96 [-Wformat-overflow=] 950 | sprintf(temp, ": %s - %s (bp) on the genome", temp_1, temp_2); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintSequenceToFile.isra.0’ at prtgene.c:950:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 25 and 105 bytes into a destination of size 101 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbidesk.a ar cru libncbidesk.a drawseq.o dotmatrx.o fea2seg.o fstyle.o smdlg1.o smdlg2.o smdlg3.o smtools.o styleman.o stylemui.o glbpic.o layout.o saldist.o saled.o salfiles.o salpanel.o salparam.o salsa.o seqfltr.o seqgraph.o seqgrphx.o seqmtrx.o seqpcc.o seqanal.o aacomp.o seqscrl.o valdlg.o vsm.o vsmfile.o vsmutil.o udvgraph.o udvopen.o udvpanel.o dotvibrant.o dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbidesk.a ../lib ranlib ../lib/libncbidesk.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvclick.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvclick.c:248: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvclick.c: In function ‘DDV_SendBSPSelectMsg_OLD’: ddvclick.c:979:13: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 979 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ ddvclick.c: In function ‘DDV_SendBSPSelectMsg’: ddvclick.c:1090:18: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 1090 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ ddvclick.c: In function ‘DDV_DragProc’: ddvclick.c:2013:13: warning: unused variable ‘cur_pgp’ [-Wunused-variable] 2013 | ParaGPtr cur_pgp=NULL; | ^~~~~~~ ddvclick.c: In function ‘DDV_HoldProc’: ddvclick.c:2494:13: warning: unused variable ‘Scroll’ [-Wunused-variable] 2494 | Boolean Scroll=FALSE; | ^~~~~~ ddvclick.c:2490:13: warning: unused variable ‘cur_pgp’ [-Wunused-variable] 2490 | ParaGPtr cur_pgp=NULL; | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ../include/ddvpanel.h:150, from ddvclick.c:252: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvclick.c:1823:13: warning: ‘EraseOutline’ defined but not used [-Wunused-function] 1823 | static void EraseOutline(PaneL p) { | ^~~~~~~~~~~~ ddvclick.c:1811:16: warning: ‘RectanglesAreSame’ defined but not used [-Wunused-function] 1811 | static Boolean RectanglesAreSame(RecT rc1, RecT rc2) { | ^~~~~~~~~~~~~~~~~ ddvclick.c:970:13: warning: ‘DDV_SendBSPSelectMsg_OLD’ defined but not used [-Wunused-function] 970 | static void DDV_SendBSPSelectMsg_OLD(DdvMainPtr dmp,Int4 bsp_coord,Int4 SeqAlign_coord, | ^~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c:611:13: warning: ‘DDV_GetSeqAlignCoordGivenCol’ defined but not used [-Wunused-function] 611 | static Int4 DDV_GetSeqAlignCoordGivenCol(DdvMainPtr dmp, Int4 Disp_coord) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c: In function ‘DDV_GetSeqNameGivenRow’: ddvclick.c:956:6: warning: ‘sip’ may be used uninitialized [-Wmaybe-uninitialized] 956 | if (!sip) | ^ ddvclick.c:942:12: note: ‘sip’ was declared here 942 | SeqIdPtr sip; | ^~~ In function ‘DDV_SendBSPSelectMsg’, inlined from ‘DDV_SelectRegion’ at ddvclick.c:2974:7, inlined from ‘DDV_ReleaseProc’ at ddvclick.c:2289:13: ddvclick.c:1127:9: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 1127 | slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c: In function ‘DDV_ReleaseProc’: ddvclick.c:1091:18: note: ‘pgp’ was declared here 1091 | ParaGPtr pgp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvgraph.c:210: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvgraph.c: In function ‘DDV_DrawSequence’: ddvgraph.c:701:31: warning: unused variable ‘pos’ [-Wunused-variable] 701 | Int2 decal=1,i,x,y,pos=0; | ^~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ddvgraph.c:215: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvopen.c:372: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvopen.c: In function ‘DDV_GetAndCheckSeqAlign’: ddvopen.c:1739:17: warning: variable ‘nRet’ set but not used [-Wunused-but-set-variable] 1739 | Uint2 nRet=DVV_MSG_M_OK; | ^~~~ ddvopen.c: In function ‘DDV_FOpenAcceptProc’: ddvopen.c:1932:33: warning: variable ‘nRet’ set but not used [-Wunused-but-set-variable] 1932 | Uint2 nRet=DVV_MSG_M_OK,The_entityID; | ^~~~ ddvopen.c: In function ‘DDV_NetOpen_okProc’: ddvopen.c:2141:25: warning: variable ‘AccessType’ set but not used [-Wunused-but-set-variable] 2141 | Int2 AccessType,procval; | ^~~~~~~~~~ ddvopen.c: In function ‘DDV_StartMainWin_Slave’: ddvopen.c:2411:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 2411 | else | ^~~~ ddvopen.c:2417:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 2417 | if (!w) return(NULL); | ^~ ddvopen.c: In function ‘DDV_ImportBioseqDlg’: ddvopen.c:2819:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 2819 | ButtoN b; | ^ ddvopen.c: In function ‘DDV_HideDlg’: ddvopen.c:3135:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 3135 | ButtoN b; | ^ In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from ddvopen.c:376: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ddvopen.c:377: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvopen.c:2111:16: warning: ‘DDV_IsInt’ defined but not used [-Wunused-function] 2111 | static Boolean DDV_IsInt(CharPtr szAccess) | ^~~~~~~~~ ddvopen.c:1285:13: warning: ‘DDV_NoConvert’ defined but not used [-Wunused-function] 1285 | static void DDV_NoConvert(ButtoN g) { | ^~~~~~~~~~~~~ ddvopen.c:1272:13: warning: ‘DDV_Convert’ defined but not used [-Wunused-function] 1272 | static void DDV_Convert(ButtoN g) { | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ddvpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvpanel.c:389: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvpanel.c: In function ‘DDV_CreateViewerPanel’: ddvpanel.c:1177:8: warning: variable ‘cxChar’ set but not used [-Wunused-but-set-variable] 1177 | Int2 cxChar,cyChar; | ^~~~~~ ddvpanel.c: In function ‘DDV_DispStyles_OkProc’: ddvpanel.c:1543:21: warning: unused variable ‘szBuf’ [-Wunused-variable] 1543 | Char szBuf[15]={""}; | ^~~~~ ddvpanel.c: In function ‘DDV_ExportTexte’: ddvpanel.c:2799:40: warning: variable ‘browse’ set but not used [-Wunused-but-set-variable] 2799 | ButtoN chk2,chk3,chk4,chk5,chk6,browse,ok; | ^~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ../include/ddvpanel.h:150, from ddvpanel.c:392: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3377:13: warning: ‘write_annot’ defined but not used [-Wunused-function] 3377 | static void write_annot(SeqAlignPtr align) | ^~~~~~~~~~~ ddvpanel.c:3296:13: warning: ‘DDV_MoveRightBoundaryRight’ defined but not used [-Wunused-function] 3296 | static void DDV_MoveRightBoundaryRight(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3290:13: warning: ‘DDV_MoveRightBoundaryLeft’ defined but not used [-Wunused-function] 3290 | static void DDV_MoveRightBoundaryLeft(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3284:13: warning: ‘DDV_MoveLeftBoundaryRight’ defined but not used [-Wunused-function] 3284 | static void DDV_MoveLeftBoundaryRight(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3278:13: warning: ‘DDV_MoveLeftBoundaryLeft’ defined but not used [-Wunused-function] 3278 | static void DDV_MoveLeftBoundaryLeft(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3272:13: warning: ‘DDV_MoveRowRight’ defined but not used [-Wunused-function] 3272 | static void DDV_MoveRowRight(IteM i) | ^~~~~~~~~~~~~~~~ ddvpanel.c:3266:13: warning: ‘DDV_MoveRowLeft’ defined but not used [-Wunused-function] 3266 | static void DDV_MoveRowLeft(IteM i) | ^~~~~~~~~~~~~~~ ddvpanel.c:3024:13: warning: ‘DDV_DeleteRow’ defined but not used [-Wunused-function] 3024 | static void DDV_DeleteRow(IteM i) | ^~~~~~~~~~~~~ ddvpanel.c: In function ‘DDV_SortPGPLineNum’: ddvpanel.c:2441:23: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 2441 | n+=pgp->nLines; | ~~~^~~~~~~~ ddvpanel.c:2431:12: note: ‘pgp’ was declared here 2431 | ParaGPtr pgp; | ^~~ rm -f libddvlib.a ar cru libddvlib.a ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libddvlib.a ../lib ranlib ../lib/libddvlib.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF corematx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corematx.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dvncode.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from dvncode.c:69: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb1.c: In function ‘BiostrucAsnRead’: objmmdb1.c:90:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 90 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucIdFree’: objmmdb1.c:323:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 323 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucIdAsnRead’: objmmdb1.c:358:12: warning: unused variable ‘isError’ [-Wunused-variable] 358 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucSetAsnRead’: objmmdb1.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucAnnotSetAsnRead’: objmmdb1.c:716:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 716 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucResidueGraphSetAsnRead’: objmmdb1.c:885:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 885 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucDescrFree’: objmmdb1.c:1015:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1015 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucDescrAsnRead’: objmmdb1.c:1059:12: warning: unused variable ‘isError’ [-Wunused-variable] 1059 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucHistoryAsnRead’: objmmdb1.c:1270:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1270 | AsnReadFunc func; | ^~~~ objmmdb1.c:1269:12: warning: unused variable ‘isError’ [-Wunused-variable] 1269 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucReplaceAsnRead’: objmmdb1.c:1450:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1450 | AsnReadFunc func; | ^~~~ objmmdb1.c:1449:12: warning: unused variable ‘isError’ [-Wunused-variable] 1449 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘VersionOfDatabase_version_of_databaseFree’: objmmdb1.c:1618:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1618 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucSourceAsnRead’: objmmdb1.c:1652:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1652 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘VersionOfDatabase_version_of_databaseAsnRead’: objmmdb1.c:1753:12: warning: unused variable ‘isError’ [-Wunused-variable] 1753 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucGraphAsnRead’: objmmdb1.c:2001:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2001 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiomolDescrFree’: objmmdb1.c:2139:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2139 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiomolDescrAsnRead’: objmmdb1.c:2189:12: warning: unused variable ‘isError’ [-Wunused-variable] 2189 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueGraphAsnRead’: objmmdb1.c:2446:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2446 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘MoleculeGraphAsnRead’: objmmdb1.c:2654:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2654 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘InterResidueBondAsnRead’: objmmdb1.c:2856:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2856 | AsnReadFunc func; | ^~~~ objmmdb1.c:2855:12: warning: unused variable ‘isError’ [-Wunused-variable] 2855 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueAsnRead’: objmmdb1.c:3037:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3037 | AsnReadFunc func; | ^~~~ objmmdb1.c:3036:12: warning: unused variable ‘isError’ [-Wunused-variable] 3036 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueGraphPntrFree’: objmmdb1.c:3177:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3177 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘ResidueGraphPntrAsnRead’: objmmdb1.c:3212:12: warning: unused variable ‘isError’ [-Wunused-variable] 3212 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucGraphPntrAsnRead’: objmmdb1.c:3399:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3399 | AsnReadFunc func; | ^~~~ objmmdb1.c:3398:12: warning: unused variable ‘isError’ [-Wunused-variable] 3398 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucResidueGraphSetPntrAsnRead’: objmmdb1.c:3565:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3565 | AsnReadFunc func; | ^~~~ objmmdb1.c:3564:12: warning: unused variable ‘isError’ [-Wunused-variable] 3564 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomAsnRead’: objmmdb1.c:3732:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3732 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘IntraResidueBondAsnRead’: objmmdb1.c:3924:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3924 | AsnReadFunc func; | ^~~~ objmmdb1.c:3923:12: warning: unused variable ‘isError’ [-Wunused-variable] 3923 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ChiralCenterAsnRead’: objmmdb1.c:4097:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4097 | AsnReadFunc func; | ^~~~ objmmdb1.c:4096:12: warning: unused variable ‘isError’ [-Wunused-variable] 4096 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomPntrAsnRead’: objmmdb1.c:4286:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4286 | AsnReadFunc func; | ^~~~ objmmdb1.c:4285:12: warning: unused variable ‘isError’ [-Wunused-variable] 4285 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomPntrSetAsnRead’: objmmdb1.c:4441:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4441 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:73, from objmmdb1.c:5: ../include/objmmdb2.h: At top level: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objmmdb1.c: In function ‘BiostrucIdAsnRead’: objmmdb1.c:411:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 411 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:357:10: note: ‘choice’ was declared here 357 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘BiostrucDescrAsnRead’: objmmdb1.c:1126:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1126 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:1058:10: note: ‘choice’ was declared here 1058 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘BiomolDescrAsnRead’: objmmdb1.c:2284:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2284 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:2188:10: note: ‘choice’ was declared here 2188 | Uint1 choice; | ^~~~~~ In function ‘VersionOfDatabase_version_of_databaseAsnRead’, inlined from ‘BiostrucSourceAsnRead’ at objmmdb1.c:1695:54: objmmdb1.c:1802:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1802 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c: In function ‘BiostrucSourceAsnRead’: objmmdb1.c:1752:10: note: ‘choice’ was declared here 1752 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘ResidueGraphPntrAsnRead’: objmmdb1.c:3265:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3265 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:3211:10: note: ‘choice’ was declared here 3211 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb2.c: In function ‘BiostrucModelAsnRead’: objmmdb2.c:88:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 88 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ModelDescrFree’: objmmdb2.c:242:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 242 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘ModelDescrAsnRead’: objmmdb2.c:289:12: warning: unused variable ‘isError’ [-Wunused-variable] 289 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘ModelSpaceAsnRead’: objmmdb2.c:512:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 512 | AsnReadFunc func; | ^~~~ objmmdb2.c:511:12: warning: unused variable ‘isError’ [-Wunused-variable] 511 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘Coordinates_coordinatesFree’: objmmdb2.c:709:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 709 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘ModelCoordinateSetAsnRead’: objmmdb2.c:743:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 743 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘Coordinates_coordinatesAsnRead’: objmmdb2.c:831:12: warning: unused variable ‘isError’ [-Wunused-variable] 831 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘ReferenceFrameAsnRead’: objmmdb2.c:1063:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1063 | AsnReadFunc func; | ^~~~ objmmdb2.c:1062:12: warning: unused variable ‘isError’ [-Wunused-variable] 1062 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘CoordinatesFree’: objmmdb2.c:1193:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1193 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘CoordinatesAsnRead’: objmmdb2.c:1231:12: warning: unused variable ‘isError’ [-Wunused-variable] 1231 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘AtomicCoordinatesAsnRead’: objmmdb2.c:1420:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1420 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘Surface_surfaceFree’: objmmdb2.c:1640:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1640 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘SurfaceCoordinatesAsnRead’: objmmdb2.c:1686:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1686 | AsnReadFunc func; | ^~~~ objmmdb2.c:1685:12: warning: unused variable ‘isError’ [-Wunused-variable] 1685 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘Surface_surfaceAsnRead’: objmmdb2.c:1766:12: warning: unused variable ‘isError’ [-Wunused-variable] 1766 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘DensityCoordinatesAsnRead’: objmmdb2.c:2030:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2030 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ModelSpacePointsAsnRead’: objmmdb2.c:2263:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2263 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsFree’: objmmdb2.c:2404:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2404 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsAsnRead’: objmmdb2.c:2439:12: warning: unused variable ‘isError’ [-Wunused-variable] 2439 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘AtomicOccupanciesAsnRead’: objmmdb2.c:2615:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2615 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AlternateConformationIdsAsnRead’: objmmdb2.c:2760:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2760 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ConformationEnsembleAsnRead’: objmmdb2.c:2890:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2890 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘IsotropicTemperatureFactorsAsnRead’: objmmdb2.c:3054:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3054 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AnisotropicTemperatureFactorsAsnRead’: objmmdb2.c:3221:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3221 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘TMeshAsnRead’: objmmdb2.c:3426:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3426 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘TrianglesAsnRead’: objmmdb2.c:3626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3626 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objmmdb2.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objmmdb2.c: In function ‘ModelDescrAsnRead’: objmmdb2.c:366:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 366 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:288:10: note: ‘choice’ was declared here 288 | Uint1 choice; | ^~~~~~ objmmdb2.c: In function ‘CoordinatesAsnRead’: objmmdb2.c:1281:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1281 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:1230:10: note: ‘choice’ was declared here 1230 | Uint1 choice; | ^~~~~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsAsnRead’: objmmdb2.c:2485:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2485 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:2438:10: note: ‘choice’ was declared here 2438 | Uint1 choice; | ^~~~~~ In function ‘Coordinates_coordinatesAsnRead’, inlined from ‘ModelCoordinateSetAsnRead’ at objmmdb2.c:794:40: objmmdb2.c:877:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 877 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c: In function ‘ModelCoordinateSetAsnRead’: objmmdb2.c:830:10: note: ‘choice’ was declared here 830 | Uint1 choice; | ^~~~~~ In function ‘Surface_surfaceAsnRead’, inlined from ‘SurfaceCoordinatesAsnRead’ at objmmdb2.c:1729:32: objmmdb2.c:1828:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1828 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c: In function ‘SurfaceCoordinatesAsnRead’: objmmdb2.c:1765:10: note: ‘choice’ was declared here 1765 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmmdb3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureSetAsnRead’: objmmdb3.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphPntrsFree’: objmmdb3.c:220:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 220 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘AtomPntrsAsnRead’: objmmdb3.c:443:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 443 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphAlignmentAsnRead’: objmmdb3.c:626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 626 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphInteractionAsnRead’: objmmdb3.c:824:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 824 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘SphereAsnRead’: objmmdb3.c:1024:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1024 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ConeAsnRead’: objmmdb3.c:1192:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1192 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘CylinderAsnRead’: objmmdb3.c:1372:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1372 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BrickAsnRead’: objmmdb3.c:1557:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1557 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘TransformAsnRead’: objmmdb3.c:1796:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1796 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucFeatureSetDescrFree’: objmmdb3.c:1921:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1921 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘Location_locationFree’: objmmdb3.c:2161:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2161 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2206:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2206 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘Property_propertyFree’: objmmdb3.c:2722:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2722 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘ColorPropAsnRead’: objmmdb3.c:2798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2798 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘CameraAsnRead’: objmmdb3.c:2986:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2986 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucScriptAsnRead’: objmmdb3.c:3171:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3171 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionPntrsAsnRead’: objmmdb3.c:3330:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3330 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionSimilarityAsnRead’: objmmdb3.c:3648:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3648 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘OtherFeatureAsnRead’: objmmdb3.c:3825:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3825 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucMoleculePntrAsnRead’: objmmdb3.c:3999:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3999 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘MoleculePntrsAsnRead’: objmmdb3.c:4342:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4342 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ResidueExplicitPntrsAsnRead’: objmmdb3.c:4505:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4505 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ResidueIntervalPntrAsnRead’: objmmdb3.c:4673:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4673 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionCoordinatesAsnRead’: objmmdb3.c:4845:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4845 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionBoundaryFree’: objmmdb3.c:4981:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4981 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘AlignStatsAsnRead’: objmmdb3.c:5212:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5212 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RealValueAsnRead’: objmmdb3.c:5454:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5454 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ModelSpacePointAsnRead’: objmmdb3.c:5615:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5615 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘MoveFree’: objmmdb3.c:5759:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 5759 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘RotMatrixAsnRead’: objmmdb3.c:5967:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5967 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘TransMatrixAsnRead’: objmmdb3.c:6200:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6200 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘GLMatrixAsnRead’: objmmdb3.c:6379:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6379 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucScriptStepAsnRead’: objmmdb3.c:6680:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6680 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objmmdb3.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ objmmdb3.c: In function ‘ChemGraphPntrsAsnRead’: objmmdb3.c:307:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 307 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:257:10: note: ‘choice’ was declared here 257 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘BiostrucFeatureSetDescrAsnRead’: objmmdb3.c:2024:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2024 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:1961:10: note: ‘choice’ was declared here 1961 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘ResiduePntrsAsnRead’: objmmdb3.c:4213:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4213 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:4162:10: note: ‘choice’ was declared here 4162 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘RegionBoundaryAsnRead’: objmmdb3.c:5075:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5075 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:5021:10: note: ‘choice’ was declared here 5021 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘MoveAsnRead’: objmmdb3.c:5839:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5839 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:5793:10: note: ‘choice’ was declared here 5793 | Uint1 choice; | ^~~~~~ In function ‘Region_regionAsnRead’, inlined from ‘RegionPntrsAsnRead’ at objmmdb3.c:3373:30: objmmdb3.c:3464:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3464 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘RegionPntrsAsnRead’: objmmdb3.c:3409:10: note: ‘choice’ was declared here 3409 | Uint1 choice; | ^~~~~~ In function ‘Property_propertyAsnRead’, inlined from ‘BiostrucFeatureAsnRead’ at objmmdb3.c:2265:34: objmmdb3.c:2691:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2691 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2626:10: note: ‘choice’ was declared here 2626 | Uint1 choice; | ^~~~~~ In function ‘Location_locationAsnRead’, inlined from ‘BiostrucFeatureAsnRead’ at objmmdb3.c:2272:34: objmmdb3.c:2370:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2370 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2308:10: note: ‘choice’ was declared here 2308 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objcn3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objcn3d.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleDictionaryAsnRead’: objcn3d.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dUserAnnotationsAsnRead’: objcn3d.c:251:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 251 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dColorAsnRead’: objcn3d.c:415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 415 | AsnReadFunc func; | ^~~~ objcn3d.c:414:12: warning: unused variable ‘isError’ [-Wunused-variable] 414 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dBackboneStyleAsnRead’: objcn3d.c:605:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 605 | AsnReadFunc func; | ^~~~ objcn3d.c:604:12: warning: unused variable ‘isError’ [-Wunused-variable] 604 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dGeneralStyleAsnRead’: objcn3d.c:789:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 789 | AsnReadFunc func; | ^~~~ objcn3d.c:788:12: warning: unused variable ‘isError’ [-Wunused-variable] 788 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dBackboneLabelStyleAsnRead’: objcn3d.c:972:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 972 | AsnReadFunc func; | ^~~~ objcn3d.c:971:12: warning: unused variable ‘isError’ [-Wunused-variable] 971 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleSettingsAsnRead’: objcn3d.c:1175:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1175 | AsnReadFunc func; | ^~~~ objcn3d.c:1174:12: warning: unused variable ‘isError’ [-Wunused-variable] 1174 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleSettingsSetAsnRead’: objcn3d.c:1578:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1578 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dStyleTableItemAsnRead’: objcn3d.c:1707:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1707 | AsnReadFunc func; | ^~~~ objcn3d.c:1706:12: warning: unused variable ‘isError’ [-Wunused-variable] 1706 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dResidueRangeAsnRead’: objcn3d.c:1872:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1872 | AsnReadFunc func; | ^~~~ objcn3d.c:1871:12: warning: unused variable ‘isError’ [-Wunused-variable] 1871 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dMoleculeLocationAsnRead’: objcn3d.c:2035:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2035 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dObjectLocationAsnRead’: objcn3d.c:2198:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2198 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dUserAnnotationAsnRead’: objcn3d.c:2363:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2363 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dGLMatrixAsnRead’: objcn3d.c:2555:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2555 | AsnReadFunc func; | ^~~~ objcn3d.c:2554:12: warning: unused variable ‘isError’ [-Wunused-variable] 2554 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dVectorAsnRead’: objcn3d.c:2843:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2843 | AsnReadFunc func; | ^~~~ objcn3d.c:2842:12: warning: unused variable ‘isError’ [-Wunused-variable] 2842 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dViewSettingsAsnRead’: objcn3d.c:3016:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3016 | AsnReadFunc func; | ^~~~ objcn3d.c:3015:12: warning: unused variable ‘isError’ [-Wunused-variable] 3015 | Boolean isError = FALSE; | ^~~~~~~ In file included from ../include/mapcn3d.h:8, from objcn3d.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/mmdbapi1.h:232, from ../include/mmdbapi.h:92, from mmdbapi.c:116: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi.c: In function ‘MakeAModelstruc’: mmdbapi.c:192:11: warning: unused variable ‘iCount’ [-Wunused-variable] 192 | Int4 iCount = 0; | ^~~~~~ mmdbapi.c:189:11: warning: unused variable ‘pdnmsCount’ [-Wunused-variable] 189 | PDNMS pdnmsCount = NULL; | ^~~~~~~~~~ mmdbapi.c: In function ‘AddPFBSelect’: mmdbapi.c:532:11: warning: unused variable ‘pmsdStruc’ [-Wunused-variable] 532 | PMSD pmsdStruc = NULL; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi1.c:294: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi1.c: In function ‘FreeAtomicModelAsnLists’: mmdbapi1.c:1037:41: warning: unused variable ‘pcoThis’ [-Wunused-variable] 1037 | CoordinatesPtr pcoThis = NULL; | ^~~~~~~ mmdbapi1.c: In function ‘FetchBS’: mmdbapi1.c:1242:13: warning: unused variable ‘bIsNetwork’ [-Wunused-variable] 1242 | Boolean bIsNetwork = FALSE; | ^~~~~~~~~~ mmdbapi1.c: In function ‘FreeSurfaceModelAsnList’: mmdbapi1.c:1627:16: warning: variable ‘pvnX’ set but not used [-Wunused-but-set-variable] 1627 | ValNodePtr pvnX = NULL; | ^~~~ mmdbapi1.c: In function ‘MakeChemGraphNodeList’: mmdbapi1.c:2343:16: warning: variable ‘pvnThis’ set but not used [-Wunused-but-set-variable] 2343 | ValNodePtr pvnThis = NULL; | ^~~~~~~ mmdbapi1.c: In function ‘DoApplyTransform’: mmdbapi1.c:2573:8: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2573 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘DoReverseTransform’: mmdbapi1.c:2713:8: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2713 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘InstBSAnnotSet’: mmdbapi1.c:2860:8: warning: unused variable ‘psfsThis’ [-Wunused-variable] 2860 | PSFS psfsThis = NULL; | ^~~~~~~~ mmdbapi1.c:2859:22: warning: unused variable ‘pbsfThis’ [-Wunused-variable] 2859 | BiostrucFeaturePtr pbsfThis = NULL; | ^~~~~~~~ mmdbapi1.c:2855:9: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2855 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:2978:19: warning: unused variable ‘loc1’ [-Wunused-variable] 2978 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c:2967:22: warning: unused variable ‘pbsf’ [-Wunused-variable] 2967 | BiostrucFeaturePtr pbsf=NULL; | ^~~~ mmdbapi1.c: In function ‘fnPBSFtoPSA’: mmdbapi1.c:3174:19: warning: unused variable ‘loc1’ [-Wunused-variable] 3174 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3408:19: warning: unused variable ‘loc1’ [-Wunused-variable] 3408 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c:3397:22: warning: unused variable ‘pbsf’ [-Wunused-variable] 3397 | BiostrucFeaturePtr pbsf=NULL; | ^~~~ mmdbapi1.c: In function ‘InstallAlignedSlave’: mmdbapi1.c:3877:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 3877 | Int2 iTest; | ^~~~~ mmdbapi1.c:3874:9: warning: unused variable ‘psfsThis’ [-Wunused-variable] 3874 | PSFS psfsThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiostrucAddFeature’: mmdbapi1.c:4184:11: warning: variable ‘ncbiVast’ set but not used [-Wunused-but-set-variable] 4184 | Boolean ncbiVast = FALSE; | ^~~~~~~~ mmdbapi1.c:4182:11: warning: variable ‘pdbFootnote’ set but not used [-Wunused-but-set-variable] 4182 | Boolean pdbFootnote = FALSE; | ^~~~~~~~~~~ mmdbapi1.c:4181:11: warning: variable ‘pdbSite’ set but not used [-Wunused-but-set-variable] 4181 | Boolean pdbSite = FALSE; | ^~~~~~~ mmdbapi1.c:4172:15: warning: unused variable ‘pdvnThis’ [-Wunused-variable] 4172 | DValNodePtr pdvnThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiostrucAsnGet’: mmdbapi1.c:5289:18: warning: variable ‘aop’ set but not used [-Wunused-but-set-variable] 5289 | AsnOptionPtr aop; | ^~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:3083:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3083 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BiosToSeq’ at mmdbapi1.c:3083:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:3127:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 3127 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi1.c:2974:37: note: ‘slavesip’ was declared here 2974 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ mmdbapi1.c: In function ‘fnPBSFtoPSA’: mmdbapi1.c:3275:52: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3275 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘fnPBSFtoPSA’ at mmdbapi1.c:3275:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3515:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3515 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘BiostrToSeqAnnotSet’ at mmdbapi1.c:3515:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3559:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 3559 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi1.c:3404:37: note: ‘slavesip’ was declared here 3404 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ mmdbapi1.c: In function ‘InstBSAnnotSet’: mmdbapi1.c:2885:15: warning: ‘iMMDBId’ may be used uninitialized [-Wmaybe-uninitialized] 2885 | pdnmsThis = FindLoadedBiostruc(NULL, iMMDBId); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdbapi1.c:2853:8: note: ‘iMMDBId’ was declared here 2853 | Int4 iMMDBId; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi2.c:159: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi2.c: In function ‘GetAtomLocs’: mmdbapi2.c:1471:9: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1471 | if (pmadThis) | ^ mmdbapi2.c: In function ‘AssignAtomLocId’: mmdbapi2.c:1537:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1537 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignBackBone’: mmdbapi2.c:1686:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1686 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignVirtual’: mmdbapi2.c:1790:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1790 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignIons’: mmdbapi2.c:1846:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1846 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘MolFromPDBChain’: mmdbapi2.c:1931:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1931 | Int2 iTest; | ^~~~~ mmdbapi2.c: In function ‘SeqStringFromMol’: mmdbapi2.c:1948:9: warning: unused variable ‘iTest’ [-Wunused-variable] 1948 | Int4 iTest =0; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi3.c:207: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi3.c: In function ‘WritePDBHeader’: mmdbapi3.c:840:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 840 | if(org) | ^~ mmdbapi3.c:845:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 845 | src = orgstring; | ^~~ mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 840 | if(org) | ^ mmdbapi3.c: In function ‘WritePDBRemarks’: mmdbapi3.c:1389:8: warning: unused variable ‘len’ [-Wunused-variable] 1389 | int len; | ^~~ mmdbapi3.c:1388:9: warning: unused variable ‘pcThis’ [-Wunused-variable] 1388 | Char pcThis[81]; | ^~~~~~ mmdbapi3.c:1387:21: warning: unused variable ‘pbsdrLast’ [-Wunused-variable] 1387 | BiostrucDescrPtr pbsdrLast = NULL; | ^~~~~~~~~ mmdbapi3.c:1386:21: warning: unused variable ‘pbsdrThis’ [-Wunused-variable] 1386 | BiostrucDescrPtr pbsdrThis = NULL; | ^~~~~~~~~ mmdbapi3.c: In function ‘WritePDBConnect’: mmdbapi3.c:1610:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1610 | Int2 iTest; | ^~~~~ mmdbapi3.c: In function ‘WritePDBModelList’: mmdbapi3.c:1625:10: warning: variable ‘iCount’ set but not used [-Wunused-but-set-variable] 1625 | Int4 iCount; | ^~~~~~ mmdbapi3.c: In function ‘WriteKinAtom’: mmdbapi3.c:2287:11: warning: unused variable ‘pcElName’ [-Wunused-variable] 2287 | CharPtr pcElName = NULL; | ^~~~~~~~ mmdbapi3.c: In function ‘WriteFASTAMolecule’: mmdbapi3.c:3537:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 3537 | Int4 iTest =0; | ^~~~~ mmdbapi3.c: In function ‘WriteKinAtom’: mmdbapi3.c:2313:19: warning: ‘iTemp’ may be used uninitialized [-Wmaybe-uninitialized] 2313 | if (iTemp > TempsKine[iIndex]) return; /* too high */ | ^ mmdbapi3.c:2284:8: note: ‘iTemp’ was declared here 2284 | Int4 iTemp; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbapi4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/mmdbapi1.h:232, from ../include/mmdbapi.h:92, from mmdbapi4.c:106: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi4.c: In function ‘RefreshSurface’: mmdbapi4.c:147:10: warning: unused variable ‘iVal’ [-Wunused-variable] 147 | Int4 iVal = 0; | ^~~~ mmdbapi4.c: In function ‘FreeCoordinatesAsnLists’: mmdbapi4.c:335:41: warning: variable ‘pdcThis’ set but not used [-Wunused-but-set-variable] 335 | DensityCoordinatesPtr pdcThis = NULL; | ^~~~~~~ mmdbapi4.c: In function ‘FreeRedundantAsn’: mmdbapi4.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ mmdbapi4.c:370:11: warning: unused variable ‘pdnmmThis’ [-Wunused-variable] 370 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ mmdbapi4.c:367:22: warning: unused variable ‘pbsmThis’ [-Wunused-variable] 367 | BiostrucModelPtr pbsmThis = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘RefreshModelAsnMem’: mmdbapi4.c:474:41: warning: unused variable ‘iCoordSets’ [-Wunused-variable] 474 | Int4 iCoordSets = 0; | ^~~~~~~~~~ mmdbapi4.c:465:41: warning: unused variable ‘pappThis’ [-Wunused-variable] 465 | AtomPntrsPtr pappThis = NULL; | ^~~~~~~~ mmdbapi4.c:464:41: warning: unused variable ‘pmspThis’ [-Wunused-variable] 464 | ModelSpacePointsPtr pmspThis = NULL; | ^~~~~~~~ mmdbapi4.c:463:41: warning: unused variable ‘pocThis’ [-Wunused-variable] 463 | AtomicOccupanciesPtr pocThis = NULL; | ^~~~~~~ mmdbapi4.c:458:41: warning: unused variable ‘paciThis’ [-Wunused-variable] 458 | AlternateConformationIdsPtr paciThis = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘RebuildChemGraphAsn’: mmdbapi4.c:931:33: warning: unused variable ‘bOK’ [-Wunused-variable] 931 | Boolean bOK = TRUE; | ^~~ mmdbapi4.c: In function ‘WriteASNChemGraphOnly’: mmdbapi4.c:1192:10: warning: unused variable ‘iHash’ [-Wunused-variable] 1192 | Int4 iHash = 0; | ^~~~~ mmdbapi4.c: In function ‘FreeSingleModel’: mmdbapi4.c:1336:11: warning: unused variable ‘pdnml’ [-Wunused-variable] 1336 | PDNML pdnml = NULL; | ^~~~~ mmdbapi4.c:1332:22: warning: unused variable ‘pbsmTemp’ [-Wunused-variable] 1332 | BiostrucModelPtr pbsmTemp = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘WriteAsnModelList’: mmdbapi4.c:1505:14: warning: unused variable ‘paioAIP’ [-Wunused-variable] 1505 | AsnIoPtr paioAIP = NULL; | ^~~~~~~ mmdbapi4.c:1502:11: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1502 | PMLD pmldThis = NULL; | ^~~~~~~~ mmdbapi4.c:1498:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1498 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ mmdbapi4.c:1496:22: warning: unused variable ‘pbsmThis’ [-Wunused-variable] 1496 | BiostrucModelPtr pbsmThis = NULL; | ^~~~~~~~ mmdbapi4.c:1495:17: warning: unused variable ‘pBSThis’ [-Wunused-variable] 1495 | BiostrucPtr pBSThis = NULL; | ^~~~~~~ mmdbapi4.c:1494:13: warning: unused variable ‘bFirst’ [-Wunused-variable] 1494 | Boolean bFirst = TRUE; | ^~~~~~ mmdbapi4.c:1493:10: warning: unused variable ‘iTest’ [-Wunused-variable] 1493 | Int2 iTest = 0; | ^~~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1741:19: warning: unused variable ‘loc1’ [-Wunused-variable] 1741 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi4.c: In function ‘WriteAsnModelList’: mmdbapi4.c:1632:13: warning: ‘bRet’ may be used uninitialized [-Wmaybe-uninitialized] 1632 | return bRet; | ^~~~ mmdbapi4.c:1503:13: note: ‘bRet’ was declared here 1503 | Boolean bRet; | ^~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1828:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 1828 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BiostrucAnnotSetToSeqAnnot’ at mmdbapi4.c:1828:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1872:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 1872 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi4.c:1737:37: note: ‘slavesip’ was declared here 1737 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mmdbentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbentr.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vastsubs.c vastsubs.c: In function ‘LoadSubsetTable’: vastsubs.c:212:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | fscanf(fd, "%d", &ndoms); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:239:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 239 | fscanf(fd, "%d", &nsubs); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:258:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 258 | fscanf(fd, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~ vastsubs.c:287:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 287 | fscanf(fd, "%8c", domid); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:296:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 296 | fscanf(fd, "%d", &n); | ^~~~~~~~~~~~~~~~~~~~ vastsubs.c:302:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 302 | fscanf(fd, "%d %d %d", &subset[j], &grps[j], &ranks[j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:304:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | fscanf(fd, "\n"); | ^~~~~~~~~~~~~~~~ vastsubs.c:277:59: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized] 277 | SubsetArray[strindex + len++] = '\0'; | ~~~^~ vastsubs.c:202:23: note: ‘len’ was declared here 202 | Int4 i, j, n, len, strindex, ndoms, nsubs; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF prunebsc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/prunebsc.h:10, from prunebsc.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prunebsc.c: In function ‘PruneFeatureSet’: prunebsc.c:220:22: warning: variable ‘bsfpDie’ set but not used [-Wunused-but-set-variable] 220 | BiostrucFeaturePtr bsfpDie, bsfp, bsfpnew = NULL; | ^~~~~~~ prunebsc.c: In function ‘PruneModel’: prunebsc.c:272:30: warning: variable ‘mcsDie’ set but not used [-Wunused-but-set-variable] 272 | ModelCoordinateSetPtr mcs, mcsDie, mcsnew = NULL; | ^~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:559:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 559 | if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name)) | ^~~ prunebsc.c:574:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 574 | if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name)) | ^~~ prunebsc.c:663:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 663 | if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name)) | ^~~ prunebsc.c:102:8: warning: ‘mtype’ may be used uninitialized [-Wmaybe-uninitialized] 102 | Int4 mtype; | ^~~~~ In function ‘MakeHetGraphPtr’, inlined from ‘PruneBiostruc’ at prunebsc.c:544:9: prunebsc.c:182:7: warning: ‘mtype’ may be used uninitialized [-Wmaybe-uninitialized] 182 | switch(mtype) | ^~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:173:8: note: ‘mtype’ was declared here 173 | Int4 mtype, molecule_id; | ^~~~~ In file included from ../include/ncbilcl.h:159: In function ‘atoi’, inlined from ‘MakeHetGraphPtr’ at prunebsc.c:189:25, inlined from ‘PruneBiostruc’ at prunebsc.c:544:9: /usr/include/stdlib.h:483:16: warning: ‘mname’ may be used uninitialized [-Wmaybe-uninitialized] 483 | return (int) strtol (__nptr, (char **) NULL, 10); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:174:11: note: ‘mname’ was declared here 174 | CharPtr mname; | ^~~~~ prunebsc.c:562:9: warning: ‘chnid’ may be used uninitialized [-Wmaybe-uninitialized] 562 | if (*chnid == *chain) | ^~~~~~ prunebsc.c:522:11: note: ‘chnid’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~ prunebsc.c:579:8: warning: ‘mol_id’ may be used uninitialized [-Wmaybe-uninitialized] 579 | if (hetnum == mol_id) | ^ prunebsc.c:523:8: note: ‘mol_id’ was declared here 523 | Int4 mol_id, hetnum, molId1, molId2; | ^~~~~~ prunebsc.c:591:26: warning: ‘currenthet’ may be used uninitialized [-Wmaybe-uninitialized] 591 | currenthet->next = het; | ~~~~~~~~~~~~~~~~~^~~~~ prunebsc.c:528:29: note: ‘currenthet’ was declared here 528 | MoleculeGraphPtr bp, het, currenthet, currentbp; | ^~~~~~~~~~ In function ‘atoi’, inlined from ‘PruneBiostruc’ at prunebsc.c:577:14: /usr/include/stdlib.h:483:16: warning: ‘hetid’ may be used uninitialized [-Wmaybe-uninitialized] 483 | return (int) strtol (__nptr, (char **) NULL, 10); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:522:18: note: ‘hetid’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~ prunebsc.c:649:23: warning: ‘pirbnew’ may be used uninitialized [-Wmaybe-uninitialized] 649 | pirbnew->next = pirb; | ~~~~~~~~~~~~~~^~~~~~ prunebsc.c:529:29: note: ‘pirbnew’ was declared here 529 | InterResidueBondPtr pirb, pirbnew; | ^~~~~~~ In file included from ../include/ncbi.h:62: ../include/ncbistr.h:339:25: warning: ‘feature_name’ may be used uninitialized [-Wmaybe-uninitialized] 339 | #define StringICmp Nlm_StringICmp prunebsc.c:522:25: note: ‘feature_name’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objcdd.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objcdd.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objcdd.c: In function ‘CddIdFree’: objcdd.c:53:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 53 | Pointer pnt; | ^~~ objcdd.c: In function ‘CddIdAsnRead’: objcdd.c:85:12: warning: unused variable ‘isError’ [-Wunused-variable] 85 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddIdSetAsnRead’: objcdd.c:248:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 248 | AsnReadFunc func; | ^~~~ objcdd.c:245:12: warning: unused variable ‘av’ [-Wunused-variable] 245 | DataVal av; | ^~ objcdd.c: In function ‘CddAsnRead’: objcdd.c:402:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 402 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddSetAsnRead’: objcdd.c:798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 798 | AsnReadFunc func; | ^~~~ objcdd.c:795:12: warning: unused variable ‘av’ [-Wunused-variable] 795 | DataVal av; | ^~ objcdd.c: In function ‘CddTreeAsnRead’: objcdd.c:935:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 935 | AsnReadFunc func; | ^~~~ objcdd.c:934:12: warning: unused variable ‘isError’ [-Wunused-variable] 934 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddTreeSetAsnRead’: objcdd.c:1147:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1147 | AsnReadFunc func; | ^~~~ objcdd.c:1144:12: warning: unused variable ‘av’ [-Wunused-variable] 1144 | DataVal av; | ^~ objcdd.c: In function ‘CddPrefNodesAsnRead’: objcdd.c:1281:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1281 | AsnReadFunc func; | ^~~~ objcdd.c:1280:12: warning: unused variable ‘isError’ [-Wunused-variable] 1280 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddProjectAsnRead’: objcdd.c:1478:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1478 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddOrgRefAsnRead’: objcdd.c:1668:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1668 | AsnReadFunc func; | ^~~~ objcdd.c:1667:12: warning: unused variable ‘isError’ [-Wunused-variable] 1667 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddOrgRefSetAsnRead’: objcdd.c:1838:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1838 | AsnReadFunc func; | ^~~~ objcdd.c:1835:12: warning: unused variable ‘av’ [-Wunused-variable] 1835 | DataVal av; | ^~ objcdd.c: In function ‘CddPrefNodeDescrFree’: objcdd.c:1932:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1932 | Pointer pnt; | ^~~ objcdd.c: In function ‘CddPrefNodeDescrAsnRead’: objcdd.c:1967:12: warning: unused variable ‘isError’ [-Wunused-variable] 1967 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddPrefNodeDescrSetAsnRead’: objcdd.c:2130:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2130 | AsnReadFunc func; | ^~~~ objcdd.c:2127:12: warning: unused variable ‘av’ [-Wunused-variable] 2127 | DataVal av; | ^~ objcdd.c: In function ‘GlobalIdAsnRead’: objcdd.c:2263:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2263 | AsnReadFunc func; | ^~~~ objcdd.c:2262:12: warning: unused variable ‘isError’ [-Wunused-variable] 2262 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddRepeatAsnRead’: objcdd.c:2450:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2450 | AsnReadFunc func; | ^~~~ objcdd.c:2449:12: warning: unused variable ‘isError’ [-Wunused-variable] 2449 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddBookRefAsnRead’: objcdd.c:2627:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2627 | AsnReadFunc func; | ^~~~ objcdd.c:2626:12: warning: unused variable ‘isError’ [-Wunused-variable] 2626 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddDescrSetAsnRead’: objcdd.c:3183:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3183 | AsnReadFunc func; | ^~~~ objcdd.c:3180:12: warning: unused variable ‘av’ [-Wunused-variable] 3180 | DataVal av; | ^~ objcdd.c: In function ‘MatrixAsnRead’: objcdd.c:3315:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3315 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘TriangleAsnRead’: objcdd.c:3504:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3504 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘UpdateCommentFree’: objcdd.c:3641:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3641 | Pointer pnt; | ^~~ objcdd.c: In function ‘UpdateCommentAsnRead’: objcdd.c:3685:12: warning: unused variable ‘isError’ [-Wunused-variable] 3685 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘UpdateAlignAsnRead’: objcdd.c:3889:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3889 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘RejectIdAsnRead’: objcdd.c:4064:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4064 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘FeatureEvidenceFree’: objcdd.c:4188:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4188 | Pointer pnt; | ^~~ objcdd.c: In function ‘FeatureEvidenceAsnRead’: objcdd.c:4232:12: warning: unused variable ‘isError’ [-Wunused-variable] 4232 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘AlignAnnotAsnRead’: objcdd.c:4437:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4437 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘AlignAnnotSetAsnRead’: objcdd.c:4606:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4606 | AsnReadFunc func; | ^~~~ objcdd.c:4603:12: warning: unused variable ‘av’ [-Wunused-variable] 4603 | DataVal av; | ^~ objcdd.c: In function ‘DomainParentAsnRead’: objcdd.c:4738:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4738 | AsnReadFunc func; | ^~~~ objcdd.c:4737:12: warning: unused variable ‘isError’ [-Wunused-variable] 4737 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘SequenceTreeAsnRead’: objcdd.c:4919:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4919 | AsnReadFunc func; | ^~~~ objcdd.c:4918:12: warning: unused variable ‘isError’ [-Wunused-variable] 4918 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘AlgorithmTypeAsnRead’: objcdd.c:5107:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5107 | AsnReadFunc func; | ^~~~ objcdd.c:5106:12: warning: unused variable ‘isError’ [-Wunused-variable] 5106 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘SeqTreeNodeAsnRead’: objcdd.c:5410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5410 | AsnReadFunc func; | ^~~~ objcdd.c:5409:12: warning: unused variable ‘isError’ [-Wunused-variable] 5409 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘Children_footprintAsnRead’: objcdd.c:5595:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5595 | AsnReadFunc func; | ^~~~ objcdd.c:5594:12: warning: unused variable ‘isError’ [-Wunused-variable] 5594 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘NodeAnnotationAsnRead’: objcdd.c:5887:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5887 | AsnReadFunc func; | ^~~~ objcdd.c:5886:12: warning: unused variable ‘isError’ [-Wunused-variable] 5886 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddViewerRectAsnRead’: objcdd.c:6053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6053 | AsnReadFunc func; | ^~~~ objcdd.c:6052:12: warning: unused variable ‘isError’ [-Wunused-variable] 6052 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddViewerAsnRead’: objcdd.c:6235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6235 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddScriptAsnRead’: objcdd.c:6410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6410 | AsnReadFunc func; | ^~~~ objcdd.c:6409:12: warning: unused variable ‘isError’ [-Wunused-variable] 6409 | Boolean isError = FALSE; | ^~~~~~~ In file included from objcdd.c:6: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from objcdd.c:7: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objcdd.c: In function ‘CddIdAsnRead’: objcdd.c:134:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 134 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:84:10: note: ‘choice’ was declared here 84 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘CddPrefNodeDescrAsnRead’: objcdd.c:2016:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2016 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:1966:10: note: ‘choice’ was declared here 1966 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘CddDescrAsnRead’: objcdd.c:3007:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3007 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:2868:10: note: ‘choice’ was declared here 2868 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘UpdateCommentAsnRead’: objcdd.c:3746:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3746 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:3684:10: note: ‘choice’ was declared here 3684 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘FeatureEvidenceAsnRead’: objcdd.c:4293:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4293 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:4231:10: note: ‘choice’ was declared here 4231 | Uint1 choice; | ^~~~~~ In function ‘Children_childrenAsnRead’, inlined from ‘SeqTreeNodeAsnRead’ at objcdd.c:5467:34: objcdd.c:5561:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5561 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c: In function ‘SeqTreeNodeAsnRead’: objcdd.c:5510:10: note: ‘choice’ was declared here 5510 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cddutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddutil.c:336: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cddutil.c: In function ‘CddGetPmIds’: cddutil.c:649:17: warning: unused variable ‘bRefOpen’ [-Wunused-variable] 649 | Boolean bRefOpen = FALSE; | ^~~~~~~~ cddutil.c: In function ‘CddGetAnnotNames’: cddutil.c:807:19: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 807 | ValNodePtr vnp, vnpHead = NULL; | ^~~ cddutil.c: In function ‘CddCheckForRepeats’: cddutil.c:1034:7: warning: the address of ‘CddHasConsensus’ will always evaluate as ‘true’ [-Waddress] 1034 | if (!CddHasConsensus) return FALSE; | ^ cddutil.c:1013:23: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 1013 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddMSLDenDiagToMSLDenSeg’: cddutil.c:1663:30: warning: variable ‘lasts’ set but not used [-Wunused-but-set-variable] 1663 | Int4 lastm, lasts; | ^~~~~ cddutil.c:1663:23: warning: variable ‘lastm’ set but not used [-Wunused-but-set-variable] 1663 | Int4 lastm, lasts; | ^~~~~ cddutil.c: In function ‘SeqAlignInform’: cddutil.c:1938:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 1938 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddAlignInform’: cddutil.c:2125:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2125 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddPssmInform’: cddutil.c:2248:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2248 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddPosFreqInform’: cddutil.c:2306:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2306 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComputation’: cddutil.c:2368:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 2368 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c:2365:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2365 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddCposComputation’: cddutil.c:2571:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 2571 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c:2568:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2568 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddRetrieveBioseqById’: cddutil.c:3379:15: warning: unused variable ‘retcode’ [-Wunused-variable] 3379 | Int2 retcode = 1; | ^~~~~~~ cddutil.c:3377:15: warning: unused variable ‘uid’ [-Wunused-variable] 3377 | Int4 uid = 0; | ^~~ cddutil.c: In function ‘CddCalculateTriangle’: cddutil.c:3534:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3534 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c:3534:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3534 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c: In function ‘CddCalculateQuerySim’: cddutil.c:3653:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3653 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c:3653:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3653 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c: In function ‘CddConsensus’: cddutil.c:3853:49: warning: variable ‘m_end’ set but not used [-Wunused-but-set-variable] 3853 | Int4 m_last, m_frst, s_insert, m_end; | ^~~~~ cddutil.c: In function ‘CddCposCompPart1’: cddutil.c:4247:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 4247 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddGetNewIndexForThreading’: cddutil.c:4392:14: warning: unused variable ‘Index’ [-Wunused-variable] 4392 | Int4 i, Index=0; | ^~~~~ cddutil.c: In function ‘CddCposComp’: cddutil.c:4474:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 4474 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComp2KBP’: cddutil.c:4838:14: warning: the comparison will always evaluate as ‘true’ for the address of ‘ckptFileName’ will never be NULL [-Waddress] 4838 | if (NULL != ckptFileName) | ^~ cddutil.c:4752:27: note: ‘ckptFileName’ declared here 4752 | Char ckptFileName[PATH_MAX]; | ^~~~~~~~~~~~ cddutil.c:4745:59: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 4745 | ValNodePtr ColumnHead, LetterHead, newRow, RowHead, newLetter; | ^~~~~~~ cddutil.c: In function ‘CddDumpTaxLinks’: cddutil.c:5727:16: warning: unused variable ‘txid’ [-Wunused-variable] 5727 | Int4 txid = 0, gi = 0; | ^~~~ cddutil.c: At top level: cddutil.c:6267:1: warning: "/*" within comment [-Wcomment] 6267 | /*---------------------------------------------------------------------------*/ | In file included from ../include/cddutil.h:205, from cddutil.c:353: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:589:25: warning: ‘CddFindSeqIdInSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 589 | static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location); | ^~~~~~~~~~~~~~~~~~~~ cddutil.c:4661:16: warning: ‘CddtakeMatrixCheckpoint’ defined but not used [-Wunused-function] 4661 | static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from cddutil.c:349: ../include/cdd.h:343:21: warning: ‘amp’ defined but not used [-Wunused-variable] 343 | static AsnModulePtr amp = ampx; | ^~~ ../include/cdd.h:342:19: warning: ‘at’ defined but not used [-Wunused-variable] 342 | static AsnTypePtr at = atx; | ^~ ../include/cdd.h:341:23: warning: ‘avn’ defined but not used [-Wunused-variable] 341 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/cdd.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "cdd.h24"; | ^~~~~~~~~~~ In file included from ../include/ncbi.h:62: cddutil.c: In function ‘CddRegularizeFileName’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen cddutil.c: In function ‘CddCopyMSLDenDiag’: cddutil.c:3015:25: warning: ‘ddpTail’ may be used uninitialized [-Wmaybe-uninitialized] 3015 | ddpTail->next = ddpNew; | ~~~~~~~~~~~~~~^~~~~~~~ cddutil.c:2992:29: note: ‘ddpTail’ was declared here 2992 | DenseDiagPtr ddp, ddpNew, ddpTail; | ^~~~~~~ cddutil.c: In function ‘CddCalculateTriangle’: cddutil.c:3535:7: warning: ‘buffer1’ may be used uninitialized [-Wmaybe-uninitialized] 3535 | if (buffer1) MemFree(buffer1); | ^ cddutil.c:3415:19: note: ‘buffer1’ was declared here 3415 | Uint1Ptr buffer1, buffer2, buffer3; | ^~~~~~~ cddutil.c:3524:22: warning: ‘pscTail’ may be used uninitialized [-Wmaybe-uninitialized] 3524 | pscTail->next = psc; pscTail = psc; psc = NULL; | ~~~~~~~~~~~~~~^~~~~ cddutil.c:3413:38: note: ‘pscTail’ was declared here 3413 | ScorePtr pscHead=NULL, psc, pscTail; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComp2KBP’: cddutil.c:4974:11: warning: ‘pssm’ may be used uninitialized [-Wmaybe-uninitialized] 4974 | return(pssm); | ^ cddutil.c:4764:27: note: ‘pssm’ was declared here 4764 | Seq_Mtf* pssm; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cddposutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddposutil.c:119: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cddposutil.c: In function ‘CddfindThreshSequences’: cddposutil.c:359:15: warning: variable ‘thisId’ set but not used [-Wunused-but-set-variable] 359 | SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */ | ^~~~~~ cddposutil.c: In function ‘CddfindDenseDiagThreshSequences’: cddposutil.c:386:16: warning: variable ‘thisId’ set but not used [-Wunused-but-set-variable] 386 | SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */ | ^~~~~~ cddposutil.c: In function ‘CddposFreqsToMatrix’: cddposutil.c:1038:45: warning: operation on ‘*(*(posSearch->posPrivateMatrix + (sizetype)((long unsigned int)length * 8)) + (sizetype)((long unsigned int)a * 4))’ may be undefined [-Wsequence-point] 1038 | posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN; cddposutil.c: In function ‘CddposDenseDiagDemographics’: cddposutil.c:1094:17: warning: unused variable ‘is_new_id’ [-Wunused-variable] 1094 | Boolean is_new_id = FALSE; | ^~~~~~~~~ cddposutil.c:1093:17: warning: unused variable ‘segIndex’ [-Wunused-variable] 1093 | Int4 segIndex; /*Index for which piece we are at*/ | ^~~~~~~~ cddposutil.c:1092:25: warning: variable ‘startS’ set but not used [-Wunused-but-set-variable] 1092 | Int4 startQ, startS; /*Indices into array of starting positions*/ | ^~~~~~ cddposutil.c:1092:17: warning: variable ‘startQ’ set but not used [-Wunused-but-set-variable] 1092 | Int4 startQ, startS; /*Indices into array of starting positions*/ | ^~~~~~ cddposutil.c:1091:17: warning: unused variable ‘curId’ [-Wunused-variable] 1091 | SeqIdPtr curId; /*Used to compare seq. coming from different SeqAligns*/ | ^~~~~ cddposutil.c: In function ‘CddSetUpSearchInternalByLoc’: cddposutil.c:1246:53: warning: unused variable ‘last_length_adjustment’ [-Wunused-variable] 1246 | index, length, length_adjustment=0, last_length_adjustment, min_query_length; | ^~~~~~~~~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddSetUpSearchWithReadDb’: cddposutil.c:2040:55: warning: variable ‘final_db_seq’ set but not used [-Wunused-but-set-variable] 2040 | Int4 final_virtual_db_seq=0, final_db_seq=0; | ^~~~~~~~~~~~ cddposutil.c:2006:44: warning: unused variable ‘virtual_oid_bit’ [-Wunused-variable] 2006 | Uint4 oid_bit, virtual_oid_bit; | ^~~~~~~~~~~~~~~ cddposutil.c:2006:35: warning: unused variable ‘oid_bit’ [-Wunused-variable] 2006 | Uint4 oid_bit, virtual_oid_bit; | ^~~~~~~ cddposutil.c:2005:47: warning: unused variable ‘virtual_mask_index’ [-Wunused-variable] 2005 | Int4 mask_index, virtual_mask_index; | ^~~~~~~~~~~~~~~~~~ cddposutil.c:2005:35: warning: unused variable ‘mask_index’ [-Wunused-variable] 2005 | Int4 mask_index, virtual_mask_index; | ^~~~~~~~~~ cddposutil.c:2004:31: warning: unused variable ‘alias_oidlist’ [-Wunused-variable] 2004 | OIDListPtr alias_oidlist; | ^~~~~~~~~~~~~ cddposutil.c:2003:33: warning: unused variable ‘use_private_gilist’ [-Wunused-variable] 2003 | Boolean use_private_gilist = FALSE; | ^~~~~~~~~~~~~~~~~~ cddposutil.c:2000:23: warning: unused variable ‘vnp’ [-Wunused-variable] 2000 | ValNodePtr vnp; | ^~~ cddposutil.c: In function ‘CddposReadAlignment’: cddposutil.c:2226:16: warning: variable ‘alignPos’ set but not used [-Wunused-but-set-variable] 2226 | Int4 alignPos, queryOffset, subjectOffset, matchLength; | ^~~~~~~~ In file included from ../include/cddutil.h:205, from cddposutil.c:131: ../include/objcdd.h: At top level: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:507:27: warning: ‘CddReadBlastOptions’ declared ‘static’ but never defined [-Wunused-function] 507 | static PGPBlastOptionsPtr CddReadBlastOptions(BioseqPtr bsp, Int4 iPseudo, CharPtr matrix_name); | ^~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:512:13: warning: ‘BlastKarlinBlkCopy’ declared ‘static’ but never defined [-Wunused-function] 512 | static void BlastKarlinBlkCopy(BLAST_KarlinBlkPtr kbp_in,BLAST_KarlinBlkPtr kbp_out); | ^~~~~~~~~~~~~~~~~~ ../include/cddutil.h:516:13: warning: ‘CddputMatrixKbp’ declared ‘static’ but never defined [-Wunused-function] 516 | static void CddputMatrixKbp(FILE *checkFile, BLAST_KarlinBlkPtr kbp, | ^~~~~~~~~~~~~~~ ../include/cddutil.h:518:13: warning: ‘CddputMatrixMatrix’ declared ‘static’ but never defined [-Wunused-function] 518 | static void CddputMatrixMatrix(FILE *checkFile, | ^~~~~~~~~~~~~~~~~~ ../include/cddutil.h:522:16: warning: ‘CddtakeMatrixCheckpoint’ declared ‘static’ but never defined [-Wunused-function] 522 | static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch, | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:589:25: warning: ‘CddFindSeqIdInSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 589 | static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location); | ^~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:591:25: warning: ‘CddRelocateSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 591 | static void CddRelocateSeqLoc(SeqLocPtr location, SeqIdPtr sip, Int4 *ali); | ^~~~~~~~~~~~~~~~~ ../include/cddutil.h:592:25: warning: ‘CddSeqLocInExpAlign’ declared ‘static’ but never defined [-Wunused-function] 592 | static Int4 CddSeqLocInExpAlign(SeqLocPtr location, CddExpAlignPtr eap); | ^~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:593:25: warning: ‘CddFindSeqIdInAlignAnnot’ declared ‘static’ but never defined [-Wunused-function] 593 | static SeqIdPtr CddFindSeqIdInAlignAnnot(AlignAnnotPtr oldannot); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:623:24: warning: ‘HitYet’ declared ‘static’ but never defined [-Wunused-function] 623 | static Boolean HitYet(Int4Ptr retlist, Int4 index, Int4 i); | ^~~~~~ ../include/cddutil.h:649:16: warning: ‘CddFixForXML’ declared ‘static’ but never defined [-Wunused-function] 649 | static CharPtr CddFixForXML(CharPtr pc); | ^~~~~~~~~~~~ cddposutil.c:971:13: warning: ‘CddfreePosFreqs’ defined but not used [-Wunused-function] 971 | static void CddfreePosFreqs(Nlm_FloatHi ** posFreqs, Int4 length) | ^~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddposComputeSequenceWeights’: cddposutil.c:829:10: warning: ‘Sigma’ may be used uninitialized [-Wmaybe-uninitialized] 829 | if (Sigma > 0) { | ^ cddposutil.c:747:16: note: ‘Sigma’ was declared here 747 | Nlm_FloatHi Sigma; /*Number of different characters occurring in matches | ^~~~~ cddposutil.c:840:35: warning: ‘intervalSigma’ may be used uninitialized [-Wmaybe-uninitialized] 840 | posSearch->posSigma[qplace] = intervalSigma; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ cddposutil.c:749:16: note: ‘intervalSigma’ was declared here 749 | Nlm_FloatHi intervalSigma; /*Same as Sigma but includes identical columns*/ | ^~~~~~~~~~~~~ cddposutil.c: In function ‘CddposDemographics’: cddposutil.c:1199:24: warning: ‘retrievalOffset’ may be used uninitialized [-Wmaybe-uninitialized] 1199 | subjectOffset = curSegs->starts[startS] - retrievalOffset; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cddposutil.c:1154:44: note: ‘retrievalOffset’ was declared here 1154 | Int4 queryOffset, subjectOffset, retrievalOffset; /*offsets needed to make a match align*/ | ^~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddSetUpSearchWithReadDb’: cddposutil.c:2041:86: warning: ‘total_virtual_mask’ may be used uninitialized [-Wmaybe-uninitialized] 2041 | Int4 mask, oid, virtual_oid, maskindex, virtual_mask_index, total_virtual_mask, base; | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF objmime.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmime.c:76: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmime.c: In function ‘NcbiMimeAsn1Free’: objmime.c:126:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 126 | Pointer pnt; | ^~~ objmime.c: In function ‘NcbiMimeAsn1AsnRead’: objmime.c:173:12: warning: unused variable ‘isError’ [-Wunused-variable] 173 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘Data_dataFree’: objmime.c:382:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 382 | Pointer pnt; | ^~~ objmime.c: In function ‘EntrezGeneralAsnRead’: objmime.c:428:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 428 | AsnReadFunc func; | ^~~~ objmime.c:427:12: warning: unused variable ‘isError’ [-Wunused-variable] 427 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘Data_dataAsnRead’: objmime.c:522:12: warning: unused variable ‘isError’ [-Wunused-variable] 522 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘BiostrucAlignAsnRead’: objmime.c:801:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 801 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucAlignSeqAsnRead’: objmime.c:1027:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1027 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucSeqAsnRead’: objmime.c:1220:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1220 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucSeqsAsnRead’: objmime.c:1415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1415 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘SeqAlignData_seq_align_dataFree’: objmime.c:1613:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1613 | Pointer pnt; | ^~~ objmime.c: In function ‘BiostrucSeqsAlignsCddAsnRead’: objmime.c:1647:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1647 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘SeqAlignData_seq_align_dataAsnRead’: objmime.c:1734:12: warning: unused variable ‘isError’ [-Wunused-variable] 1734 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘BundleSeqsAlignsAsnRead’: objmime.c:1973:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1973 | AsnReadFunc func; | ^~~~ In file included from ../include/mapmime.h:4, from objmime.c:81: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/mapmime.h:6: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ objmime.c: In function ‘NcbiMimeAsn1AsnRead’: objmime.c:235:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 235 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c:172:10: note: ‘choice’ was declared here 172 | Uint1 choice; | ^~~~~~ In function ‘Data_dataAsnRead’, inlined from ‘EntrezGeneralAsnRead’ at objmime.c:471:26: objmime.c:584:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 584 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c: In function ‘EntrezGeneralAsnRead’: objmime.c:521:10: note: ‘choice’ was declared here 521 | Uint1 choice; | ^~~~~~ In function ‘SeqAlignData_seq_align_dataAsnRead’, inlined from ‘BiostrucSeqsAlignsCddAsnRead’ at objmime.c:1683:44: objmime.c:1780:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1780 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c: In function ‘BiostrucSeqsAlignsCddAsnRead’: objmime.c:1733:10: note: ‘choice’ was declared here 1733 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF strucapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from strucapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdalgs.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdatd.c thrdatd.c: In function ‘atd’: thrdatd.c:859:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 859 | for(i=0;ial[i]); printf("sai->al\n"); | ^~~ thrdatd.c:859:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 859 | for(i=0;ial[i]); printf("sai->al\n"); | ^~~~~~ thrdatd.c:860:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 860 | for(i=0;inmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n"); | ^~~ thrdatd.c:860:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 860 | for(i=0;inmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n"); | ^~~~~~ thrdatd.c:862:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 862 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~ thrdatd.c:862:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 862 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~~~~ thrdatd.c:863:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 863 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~ thrdatd.c:863:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 863 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~~~~ thrdatd.c:864:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 864 | for(i=0;inlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n"); | ^~~ thrdatd.c:864:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 864 | for(i=0;inlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n"); | ^~~~~~ thrdatd.c:865:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 865 | for(i=0;inmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n"); | ^~~ thrdatd.c:865:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 865 | for(i=0;inmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n"); | ^~~~~~ thrdatd.c:1014:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1014 | for(k=0;kal[k]); printf("sai->al\n"); | ^~~ thrdatd.c:1014:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1014 | for(k=0;kal[k]); printf("sai->al\n"); | ^~~~~~ thrdatd.c:1015:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1015 | for(k=0;ksq[k]); printf("sai->sq\n"); | ^~~ thrdatd.c:1015:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1015 | for(k=0;ksq[k]); printf("sai->sq\n"); | ^~~~~~ thrdatd.c:1017:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1017 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~ thrdatd.c:1017:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1017 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~~~~ thrdatd.c:1018:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1018 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~ thrdatd.c:1018:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1018 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~~~~ thrdatd.c:1019:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1019 | for(i=0;ilp[i]); printf("sli->lp\n"); | ^~~ thrdatd.c:1019:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1019 | for(i=0;ilp[i]); printf("sli->lp\n"); | ^~~~~~ thrdatd.c:1020:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1020 | for(i=0;icr[i]); printf("sli->cr\n"); | ^~~ thrdatd.c:1020:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1020 | for(i=0;icr[i]); printf("sli->cr\n"); | ^~~~~~ thrdatd.c:1244:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1244 | for(i=0;igss[i]); free(spe->gss); | ^~~ thrdatd.c:1244:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1244 | for(i=0;igss[i]); free(spe->gss); | ^~~~ thrdatd.c:1251:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1251 | for(i=0; inrr[i]); free(spn->nrr); | ^~~ thrdatd.c:1251:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1251 | for(i=0; inrr[i]); free(spn->nrr); | ^~~~ thrdatd.c:1255:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1255 | for(i=0; inrp[i]); free(spn->nrp); | ^~~ thrdatd.c:1255:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1255 | for(i=0; inrp[i]); free(spn->nrp); | ^~~~ thrdatd.c:1259:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1259 | for(i=0; inrf[i]); free(spn->nrf); | ^~~ thrdatd.c:1259:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1259 | for(i=0; inrf[i]); free(spn->nrf); | ^~~~ thrdatd.c:1260:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1260 | for(i=0; ifrf[i]); free(spn->frf); | ^~~ thrdatd.c:1260:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1260 | for(i=0; ifrf[i]); free(spn->frf); | ^~~~ thrdatd.c:201:8: warning: variable ‘hh’ set but not used [-Wunused-but-set-variable] 201 | float hh; | ^~ thrdatd.c:198:9: warning: variable ‘rf’ set but not used [-Wunused-but-set-variable] 198 | int rf; /* Reference position for a core element */ | ^~ thrdatd.c:188:17: warning: unused variable ‘m’ [-Wunused-variable] 188 | int i,j,k,l,m,n; /* Counters */ | ^ thrdatd.c:188:15: warning: unused variable ‘l’ [-Wunused-variable] 188 | int i,j,k,l,m,n; /* Counters */ | ^ thrdatd.c:171:9: warning: variable ‘nrp’ set but not used [-Wunused-but-set-variable] 171 | int nrp; /* Number of residue-peptide contacts in motif */ | ^~~ thrdatd.c:170:9: warning: variable ‘nrr’ set but not used [-Wunused-but-set-variable] 170 | int nrr; /* Number of residue-residue contacts in motif */ | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdbwfi.c thrdbwfi.c: In function ‘bwfi’: thrdbwfi.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] 114 | } | ^ thrdbwfi.c:89:30: warning: ‘nz’ may be used uninitialized [-Wmaybe-uninitialized] 89 | cw=0.; ct=ttb->mx; for(i=0; i<=nz; i++) { | ~^~~~ thrdbwfi.c:63:9: note: ‘nz’ was declared here 63 | int nz; /* Number of threads with non-zero Boltzmann weight */ | ^~ thrdbwfi.c:64:9: warning: ‘nt’ may be used uninitialized [-Wmaybe-uninitialized] 64 | int nt; /* Number of threads within specified ensemble cutoff */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcpal.c thrdcpal.c: In function ‘cpal’: thrdcpal.c:210:1: warning: control reaches end of non-void function [-Wreturn-type] 210 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcpll.c thrdcpll.c: In function ‘cpll’: thrdcpll.c:74:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 74 | int nrt; /* Number of residue types */ | ^~~ thrdcpll.c:229:1: warning: control reaches end of non-void function [-Wreturn-type] 229 | } | ^ thrdcpll.c:220:29: warning: ‘r2’ may be used uninitialized [-Wmaybe-uninitialized] 220 | cl->rf.t2[k]=r2; | ~~~~~~~~~~~~^~~ thrdcpll.c:78:12: note: ‘r2’ was declared here 78 | int r1,r2; /* Motif residue positions */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcprl.c thrdcprl.c: In function ‘cprl’: thrdcprl.c:261:1: warning: control reaches end of non-void function [-Wreturn-type] 261 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdcxei.c thrdcxei.c: In function ‘cxei’: thrdcxei.c:94:15: warning: variable ‘ms’ set but not used [-Wunused-but-set-variable] 94 | int ntot, ms; | ^~ thrdcxei.c:205:1: warning: control reaches end of non-void function [-Wreturn-type] 205 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrddgri.c thrddgri.c: In function ‘g’: thrddgri.c:72:9: warning: variable ‘s0’ set but not used [-Wunused-but-set-variable] 72 | int s0; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdrsmp.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsal0.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsalr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsalu.c thrdsalu.c: In function ‘salu’: thrdsalu.c:83:1: warning: control reaches end of non-void function [-Wreturn-type] 83 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdsgoi.c thrdsgoi.c: In function ‘sgoi’: thrdsgoi.c:98:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 98 | for(i=0; i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslo0.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslor.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdslou.c thrdslou.c: In function ‘slou’: thrdslou.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] 114 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspci.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspea.c thrdspea.c: In function ‘spea’: thrdspea.c:91:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 91 | int nrt; /* Number of residue types in potential */ | ^~~ thrdspea.c:189:1: warning: control reaches end of non-void function [-Wreturn-type] 189 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspel.c thrdspel.c: In function ‘spel’: thrdspel.c:88:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 88 | int nrt; /* Number of residue types in potential */ | ^~~ thrdspel.c:188:1: warning: control reaches end of non-void function [-Wreturn-type] 188 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdspni.c thrdspni.c: In function ‘spni’: thrdspni.c:238:1: warning: control reaches end of non-void function [-Wreturn-type] 238 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdttb0.c thrdttb0.c: In function ‘ttb0’: thrdttb0.c:75:1: warning: control reaches end of non-void function [-Wreturn-type] 75 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdttbi.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF thrdzsc.c thrdzsc.c: In function ‘zsc’: thrdzsc.c:107:11: warning: unused variable ‘gs’ [-Wunused-variable] 107 | int g,gs; | ^~ thrdzsc.c:102:20: warning: unused variable ‘zsc’ [-Wunused-variable] 102 | float tg,tgp,tgm,zsc; /* Energy of shuffled sequence */ | ^~~ thrdzsc.c:95:9: warning: unused variable ‘ps’ [-Wunused-variable] 95 | int ps,ms,cs, | ^~ thrdzsc.c:80:9: warning: unused variable ‘temp’ [-Wunused-variable] 80 | int temp; /* Random index of the query sequence */ | ^~~~ thrdzsc.c:79:9: warning: unused variable ‘kk’ [-Wunused-variable] 79 | kk,itr,ii,jj; /* Counters */ | ^~ thrdzsc.c:369:1: warning: control reaches end of non-void function [-Wreturn-type] 369 | } | ^ thrdzsc.c:357:46: warning: ‘tg_max’ may be used uninitialized [-Wmaybe-uninitialized] 357 | ttb->zsc[i_max]=ScalingFactor*(tg_max-avg)/disp; | ~~~~~~~^~~~~ thrdzsc.c:103:9: note: ‘tg_max’ was declared here 103 | float tg_max; /* Energy of a given thread */ | ^~~~~~ rm -f libncbimmdb.a ar cru libncbimmdb.a corematx.o dvncode.o objmmdb1.o objmmdb2.o objmmdb3.o objcn3d.o mmdbapi.o mmdbapi1.o mmdbapi2.o mmdbapi3.o mmdbapi4.o mmdbentr.o vastsubs.o prunebsc.o objcdd.o cddutil.o cddposutil.o objmime.o strucapi.o thrdalgs.o thrdatd.o thrdbwfi.o thrdcpal.o thrdcpll.o thrdcprl.o thrdcxei.o thrddgri.o thrdrsmp.o thrdsal0.o thrdsalr.o thrdsalu.o thrdsgoi.o thrdslo0.o thrdslor.o thrdslou.o thrdspci.o thrdspea.o thrdspel.o thrdspni.o thrdttb0.o thrdttbi.o thrdzsc.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbimmdb.a ../lib ranlib ../lib/libncbimmdb.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF csim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from csim.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ csim.c: In function ‘set_pam_200’: csim.c:163:29: warning: missing braces around initializer [-Wmissing-braces] 163 | static Int2 wgts[23][23] = { /* the PAM200 matrix */ | ^ 164 | 165 | 2,-2, 0, 0,-2,-1, 0, 1,-1,-1,-2,-1,-1,-3, 1, 1, 1,-5,-3, 0, 1, 1, 0, | { } 166 | -2, 5, 0,-1,-3, 1,-1,-3, 1,-2,-2, 2, 0,-3, 0, 0,-1, 1,-4,-2, 0, 1, 0, | { } 167 | 0, 0, 2, 2,-3, 0, 1, 0, 1,-1,-2, 1,-2,-2, 0, 1, 0,-4,-1,-2, 3, 2, 0, | { } 168 | 0,-1, 2, 3,-4, 1, 3, 0, 0,-2,-3, 0,-2,-4,-1, 0, 0,-6,-3,-2, 4, 3, 0, | { } 169 | -2,-3,-3,-4, 8,-4,-4,-3,-3,-2,-5,-4,-4,-4,-2, 0,-2,-6, 0,-2,-3,-3, 0, | { } 170 | -1, 1, 0, 1,-4, 4, 2,-1, 2,-2,-1, 0,-1,-4, 0,-1,-1,-4,-3,-2, 2, 4, 0, | { } 171 | 0,-1, 1, 3,-4, 2, 3, 0, 0,-2,-3, 0,-2,-4, 0, 0, 0,-6,-3,-2, 3, 4, 0, | { } 172 | 1,-3, 0, 0,-3,-1, 0, 4,-2,-2,-3,-2,-3,-3,-1, 1, 0,-5,-4,-1, 1, 0, 0, | { } 173 | -1, 1, 1, 0,-3, 2, 0,-2, 5,-2,-2, 0,-2,-1, 0,-1,-1,-3, 0,-2, 2, 2, 0, | { } 174 | -1,-2,-1,-2,-2,-2,-2,-2,-2, 4, 2,-1, 2, 1,-2,-1, 0,-5,-1, 3,-1,-1, 0, | { } 175 | -2,-2,-2,-3,-5,-1,-3,-3,-2, 2, 4,-2, 3, 1,-2,-2,-1,-4,-1, 1,-2,-1, 0, | { } 176 | -1, 2, 1, 0,-4, 0, 0,-2, 0,-1,-2, 4, 1,-4,-1, 0, 0,-3,-4,-2, 1, 1, 0, | { } 177 | -1, 0,-2,-2,-4,-1,-2,-3,-2, 2, 3, 1, 5, 0,-2,-1, 0,-4,-2, 1,-1, 0, 0, | { } 178 | -3,-3,-2,-4,-4,-4,-4,-3,-1, 1, 1,-4, 0, 7,-4,-2,-2, 0, 5,-1,-2,-3, 0, | { } 179 | 1, 0, 0,-1,-2, 0, 0,-1, 0,-2,-2,-1,-2,-4, 5, 1, 0,-5,-4,-1, 0, 1, 0, | { } 180 | 1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-2, 0,-1,-2, 1, 2, 1,-2,-2,-1, 1, 1, 0, | { } 181 | 1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-1, 0, 0,-2, 0, 1, 3,-4,-2, 0, 1, 0, 0, | { } 182 | -5, 1,-4,-6,-6,-4,-6,-5,-3,-5,-4,-3,-4, 0,-5,-2,-4,12, 0,-6,-3,-4, 0, | { } 183 | -3,-4,-1,-3, 0,-3,-3,-4, 0,-1,-1,-4,-2, 5,-4,-2,-2, 0, 7,-2,-1,-2, 0, | { } 184 | 0,-2,-2,-2,-2,-2,-2,-1,-2, 3, 1,-2, 1,-1,-1,-1, 0,-6,-2, 4,-1,-1, 0, | { } 185 | 1, 0, 3, 4,-3, 2, 3, 1, 2,-1,-2, 1,-1,-2, 0, 1, 1,-3,-1,-1, 4, 4, 0, | { } 186 | 1, 1, 2, 3,-3, 4, 4, 0, 2,-1,-1, 1, 0,-3, 1, 1, 0,-4,-2,-1, 4, 5, 0, | { } 187 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, | { 188 | }; | } csim.c:196:16: warning: array subscript has type ‘char’ [-Wchar-subscripts] 196 | V[achars[i]][achars[j]]=10*(wgts[i][j]); | ~~~~~~^~~ csim.c:196:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 196 | V[achars[i]][achars[j]]=10*(wgts[i][j]); | ~~~~~~^~~ csim.c: In function ‘set_pam_file’: csim.c:228:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 228 | V[alph[i]][alph[j]]=(Int2)(10*weight); | ~~~~^~~ csim.c:228:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 228 | V[alph[i]][alph[j]]=(Int2)(10*weight); | ~~~~^~~ csim.c: In function ‘big_pass’: csim.c:668:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 668 | va = v[A[i]]; | ~^~~ csim.c:692:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 692 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c: In function ‘diff1’: csim.c:799:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 799 | va = v[A[1]]; | ~^~~ csim.c:805:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 805 | { c = va[B[j]] - ( GAP(j-1) + GAP(N-j) ); | ~^~~ csim.c:849:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 849 | va = v[A[i]]; | ~^~~ csim.c:853:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 853 | DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:853:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 853 | DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:874:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 874 | va = v[A[i+1]]; | ~^~~~~ csim.c:878:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]]) | ~^~~~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:878:60: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]]) | ~^~~~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:893:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 893 | if (c > midc || CC[j] != DD[j] && RR[j] == SS[j]) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ csim.c: In function ‘locate’: csim.c:974:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 974 | va = v[A[i]]; | ~^~~ csim.c:991:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 991 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1030:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1030 | va = v[A[(plist->m1)]]; | ~^~~~~~~~~~~~~ csim.c:1043:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1043 | DIAG((plist->m1), j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1061:45: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1061 | if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1062:64: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1062 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1071:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1071 | if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1072:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1072 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1084:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1084 | va = v[B[(plist->n1)]]; | ~^~~~~~~~~~~~~ csim.c:1110:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1110 | DIAG(i, (plist->n1), c, p+va[A[i]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1128:45: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1128 | if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1129:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1129 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1138:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1138 | if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1139:61: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1139 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1144:29: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1144 | if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) ) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ csim.c: In function ‘small_pass’: csim.c:1186:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1186 | va = v[A[i]]; | ~^~~ csim.c:1212:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1212 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c: In function ‘display’: csim.c:1360:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1360 | if (i < M || j < N) | ^ csim.c: In function ‘set_pam_file’: csim.c:227:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 227 | fscanf(fp, "%f", &weight); /**get the matrix**/ | ^~~~~~~~~~~~~~~~~~~~~~~~~ csim.c: At top level: csim.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: csim.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF db_slist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/list.h:56, from db_slist.c:97: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ db_slist.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from dust.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dust.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: dust.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_dust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from blast_dust.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_dust.c:39:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 39 | static char const rcsid[] = | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF falign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from falign.c:92: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ falign.c: In function ‘fbld_table’: falign.c:490:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 490 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:494:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 494 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘bbld_table’: falign.c:517:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 517 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:521:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 521 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rcbld_table’: falign.c:544:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 544 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:548:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 548 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘ex_table’: falign.c:567:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 567 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘free_all’: falign.c:668:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 668 | if (df = cdiag_prev[l]) { | ^~ falign.c: In function ‘scan’: falign.c:688:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 688 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:694:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 694 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c:710:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 710 | if (df = diag_prev[len1+len2-1-pos]) { | ^~ falign.c:719:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 719 | if (df=diag_prev[l]) { | ^~ falign.c: In function ‘fscan’: falign.c:763:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 763 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:769:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 769 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘bscan’: falign.c:794:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 794 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:800:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 800 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rfscan’: falign.c:870:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 870 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:876:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 876 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c:881:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 881 | if (df = diag_prev[len1+se2-pos]) { | ^~ falign.c:889:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 889 | if (df = diag_prev[len1+se2-pos]) { | ^~ falign.c: In function ‘trcscan’: falign.c:1476:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1476 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:1482:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1482 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rclocal’: falign.c:1547:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1547 | if (pf = diag_prev[ocur_diag]) { | ^~ falign.c: In function ‘enterS’: falign.c:1897:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1897 | if (s = findS(f->bgf)) { | ^ falign.c: In function ‘local’: falign.c:1958:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1958 | if (pf = diag_prev[cur_diag]) { | ^~ falign.c: In function ‘align’: falign.c:1999:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1999 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: In function ‘calign’: falign.c:2054:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2054 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: In function ‘malign’: falign.c:2109:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2109 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: At top level: falign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: falign.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF g_any.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from g_any.c:89: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ g_any.c: In function ‘k_align’: g_any.c:212:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 212 | va = vv[A[i+1]]; | ~^~~~~ g_any.c:229:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 229 | if (j < J2) c = s + va[B[j+1]]; | ~^~~~~ g_any.c:319:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 319 | b2 = PP[t1][b1]; | ^ g_any.c:322:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 322 | t2 = PT[t1][b1]; | ^ g_any.c: In function ‘z_ALIGN’: g_any.c:367:14: warning: variable ‘check_score’ set but not used [-Wunused-but-set-variable] 367 | Int4 check_score; | ^~~~~~~~~~~ g_any.c: In function ‘CHECK_SCORE’: g_any.c:492:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 492 | score = vv[A[++i]][B[++j]] + score; | ~^~~~~ g_any.c:492:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] 492 | score = vv[A[++i]][B[++j]] + score; | ~^~~~~ g_any.c: At top level: g_any.c:428:35: warning: ‘CLINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:428:24: warning: ‘BLINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:428:13: warning: ‘ALINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sim2.c sim2.c: In function ‘SIM2’: sim2.c:19:23: warning: unused variable ‘compB’ [-Wunused-variable] 19 | CharPtr A, B, compB = NULL; | ^~~~~ sim2.c:17:33: warning: unused variable ‘sapC’ [-Wunused-variable] 17 | SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC; | ^~~~ sim2.c: At top level: sim2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim2.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sim3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from sim3.c:28: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sim3.c: In function ‘locate’: sim3.c:103:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 103 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:105:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 105 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:113:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 113 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:115:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 115 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:129:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 129 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:133:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 133 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:152:60: warning: array subscript has type ‘char’ [-Wchar-subscripts] 152 | ecode1 = ((ecode1 & mask) << 2) + encoding[*q++]; | ^~~~ sim3.c:155:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 155 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c: At top level: sim3.c:1067:16: warning: ‘is_end_seg’ defined but not used [-Wunused-function] 1067 | static Boolean is_end_seg(EditScriptPtr curr, EditScriptPtr head) | ^~~~~~~~~~ sim3.c:1056:13: warning: ‘get_current_pos’ defined but not used [-Wunused-function] 1056 | static Int4 get_current_pos(Int4Ptr pos, Int4 length) | ^~~~~~~~~~~~~~~ sim3.c:1048:13: warning: ‘get_start_pos’ defined but not used [-Wunused-function] 1048 | static Int4 get_start_pos(SeqLocPtr slp) | ^~~~~~~~~~~~~ sim3.c:806:13: warning: ‘Print_Script’ defined but not used [-Wunused-function] 806 | static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, CharPtr A, CharPtr B) | ^~~~~~~~~~~~ sim3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim3.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sim3.c: In function ‘locate’: sim3.c:229:13: warning: ‘paired_fj’ may be used uninitialized [-Wmaybe-uninitialized] 229 | *j1 = paired_fj; | ~~~~^~~~~~~~~~~ sim3.c:79:14: note: ‘paired_fj’ was declared here 79 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim3.c:230:24: warning: ‘paired_bj’ may be used uninitialized [-Wmaybe-uninitialized] 230 | *j2 = paired_bj+1; | ~~~~~~~~~^~ sim3.c:79:25: note: ‘paired_bj’ was declared here 79 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim3.c: In function ‘path’: sim3.c:720:12: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 720 | if(head2) | ^~~~~ sim3.c:481:37: note: ‘head2’ declared here 481 | EditScriptPtr head1, tail1, head2, tail2; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sim4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from sim4.c:18: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sim4.c: In function ‘sim4x’: sim4.c:630:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 630 | while(i1 = sgp->Blist[i].next) { | ^~ sim4.c: In function ‘greedy’: sim4.c:1770:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1770 | if (row == 0 && col == 0) | ^ sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1794 | if (row == 0) | ^ sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1838 | if (col == 0) | ^ sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1962 | if (row == m && col == n) | ^ sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1991 | if (row == m) | ^ sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2037 | if (col == n) | ^ sim4.c: In function ‘DISPLAY’: sim4.c:2625:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2625 | if (a >= ALINE+50 || i >= M && j >= N) | ~~~~~~~^~~~~~~~~ sim4.c: At top level: sim4.c:2592:13: warning: ‘DISPLAY’ defined but not used [-Wunused-function] 2592 | static void DISPLAY(Int1 A[], Int1 B[], Int4 M, Int4 N, Int4 S[], Int4 AP, Int4 BP) | ^~~~~~~ sim4.c:2563:13: warning: ‘S2A’ defined but not used [-Wunused-function] 2563 | static void S2A(EditScriptPtr head, Int4Ptr S) | ^~~ sim4.c:2499:13: warning: ‘Print_Script’ defined but not used [-Wunused-function] 2499 | static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, data_t *data) | ^~~~~~~~~~~~ sim4.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim4.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sim4.c: In function ‘path’: sim4.c:2467:7: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 2467 | if (head2) *tail = tail2; | ^~~~~ sim4.c:2262:31: note: ‘head2’ declared here 2262 | EditScriptPtr head1, tail1, head2, tail2; | ^~~~~ sim4.c: In function ‘locate’: sim4.c:2918:7: warning: ‘paired_fj’ may be used uninitialized [-Wmaybe-uninitialized] 2918 | *j1 = paired_fj; | ~~~~^~~~~~~~~~~ sim4.c:2765:8: note: ‘paired_fj’ was declared here 2765 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim4.c:2919:19: warning: ‘paired_bj’ may be used uninitialized [-Wmaybe-uninitialized] 2919 | *j2 = paired_bj + 1; | ~~~~~~~~~~^~~ sim4.c:2765:19: note: ‘paired_bj’ was declared here 2765 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ In function ‘greedy’, inlined from ‘sim4x’ at sim4.c:703:12: sim4.c:2112:22: warning: ‘back’ may be used uninitialized [-Wmaybe-uninitialized] 2112 | if (m-min_row[back]>=max_row[forth]) { | ^ sim4.c: In function ‘sim4x’: sim4.c:1609:12: note: ‘back’ was declared here 1609 | Int4 back, forth; /* backward and forward limits at exit */ | ^~~~ In function ‘greedy’, inlined from ‘sim4x’ at sim4.c:703:12: sim4.c:2112:37: warning: ‘forth’ may be used uninitialized [-Wmaybe-uninitialized] 2112 | if (m-min_row[back]>=max_row[forth]) { | ^ sim4.c: In function ‘sim4x’: sim4.c:1609:18: note: ‘forth’ was declared here 1609 | Int4 back, forth; /* backward and forward limits at exit */ | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF simutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from simutil.c:103: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ simutil.c: In function ‘make_align’: simutil.c:495:9: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 495 | Uint1 strand; | ^~~~~~ simutil.c: At top level: simutil.c:848:16: warning: ‘is_alu_seq’ defined but not used [-Wunused-function] 848 | static Boolean is_alu_seq(CharPtr name) | ^~~~~~~~~~ simutil.c:814:16: warning: ‘re_cal_score’ defined but not used [-Wunused-function] 814 | static FloatHi re_cal_score(RecordEndsPtr o_rep, RecordEndsPtr n_rep) | ^~~~~~~~~~~~ simutil.c:344:17: warning: ‘convert’ defined but not used [-Wunused-function] 344 | static ScorePtr convert(Int4Ptr x, Int4Ptr y, Int4Ptr start, Int4Ptr length, Int4 n, SeqLocPtr locx, SeqLocPtr locy, Int2Ptr numseg, FloatHiPtr SegScores) | ^~~~~~~ simutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: simutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF slist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/list.h:56, from slist.c:101: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ slist.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF sec.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from sec.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sec.c: In function ‘Region’: sec.c:268:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 268 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:268:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 268 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:292:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 292 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:292:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 292 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:321:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 321 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:321:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 321 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:345:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 345 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:345:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 345 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:428:68: warning: array subscript has type ‘char’ [-Wchar-subscripts] 428 | diag_score = diag_score + V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:428:77: warning: array subscript has type ‘char’ [-Wchar-subscripts] 428 | diag_score = diag_score + V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c: At top level: sec.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sec.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sec.c: In function ‘Region’: sec.c:504:39: warning: ‘LB’ may be used uninitialized [-Wmaybe-uninitialized] 504 | LB[i] = old_l; | ~~~~~~^~~~~~~ sec.c:158:17: note: ‘LB’ was declared here 158 | Int4Ptr LB; | ^~ sec.c:505:39: warning: ‘RB’ may be used uninitialized [-Wmaybe-uninitialized] 505 | RB[i] = tr; | ~~~~~~^~~~ sec.c:159:17: note: ‘RB’ was declared here 159 | Int4Ptr RB; | ^~ sec.c:405:47: warning: ‘bi’ may be used uninitialized [-Wmaybe-uninitialized] 405 | c = ((FloatHi)z_ALIGN(seq1-1,seq2-1,bi,bj,ei,ej,LB,RB,V,G,H,S+fk))/DIGIT + (FloatHi)fk + (FloatHi)lk; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sec.c:163:14: note: ‘bi’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:71:37: warning: ‘bj’ may be used uninitialized [-Wmaybe-uninitialized] 71 | #define Max(x,y) ((x) >= (y) ? (x) : (y)) | ~~~~~~~~~~~~~~~~~~^~~~~~ sec.c:163:18: note: ‘bj’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:400:51: warning: ‘ei’ may be used uninitialized [-Wmaybe-uninitialized] 400 | for (i = pi; i <= ei; ++i) { | ~~^~~~~ sec.c:163:22: note: ‘ei’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:502:31: warning: ‘ej’ may be used uninitialized [-Wmaybe-uninitialized] 502 | tr = Min(cj + Width, ej); | ^ sec.c:163:26: note: ‘ej’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:503:43: warning: ‘pi’ may be used uninitialized [-Wmaybe-uninitialized] 503 | for (i = pi; i <= ci; ++i) { | ~~^~~~~ sec.c:172:14: note: ‘pi’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~ sec.c:493:44: warning: ‘ppi’ may be used uninitialized [-Wmaybe-uninitialized] 493 | for (i = ppi; i <= ci; ++i) { | ~~^~~~~ sec.c:172:22: note: ‘ppi’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~~ sec.c:72:37: warning: ‘ppj’ may be used uninitialized [-Wmaybe-uninitialized] 72 | #define Min(x,y) ((x) <= (y) ? (x) : (y)) | ~~~~~~~~~~~~~~~~~~^~~~~~ sec.c:172:27: note: ‘ppj’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~~ sec.c:504:39: warning: ‘old_l’ may be used uninitialized [-Wmaybe-uninitialized] 504 | LB[i] = old_l; | ~~~~~~^~~~~~~ sec.c:185:14: note: ‘old_l’ was declared here 185 | Int4 old_l, tl, tr; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF tfuns.c tfuns.c: In function ‘find_orf’: tfuns.c:866:33: warning: unused variable ‘into’ [-Wunused-variable] 866 | IntFuzzPtr infrom=NULL, into=NULL; | ^~~~ tfuns.c:866:20: warning: unused variable ‘infrom’ [-Wunused-variable] 866 | IntFuzzPtr infrom=NULL, into=NULL; | ^~~~~~ tfuns.c: At top level: tfuns.c:977:13: warning: ‘find_orf_from_circle’ defined but not used [-Wunused-function] 977 | static void find_orf_from_circle (SeqPortPtr spp, Boolean flagIsCircle, | ^~~~~~~~~~~~~~~~~~~~ tfuns.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: tfuns.c,v 6.17 2015/08/17 17:15:09 bollin Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF toasn3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from toasn3.c:10: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ toasn3.c: In function ‘FindOrg’: toasn3.c:1444:17: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 1444 | Int4 len; | ^~~ toasn3.c: In function ‘CheckQualsWithComm’: toasn3.c:1731:18: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 1731 | OrgRefPtr orp; | ^~~ toasn3.c: In function ‘CheckQuals’: toasn3.c:1768:18: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 1768 | OrgRefPtr orp; | ^~~ toasn3.c: In function ‘CountSourceFeat’: toasn3.c:2570:13: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2570 | Pointer pnt; | ^~~ toasn3.c:2561:19: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2561 | ValNodePtr vnp; | ^~~ toasn3.c: In function ‘TASNTrimInternalSemicolons’: toasn3.c:4155:12: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 4155 | CharPtr tmp; | ^~~ toasn3.c: In function ‘ImpFeatToProtRef’: toasn3.c:4861:13: warning: variable ‘lfree’ set but not used [-Wunused-but-set-variable] 4861 | Boolean lfree = FALSE, partial5, partial3; | ^~~~~ toasn3.c: In function ‘RemovePeptideImpFeats’: toasn3.c:5160:24: warning: variable ‘ifp’ set but not used [-Wunused-but-set-variable] 5160 | ImpFeatPtr ifp; | ^~~ toasn3.c: At top level: toasn3.c:1711:16: warning: ‘GetQualValue’ defined but not used [-Wunused-function] 1711 | static CharPtr GetQualValue(GBQualPtr gbqual, CharPtr qual) | ^~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from toasn3.c:19: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ toasn3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: toasn3.c,v 6.150 2016/11/02 23:36:09 kans Exp $"; | ^~~~~ toasn3.c: In function ‘CdEndCheck’: toasn3.c:4662:15: warning: ‘oldfrom’ may be used uninitialized [-Wmaybe-uninitialized] 4662 | sip->from = oldfrom; | ~~~~~~~~~~^~~~~~~~~ toasn3.c:4441:31: note: ‘oldfrom’ was declared here 4441 | Int4 len, remainder, aas, oldfrom, oldto, protlen, i, oldnum; | ^~~~~~~ toasn3.c:4663:13: warning: ‘oldto’ may be used uninitialized [-Wmaybe-uninitialized] 4663 | sip->to = oldto; | ~~~~~~~~^~~~~~~ toasn3.c:4441:40: note: ‘oldto’ was declared here 4441 | Int4 len, remainder, aas, oldfrom, oldto, protlen, i, oldnum; | ^~~~~ toasn3.c:4665:18: warning: ‘m_oldfrom’ may be used uninitialized [-Wmaybe-uninitialized] 4665 | msip->from = m_oldfrom; | ~~~~~~~~~~~^~~~~~~~~~~ toasn3.c:4442:10: note: ‘m_oldfrom’ was declared here 4442 | Int4 m_oldfrom, m_oldto; | ^~~~~~~~~ toasn3.c:4666:16: warning: ‘m_oldto’ may be used uninitialized [-Wmaybe-uninitialized] 4666 | msip->to = m_oldto; | ~~~~~~~~~^~~~~~~~~ toasn3.c:4442:21: note: ‘m_oldto’ was declared here 4442 | Int4 m_oldfrom, m_oldto; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF toporg.c toporg.c: In function ‘ChkSegset’: toporg.c:64:51: warning: variable ‘is_title’ set but not used [-Wunused-but-set-variable] 64 | Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE; | ^~~~~~~~ toporg.c:63:17: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 63 | OrgRefPtr orp; | ^~~ toporg.c:60:17: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 60 | Pointer pnt; | ^~~ toporg.c:55:17: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 55 | ValNodePtr vnp = NULL, set_vnp = NULL, upd_date_vnp = NULL; | ^~~ toporg.c: In function ‘ChkNucProt’: toporg.c:608:51: warning: variable ‘is_title’ set but not used [-Wunused-but-set-variable] 608 | Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE; | ^~~~~~~~ toporg.c: In function ‘StripBSfromParts’: toporg.c:1330:17: warning: variable ‘empty’ set but not used [-Wunused-but-set-variable] 1330 | Boolean empty; | ^~~~~ toporg.c:1329:17: warning: variable ‘bsmp’ set but not used [-Wunused-but-set-variable] 1329 | BSMapPtr bsmp; | ^~~~ toporg.c:1328:29: warning: variable ‘set_vnp’ set but not used [-Wunused-but-set-variable] 1328 | ValNodePtr descr, vnp, set_vnp; | ^~~~~~~ toporg.c: In function ‘MapsToGenref’: toporg.c:2021:17: warning: variable ‘loc’ set but not used [-Wunused-but-set-variable] 2021 | SeqLocPtr loc; | ^~~ toporg.c:2016:17: warning: variable ‘descr’ set but not used [-Wunused-but-set-variable] 2016 | ValNodePtr descr = NULL, head, last, vnp; | ^~~~~ toporg.c: In function ‘FindOldLineage’: toporg.c:2606:17: warning: variable ‘lineage’ set but not used [-Wunused-but-set-variable] 2606 | CharPtr lineage; | ^~~~~~~ toporg.c: In function ‘ArePubsMergeableForFig’: toporg.c:4796:36: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^~ toporg.c:4796:12: note: add parentheses around left hand side expression to silence this warning 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^~~~~~~~~~~~~~~~~~~~~~~ | ( ) toporg.c: In function ‘StripBadTitleFromProteinProducts’: toporg.c:5311:22: warning: variable ‘tech’ set but not used [-Wunused-but-set-variable] 5311 | Uint1 tech; | ^~~~ toporg.c: In function ‘FindPubWithFig’: toporg.c:5647:10: warning: variable ‘a’ set but not used [-Wunused-but-set-variable] 5647 | Int4 a = 0; | ^ toporg.c: In function ‘AddMissingGeneXref’: toporg.c:5955:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 5955 | Int2 count; | ^~~~~ toporg.c: In function ‘ConvertSegSetToDeltaSeqInt’: toporg.c:7093:18: warning: unused variable ‘str’ [-Wunused-variable] 7093 | CharPtr str, ttl = NULL; | ^~~ toporg.c:7086:18: warning: unused variable ‘ovp’ [-Wunused-variable] 7086 | ObjValNodePtr ovp; | ^~~ toporg.c: At top level: toporg.c:5475:13: warning: ‘SynchronizePseudogenesProc’ defined but not used [-Wunused-function] 5475 | static void SynchronizePseudogenesProc ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~ toporg.c:3119:13: warning: ‘BarCodeTechToKeyword’ defined but not used [-Wunused-function] 3119 | static void BarCodeTechToKeyword (BioseqPtr bsp, Pointer userdata) | ^~~~~~~~~~~~~~~~~~~~ toporg.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: toporg.c,v 6.251 2016/11/02 23:36:10 kans Exp $"; | ^~~~~ In function ‘CitSubsMatch’, inlined from ‘MergeEquivCitSubs’ at toporg.c:3952:13: toporg.c:3905:7: warning: ‘csp1’ may be used uninitialized [-Wmaybe-uninitialized] 3905 | if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ toporg.c: In function ‘MergeEquivCitSubs’: toporg.c:3925:18: note: ‘csp1’ was declared here 3925 | CitSubPtr csp1, csp2; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pobutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/pobutil.h:7, from pobutil.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pobutil.c: In function ‘build_repeat_feat’: pobutil.c:187:14: warning: unused variable ‘c’ [-Wunused-variable] 187 | Char c='%'; | ^ pobutil.c: In function ‘merge_StdSeg’: pobutil.c:1033:14: warning: variable ‘start_1’ set but not used [-Wunused-but-set-variable] 1033 | Int4 start_1, stop_1, start_2, stop_2; | ^~~~~~~ pobutil.c:1031:14: warning: unused variable ‘overlap’ [-Wunused-variable] 1031 | Int4 overlap = -1; | ^~~~~~~ In file included from ../include/ncbi.h:59: pobutil.c: In function ‘FindHumanRepeats’: ../include/ncbimem.h:191:21: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ pobutil.c:2380:9: note: in expansion of macro ‘MemSet’ 2380 | MemSet((Pointer) (&tmp), sizeof(ValNode), 0); | ^~~~~~ ../include/ncbimem.h:191:21: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ pobutil.c:2381:9: note: in expansion of macro ‘MemSet’ 2381 | MemSet((Pointer) (&si), sizeof(SeqInt), 0); | ^~~~~~ pobutil.c: In function ‘AluFeat’: pobutil.c:2431:17: warning: variable ‘my_userdata’ set but not used [-Wunused-but-set-variable] 2431 | Pointer my_userdata; | ^~~~~~~~~~~ pobutil.c: At top level: pobutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pobutil.c,v 6.10 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF stsutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from stsutil.c:88: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ stsutil.c: In function ‘InitSTSSearch_r’: stsutil.c:270:10: warning: unused variable ‘StsCount’ [-Wunused-variable] 270 | Int4 StsCount=0; | ^~~~~~~~ stsutil.c: In function ‘GetSTSEntry’: stsutil.c:635:13: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 635 | CharPtr p; | ^ stsutil.c: In function ‘STSCalculateHash’: stsutil.c:753:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 753 | if ((j = HashCode[*p++]) < 0) | ^~~~ stsutil.c: In function ‘STSReverse’: stsutil.c:771:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 771 | if ((*t = ComplCode[*s]) == 0) | ^~ stsutil.c: In function ‘InitHashTable’: stsutil.c:910:21: warning: variable ‘sts_uid’ set but not used [-Wunused-but-set-variable] 910 | CharPtr gb_uid, sts_uid; | ^~~~~~~ stsutil.c:910:13: warning: variable ‘gb_uid’ set but not used [-Wunused-but-set-variable] 910 | CharPtr gb_uid, sts_uid; | ^~~~~~ stsutil.c:908:23: warning: variable ‘gi’ set but not used [-Wunused-but-set-variable] 908 | Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0; | ^~ stsutil.c:908:10: warning: variable ‘id_sts’ set but not used [-Wunused-but-set-variable] 908 | Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0; | ^~~~~~ stsutil.c:907:23: warning: unused variable ‘error’ [-Wunused-variable] 907 | Int4 LineLength, error= FALSE; | ^~~~~ stsutil.c: At top level: stsutil.c:892:13: warning: ‘STSHashInitFree’ defined but not used [-Wunused-function] 892 | static void STSHashInitFree(STSHashInitPtr sts) | ^~~~~~~~~~~~~~~ stsutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: stsutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF suggadj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggadj.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggadj.c: In function ‘score_possible_splice_sites’: suggadj.c:874:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 874 | score = ( vx[seq_or_rev[putative_donor]]==3) ?10:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:875:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 875 | score += (vx[seq_or_rev[putative_acceptor]]==3 )?10:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ suggadj.c:878:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | score += ( vx[seq_or_rev[putative_donor+1]]==0 )?3:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ suggadj.c:879:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 879 | score += ( vx[seq_or_rev[putative_acceptor-1]]==2 )?3:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c: In function ‘check_split_codon’: suggadj.c:985:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 985 | val_assuming_1_from_left= vx[seq_or_rev[left_ends+1]] * 16 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:986:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 986 | vx[seq_or_rev[right_starts-2]]*4+ | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:987:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 987 | vx[seq_or_rev[right_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:998:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 998 | val_assuming_2_from_left= vx[seq_or_rev[left_ends+1]] * 16 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:999:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 999 | vx[seq_or_rev[left_ends+2]] * 4 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:1000:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1000 | vx[seq_or_rev[right_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c: In function ‘overlapping_fixer’: suggadj.c:1370:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1370 | test_val = vx[seq_or_rev[left_exon_ends]]*16 + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:1371:54: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1371 | vx[seq_or_rev[right_exon_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c:1373:66: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1373 | test_val += vx[seq_or_rev[right_exon_starts-2]]*4; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c:1375:66: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1375 | test_val += vx[seq_or_rev[left_exon_ends+1]]*4; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ suggadj.c: At top level: suggadj.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggadj.c,v 6.3 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF suggest.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggest.c:199: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggest.c: In function ‘get_frames’: suggest.c:458:35: warning: array subscript has type ‘char’ [-Wchar-subscripts] 458 | val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]]; | ~^~~ suggest.c:458:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 458 | val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]]; | ~^~~ suggest.c: At top level: suggest.c:1331:13: warning: ‘ReportSuggestIntervalsError’ defined but not used [-Wunused-function] 1331 | static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ suggest.c:1222:1: warning: ‘fprintf_m_stk_entry’ defined but not used [-Wunused-function] 1222 | fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg) | ^~~~~~~~~~~~~~~~~~~ suggest.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF suggslp.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggslp.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggslp.c: In function ‘MakeReverseSequence’: suggslp.c:190:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 190 | *t++ = r[*--s]; | ^~~~ suggslp.c: At top level: suggslp.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggslp.c,v 6.6 2009/04/16 18:35:41 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blast.c:2572: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast.c: In function ‘BlastReevaluateWithAmbiguities’: blast.c:2954:31: warning: variable ‘query_end’ set but not used [-Wunused-but-set-variable] 2954 | Uint1Ptr query_start, query_end, subject_real_start=NULL; | ^~~~~~~~~ blast.c:2949:23: warning: variable ‘hspcnt’ set but not used [-Wunused-but-set-variable] 2949 | Int4 context, hspcnt, hspcnt_max, index, index1, status; | ^~~~~~ blast.c: In function ‘BlastGetVirtualOIDList’: blast.c:3179:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3179 | if (virtual_oidlist = rdfp_chain->oidlist) { | ^~~~~~~~~~~~~~~ blast.c: In function ‘BlastGetDbChunk’: blast.c:3210:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { | ^~~~~~~~~~~~~~~ blast.c: In function ‘BlastCreateQueryDNAP’: blast.c:4100:11: warning: variable ‘strand_option’ set but not used [-Wunused-but-set-variable] 4100 | Uint1 strand_option; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastReapPartialHitlistByEvalue’: blast.c:6486:10: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 6486 | else | ^~~~ blast.c:6490:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 6490 | if( !search->mult_queries ) | ^~ blast.c: In function ‘BlastWordFinder_contig’: blast.c:7094:23: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 7094 | register Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastWordExtend’: blast.c:7835:64: warning: variable ‘leftscore’ set but not used [-Wunused-but-set-variable] 7835 | BLAST_Score leftsum, rightsum, rightscore, leftscore; | ^~~~~~~~~ blast.c: In function ‘BlastNewWordExtend’: blast.c:7982:64: warning: variable ‘leftscore’ set but not used [-Wunused-but-set-variable] 7982 | BLAST_Score leftsum, rightsum, rightscore, leftscore; | ^~~~~~~~~ blast.c: In function ‘BlastNtWordFinder_mh’: blast.c:8843:23: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 8843 | register Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c:8842:103: warning: variable ‘compression_factor’ set but not used [-Wunused-but-set-variable] 8842 | Int4 s_pos, q_off, s_off, offset, virtual_wordsize, wordsize, compressed_wordsize, compression_factor; | ^~~~~~~~~~~~~~~~~~ blast.c: In function ‘BlastNtWordFinder’: blast.c:9076:14: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 9076 | Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastSaveCurrentHitlist’: blast.c:10115:25: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 10115 | if( hitlist_max > 1 ) | ^ blast.c:9785:14: warning: variable ‘query_length’ set but not used [-Wunused-but-set-variable] 9785 | Int4 query_length; | ^~~~~~~~~~~~ blast.c: In function ‘SumHSPEvalue’: blast.c:10588:9: warning: variable ‘gap_size’ set but not used [-Wunused-but-set-variable] 10588 | Int4 gap_size, num, subject_length; | ^~~~~~~~ blast.c: In function ‘link_hsps’: blast.c:11267:17: warning: variable ‘frame_change’ set but not used [-Wunused-but-set-variable] 11267 | Boolean frame_change, linked_set, ignore_small_gaps; | ^~~~~~~~~~~~ blast.c: At top level: blast.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $"; | ^~~~~ blast.c: In function ‘blastMergeFilterLocs’: blast.c:3969:9: warning: ‘dup_slp’ may be used uninitialized [-Wmaybe-uninitialized] 3969 | BlastConvertDNASeqLoc(dup_slp, frame, length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast.c:3933:20: note: ‘dup_slp’ was declared here 3933 | SeqLocPtr slp, dup_slp, dup_head; | ^~~~~~~ blast.c: In function ‘BlastLinkHsps’: blast.c:10455:41: warning: ‘orig_hitlist’ may be used uninitialized [-Wmaybe-uninitialized] 10455 | search->current_hitlist = orig_hitlist; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blast.c:10401:35: note: ‘orig_hitlist’ was declared here 10401 | BLAST_HitListPtr hitlist, orig_hitlist; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blastutl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastutl.c:1836: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastutl.c: In function ‘BlastSeqLocFilterEx’: blastutl.c:7554:11: warning: statement with no effect [-Wunused-value] 7554 | stop_timer("after repeat filtering"); | ^ blastutl.c: In function ‘BlastPreliminaryGappedScore’: blastutl.c:9853:37: warning: variable ‘query_length’ set but not used [-Wunused-but-set-variable] 9853 | Int4 index, max_offset = 0, query_length, min_score; | ^~~~~~~~~~~~ blastutl.c: In function ‘BlastGetGappedScore’: blastutl.c:10282:11: warning: statement with no effect [-Wunused-value] 10282 | stop_timer("after BlastGappedScoreInternal"); | ^ blastutl.c: At top level: blastutl.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastutl.c,v 6.472 2010/12/10 18:47:12 madden Exp $"; | ^~~~~ blastutl.c: In function ‘BlastNtFindWords’: blastutl.c:11445:17: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 11445 | end = MIN(end, len-initial_wordsize); blastutl.c:11396:14: note: ‘end’ was declared here 11396 | Int4 end, index, index_addition, lookup_index, stop; | ^~~ blastutl.c: In function ‘BlastFindWords’: blastutl.c:11623:22: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 11623 | stop = MIN(stop, len); blastutl.c:11522:66: note: ‘stop’ was declared here 11522 | Int4 loop_increment, loop_increment2, stop; | ^~~~ blastutl.c:11695:39: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 11695 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11512:58: note: ‘diff’ was declared here 11512 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:11704:45: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 11704 | start_score = second_score+first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11512:71: note: ‘first_score’ was declared here 11512 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:11711:46: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 11711 | start_score2 += matrix[(Int4) *(str+index2)][*(words+index2)]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11513:47: note: ‘start_score’ was declared here 11513 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘BlastNewFindWords_Old’: blastutl.c:11915:39: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 11915 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11777:58: note: ‘diff’ was declared here 11777 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:11924:45: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 11924 | start_score = second_score+first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11777:71: note: ‘first_score’ was declared here 11777 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:11931:46: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 11931 | start_score2 += MtrxScorePosSearch(search->sbp, blastutl.c:11778:47: note: ‘start_score’ was declared here 11778 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘BlastNewFindWordsEx’: blastutl.c:12110:23: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 12110 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11989:50: note: ‘diff’ was declared here 11989 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:12118:29: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 12118 | start_score = second_score + first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11989:63: note: ‘first_score’ was declared here 11989 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:12124:30: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 12124 | start_score2 += posMatrix[offset+index2][*(words+index2)]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11990:39: note: ‘start_score’ was declared here 11990 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘SumBlastGetGappedAlignmentEx’: blastutl.c:9662:40: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 9662 | for (index=start; index>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blastool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastool.c:946: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastool.c: In function ‘BlastScaleMatrix’: blastool.c:3032:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 3032 | else | ^~~~ blastool.c:3035:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 3035 | if (new_lambda > lambda) | ^~ blastool.c: In function ‘OOFBlastHSPGetNumIdentical’: blastool.c:6081:9: warning: variable ‘context’ set but not used [-Wunused-but-set-variable] 6081 | Int2 context; | ^~~~~~~ blastool.c: At top level: blastool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastool.c,v 6.292 2007/03/15 20:39:17 madden Exp $"; | ^~~~~ blastool.c: In function ‘BlastCreateVirtualOIDList’: blastool.c:2556:24: warning: ‘gilist’ may be used uninitialized [-Wmaybe-uninitialized] 2556 | BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL; | ^~~~~~ blastool.c: In function ‘BlastInsertList2Heap’: blastool.c:3595:38: warning: ‘query_length’ may be used uninitialized [-Wmaybe-uninitialized] 3595 | context = hsp->query_offset / query_length; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blastool.c:3575:30: note: ‘query_length’ was declared here 3575 | Int4 begin, end, hspcnt, query_length; | ^~~~~~~~~~~~ blastool.c: In function ‘BlastFreeHeap’: blastool.c:3687:38: warning: ‘query_length’ may be used uninitialized [-Wmaybe-uninitialized] 3687 | context = hsp->query_offset / query_length; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blastool.c:3670:33: note: ‘query_length’ was declared here 3670 | Int4 begin, end, i, hspcnt, query_length; | ^~~~~~~~~~~~ blastool.c: In function ‘BlastPrintAlignInfo’: blastool.c:4800:23: warning: ‘sap’ may be used uninitialized [-Wmaybe-uninitialized] 4800 | sap->next = SeqAlignNew(); | ~~~~~~~~~~^~~~~~~~~~~~~~~ blastool.c:4589:33: note: ‘sap’ was declared here 4589 | SeqAlignPtr seqalign = NULL, sap; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blastconcat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastconcat.c:89: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastconcat.c: In function ‘BlastMakeFakeBspConcat’: blastconcat.c:648:19: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 648 | SeqLocPtr slp = NULL; | ^~~ blastconcat.c: At top level: blastconcat.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF splutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from splutil.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ splutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gapxdrop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/gapxdrop.h:150, from gapxdrop.c:368: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gapxdrop.c: In function ‘ALIGN_EX’: gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 864 | if (s == 1) | ^ gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 867 | if (s == 2) | ^ gapxdrop.c: At top level: gapxdrop.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg0.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg0.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg0.c: In function ‘g_band0_align’: bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 273 | if(leftd >= 1) | ^ bandalg0.c: At top level: bandalg0.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg1.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg1.c: In function ‘gband_quadratic’: bandalg1.c:54:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 54 | Int4 c, i, j; | ^ bandalg1.c: In function ‘g_band1_align’: bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 205 | if(leftd >= 1) | ^ bandalg1.c: At top level: bandalg1.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg2.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg2.c: In function ‘gb_linear_align’: bandalg2.c:208:24: warning: variable ‘misma’ set but not used [-Wunused-but-set-variable] 208 | register Int4 match, misma; | ^~~~~ bandalg2.c:208:17: warning: variable ‘match’ set but not used [-Wunused-but-set-variable] 208 | register Int4 match, misma; | ^~~~~ bandalg2.c:207:18: warning: variable ‘AA’ set but not used [-Wunused-but-set-variable] 207 | register Uint1 AA; | ^~ bandalg2.c: At top level: bandalg2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ bandalg2.c: In function ‘gb_linear_align’: bandalg2.c:494:22: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 494 | if (rmid > Y - X) { | ~~^~~ bandalg2.c:202:35: note: ‘X’ was declared here 202 | Int4 rmid, k =0, l=0, r, v, kt, X, Y; | ^ bandalg2.c:494:22: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 494 | if (rmid > Y - X) { | ~~^~~ bandalg2.c:202:38: note: ‘Y’ was declared here 202 | Int4 rmid, k =0, l=0, r, v, kt, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg3.c:37: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:54:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 54 | Int4 c, i, j; | ^ bandalg3.c: At top level: bandalg3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ In function ‘g_band3_align’, inlined from ‘gband_linear_qgap’ at bandalg3.c:111:7: bandalg3.c:291:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 291 | for (i = X, j = Y, e=0, c = 0; i>=0; i--, c++) { | ~^~~ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:185:25: note: ‘X’ was declared here 185 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band3_align’, inlined from ‘gband_linear_qgap’ at bandalg3.c:111:7: bandalg3.c:314:23: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 314 | else if(Y != rightd) _INS(rightd-Y) | ^ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:185:28: note: ‘Y’ was declared here 185 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg4.c:37: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg4.c: In function ‘g_band4_align_small’: bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 826 | if (e == 1) | ^ bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 829 | if (e == 2) | ^ bandalg4.c:630:8: warning: variable ‘band’ set but not used [-Wunused-but-set-variable] 630 | Int4 band, j; | ^~~~ bandalg4.c: At top level: bandalg4.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg4.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:534:12: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 534 | if(X != M || Y != N) regA = regB = 1; | ~~^~~~ bandalg4.c:183:30: note: ‘X’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ bandalg4.c:534:22: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 534 | if(X != M || Y != N) regA = regB = 1; | ~~^~~~ bandalg4.c:183:33: note: ‘Y’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ bandalg4.c:544:11: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 544 | for(; k > -1; r = k, k = data->MP[l][r], l = data->MT[l][r]){ | ~~^~~~ bandalg4.c:183:14: note: ‘k’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ In function ‘g_band4_align_small’, inlined from ‘g_band4_align’ at bandalg4.c:208:14: bandalg4.c:823:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 823 | for (i = X, j = Y, e=l, c = 0; i>=0; i--, c++) { | ~^~~ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:640:25: note: ‘X’ was declared here 640 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band4_align_small’, inlined from ‘g_band4_align’ at bandalg4.c:208:14: bandalg4.c:857:11: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 857 | else if (Y != rightd) _INS(rightd - Y); | ^ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:640:28: note: ‘Y’ was declared here 640 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalg5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg5.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:56:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 56 | Int4 c, i, j; | ^ bandalg5.c: In function ‘g_band5_align’: bandalg5.c:292:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 292 | if (e == 1) | ^ bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 295 | if (e == 2) | ^ bandalg5.c: At top level: bandalg5.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg5.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ In function ‘g_band5_align’, inlined from ‘gband_q3gap’ at bandalg5.c:109:7: bandalg5.c:289:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 289 | for (i = X, j = Y, e=0, c = 0; i>=0; i--, c++) { | ~^~~ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:146:25: note: ‘X’ was declared here 146 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band5_align’, inlined from ‘gband_q3gap’ at bandalg5.c:109:7: bandalg5.c:320:6: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 320 | if (Y != rightd) _INS(rightd - Y); | ^ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:146:28: note: ‘Y’ was declared here 146 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bandalgn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from bandalgn.c:118: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalgn.c: In function ‘ExtendSeqAlign’: bandalgn.c:1113:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 1113 | DenseDiagPtr ddp; | ^~~ bandalgn.c: In function ‘CC_ExtendSeqAlign’: bandalgn.c:1188:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 1188 | DenseDiagPtr ddp; | ^~~ bandalgn.c: At top level: bandalgn.c:699:14: warning: ‘HSblastna_to_ncbi4na’ defined but not used [-Wunused-variable] 699 | static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */ | ^~~~~~~~~~~~~~~~~~~~ bandalgn.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalgn.c,v 6.17 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ bandalgn.c: In function ‘LocalBandToEditBlock’: bandalgn.c:463:20: warning: ‘edit_block’ may be used uninitialized [-Wmaybe-uninitialized] 463 | lbsp->edit_block = edit_block; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ bandalgn.c:435:20: note: ‘edit_block’ was declared here 435 | GapXEditBlockPtr edit_block; | ^~~~~~~~~~ bandalgn.c: In function ‘SetLowUpFromBlast’: bandalgn.c:1053:28: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 1053 | if (maxsc < val) { | ^ bandalgn.c:943:17: note: ‘val’ was declared here 943 | FloatHi val, maxsc = 0; | ^~~ bandalgn.c:1056:38: warning: ‘mindi’ may be used uninitialized [-Wmaybe-uninitialized] 1056 | miny = mindi - width; | ~~~~~^~~~~~~~~~~~~~~ bandalgn.c:939:28: note: ‘mindi’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~ bandalgn.c:1055:38: warning: ‘maxdi’ may be used uninitialized [-Wmaybe-uninitialized] 1055 | maxy = maxdi + width; | ~~~~~^~~~~~~~~~~~~~~ bandalgn.c:939:34: note: ‘maxdi’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~ bandalgn.c:1060:28: warning: ‘alnlen’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | if (maxlen < alnlen) { | ^ bandalgn.c:940:37: note: ‘alnlen’ was declared here 940 | Int4 len,len1,len2,maxlen=0,alnlen,lastx,lowestx,diag; | ^~~~~~ bandalgn.c:1069:16: warning: ‘mindi_low’ may be used uninitialized [-Wmaybe-uninitialized] 1069 | miny = MIN(miny,mindi_low); bandalgn.c:939:40: note: ‘mindi_low’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~~~~~ bandalgn.c:1070:16: warning: ‘maxdi_up’ may be used uninitialized [-Wmaybe-uninitialized] 1070 | maxy = MAX(maxy,maxdi_up); bandalgn.c:939:50: note: ‘maxdi_up’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~~~~ bandalgn.c: In function ‘GetAlignExtremes’: bandalgn.c:1306:14: warning: ‘x1’ may be used uninitialized [-Wmaybe-uninitialized] 1306 | *xx1 = x1; | ~~~~~^~~~ bandalgn.c:1281:39: note: ‘x1’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1307:14: warning: ‘x2’ may be used uninitialized [-Wmaybe-uninitialized] 1307 | *xx2 = x2; | ~~~~~^~~~ bandalgn.c:1281:43: note: ‘x2’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1308:14: warning: ‘y1’ may be used uninitialized [-Wmaybe-uninitialized] 1308 | *yy1 = y1; | ~~~~~^~~~ bandalgn.c:1281:47: note: ‘y1’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1309:14: warning: ‘y2’ may be used uninitialized [-Wmaybe-uninitialized] 1309 | *yy2 = y2; | ~~~~~^~~~ bandalgn.c:1281:51: note: ‘y2’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blastkar.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastkar.c:648: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastkar.c:2373:25: warning: ‘Altschul_prob’ defined but not used [-Wunused-variable] 2373 | static BLAST_LetterProb Altschul_prob[] = { | ^~~~~~~~~~~~~ blastkar.c:2347:25: warning: ‘Dayhoff_prob’ defined but not used [-Wunused-variable] 2347 | static BLAST_LetterProb Dayhoff_prob[] = { | ^~~~~~~~~~~~ blastkar.c:1121:13: warning: ‘blosum62_20_prefs’ defined but not used [-Wunused-variable] 1121 | static Int4 blosum62_20_prefs[BLOSUM62_20_VALUES_MAX] = { | ^~~~~~~~~~~~~~~~~ blastkar.c:1053:21: warning: ‘blosum62_20_values’ defined but not used [-Wunused-variable] 1053 | static Nlm_FloatHi blosum62_20_values[BLOSUM62_20_VALUES_MAX][8] = { | ^~~~~~~~~~~~~~~~~~ blastkar.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastkar.c,v 6.115 2006/12/14 17:08:19 madden Exp $"; | ^~~~~ blastkar.c: In function ‘BlastScoreBlkMatCreate’: blastkar.c:1574:43: warning: ‘ ’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1574 | sprintf(buffer, "blastn matrix:%ld %ld", (long) sbp->reward, (long) sbp->penalty); | ^ blastkar.c:1574:25: note: directive argument in the range [-2147483648, 2147483647] 1574 | sprintf(buffer, "blastn matrix:%ld %ld", (long) sbp->reward, (long) sbp->penalty); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BlastScoreBlkMatCreate’ at blastkar.c:1574:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 38 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF actutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/actutils.h:103, from actutils.c:232: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ actutils.c: In function ‘SlideToHit’: actutils.c:346:23: warning: variable ‘done’ set but not used [-Wunused-but-set-variable] 346 | Boolean inIsland, done; | ^~~~ actutils.c:346:13: warning: variable ‘inIsland’ set but not used [-Wunused-but-set-variable] 346 | Boolean inIsland, done; | ^~~~~~~~ actutils.c: In function ‘ResolveSpinConflict’: actutils.c:1484:35: warning: unused variable ‘row2_conflict’ [-Wunused-variable] 1484 | Boolean row1_conflict = FALSE, row2_conflict = FALSE; | ^~~~~~~~~~~~~ actutils.c:1484:12: warning: unused variable ‘row1_conflict’ [-Wunused-variable] 1484 | Boolean row1_conflict = FALSE, row2_conflict = FALSE; | ^~~~~~~~~~~~~ actutils.c: In function ‘ACT_FindBestAlnByDotPlot’: actutils.c:2002:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 2002 | Uint1 strand; | ^~~~~~ actutils.c:2001:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2001 | Int4 start2; | ^~~~~~ actutils.c:2000:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2000 | Int4 start1; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ actutils.c:3132:13: warning: ‘DumpAlignments’ defined but not used [-Wunused-function] 3132 | static void DumpAlignments (SeqAlignPtr salp) | ^~~~~~~~~~~~~~ actutils.c:2927:13: warning: ‘MapBioseqToBioseqSpecial’ defined but not used [-Wunused-function] 2927 | static Int4 MapBioseqToBioseqSpecial(SeqAlignPtr sap, Int4 begin, Int4 fin, Int4 pos, Int4 which_end) | ^~~~~~~~~~~~~~~~~~~~~~~~ actutils.c:1654:16: warning: ‘SpinsConflict’ defined but not used [-Wunused-function] 1654 | static Boolean SpinsConflict (SQN_nPtr spin1, SQN_nPtr spin2, Int4 fuzz, Int4 strand) | ^~~~~~~~~~~~~ actutils.c:1392:13: warning: ‘am_fix_strand’ defined but not used [-Wunused-function] 1392 | static void am_fix_strand(SeqAlignPtr sap, Uint1 strand1, Uint1 strand2) | ^~~~~~~~~~~~~ actutils.c:1375:16: warning: ‘am_isa_gap’ defined but not used [-Wunused-function] 1375 | static Boolean am_isa_gap(Int4 start, Int4 prevstop, Uint1 strand) | ^~~~~~~~~~ actutils.c:749:13: warning: ‘StateTableSearch’ defined but not used [-Wunused-function] 749 | static void StateTableSearch (TextFsaPtr tbl, CharPtr txt, Int4Ptr state, Int4 pos, ACT_sitelistPtr PNTR asp_prev, ACT_sitelistPtr PNTR asp_head) | ^~~~~~~~~~~~~~~~ actutils.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: actutils.c,v 6.56 2008/10/22 17:19:22 bollin Exp $"; | ^~~~~ In file included from ../include/ncbi.h:59: actutils.c: In function ‘GetOldBlastAlignmentPiece’: ../include/ncbimem.h:232:23: warning: ‘program’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree actutils.c:3089:25: note: ‘program’ was declared here 3089 | CharPtr program; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF posit.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from posit.c:402: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ posit.c: In function ‘posDemographics’: posit.c:1110:17: warning: variable ‘numSeqAligns’ set but not used [-Wunused-but-set-variable] 1110 | Int4 numseq, numSeqAligns; /*number of matching sequences and SeqAligns*/ | ^~~~~~~~~~~~ posit.c: In function ‘posFreqsToMatrix’: posit.c:1679:45: warning: operation on ‘*(*(posSearch->posPrivateMatrix + (sizetype)((long unsigned int)length * 8)) + (sizetype)((long unsigned int)a * 4))’ may be undefined [-Wsequence-point] 1679 | posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN; posit.c: In function ‘posComputePseudoFreqs’: posit.c:1840:16: warning: variable ‘lambda’ set but not used [-Wunused-but-set-variable] 1840 | Nlm_FloatHi lambda; /*Karlin-Altschul parameter*/ | ^~~~~~ posit.c: In function ‘WposComputation’: posit.c:1988:13: warning: variable ‘numSeqAligns’ set but not used [-Wunused-but-set-variable] 1988 | Int4 i, numSeqAligns, numseq, qlength; | ^~~~~~~~~~~~ posit.c: In function ‘posPrintInformation’: posit.c:2319:8: warning: variable ‘querySize’ set but not used [-Wunused-but-set-variable] 2319 | Int4 querySize; | ^~~~~~~~~ posit.c: In function ‘posFindAlignmentDimensions’: posit.c:3064:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3064 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3070:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3070 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3079:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3079 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3086:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3086 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posPreprocessAlignment’: posit.c:3137:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3137 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3152:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3152 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posReadAlignment’: posit.c:3253:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3253 | fgets(nextline, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: At top level: posit.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: posit.c,v 6.88 2011/10/25 14:33:16 boratyng Exp $"; | ^~~~~ posit.c: In function ‘posFindAlignmentDimensions’: posit.c:3087:20: warning: ‘testCountSeqs’ may be used uninitialized [-Wmaybe-uninitialized] 3087 | testCountSeqs++; | ~~~~~~~~~~~~~^~ posit.c:3052:8: note: ‘testCountSeqs’ was declared here 3052 | Int4 testCountSeqs; /*counts number of sequences in each block | ^~~~~~~~~~~~~ posit.c: In function ‘posComputeSequenceWeights’: posit.c:1424:11: warning: ‘Sigma’ may be used uninitialized [-Wmaybe-uninitialized] 1424 | if (Sigma > 0) { | ^ posit.c:1314:16: note: ‘Sigma’ was declared here 1314 | Nlm_FloatHi Sigma; /*Number of different characters occurring in matches within | ^~~~~ posit.c:1447:36: warning: ‘intervalSigma’ may be used uninitialized [-Wmaybe-uninitialized] 1447 | posSearch->posSigma[qplace] = intervalSigma; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ posit.c:1316:16: note: ‘intervalSigma’ was declared here 1316 | Nlm_FloatHi intervalSigma; /*Same as Sigma but includes identical columns*/ | ^~~~~~~~~~~~~ In function ‘posReadPosFreqsScoremat’, inlined from ‘posReadCheckpoint’ at posit.c:2994:17: posit.c:2873:28: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 2873 | if (i < pssm->numColumns || j < pssm->numRows) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posReadCheckpoint’: posit.c:2702:11: note: ‘j’ was declared here 2702 | Int4 i, j, c; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF lookup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from lookup.c:308: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/blastdef.h:922, from ../include/blast.h:470, from lookup.c:309: lookup.c: In function ‘MegaBlastBuildLookupTable’: ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1047:35: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1047 | GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1051:35: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1051 | GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1078:31: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1078 | GET_EXTRA_CODE_18_OPT(seq) | bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1082:31: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1082 | GET_EXTRA_CODE_18_OPT(seq) | bit0; | ^~~~~~~~~~~~~~~~~~~~~ lookup.c:914:25: warning: variable ‘extra_code’ set but not used [-Wunused-but-set-variable] 914 | register Int4 ecode, extra_code; | ^~~~~~~~~~ lookup.c: At top level: lookup.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: lookup.c,v 6.59 2005/07/28 14:57:10 coulouri Exp $"; | ^~~~~ lookup.c: In function ‘MegaBlastBuildLookupTable’: lookup.c:1004:37: warning: ‘extra_length’ may be used uninitialized [-Wmaybe-uninitialized] 1004 | last_offset = query_length - extra_length; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ lookup.c:923:22: note: ‘extra_length’ was declared here 923 | Int2 word_length, extra_length, word_weight; | ^~~~~~~~~~~~ lookup.c:975:10: warning: ‘word_weight’ may be used uninitialized [-Wmaybe-uninitialized] 975 | if (word_weight >= 12) { | ^ lookup.c:923:36: note: ‘word_weight’ was declared here 923 | Int2 word_length, extra_length, word_weight; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF readdb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from readdb.c:2057: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ readdb.c: In function ‘readdb_parse_db_names’: readdb.c:2503:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2503 | if (**filenames == '"') | ^ readdb.c: In function ‘s_GetBlastDirInfo’: readdb.c:2734:32: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 2734 | memset(blast_dir, 0, sizeof(blast_dir)); | ^ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3167:33: warning: format ‘%lld’ expects argument of type ‘long long int *’, but argument 3 has type ‘Nlm_Int8 *’ {aka ‘long int *’} [-Wformat=] 3167 | sscanf(ptr, "%lld", &(rdbap->len)); | ~~~^ ~~~~~~~~~~~~~ | | | | | Nlm_Int8 * {aka long int *} | long long int * | %ld readdb.c: In function ‘IndexFileExists’: readdb.c:3320:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3320 | if (rdfp->cih) | ^~ readdb.c:3326:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3326 | if (rdbap->first_oid > 0) { | ^~ readdb.c:3400:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3400 | if (rdfp->cih && rdfp->aliasfilebit == 0) | ^~ readdb.c:3406:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3406 | if (rdbap->first_oid > 0) { | ^~ readdb.c: In function ‘FindBlastDBFileEx’: readdb.c:3480:33: warning: unused variable ‘envp’ [-Wunused-variable] 3480 | CharPtr buffer, buffer1, envp = NULL; | ^~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3558:25: warning: unused variable ‘envp’ [-Wunused-variable] 3558 | CharPtr charptr, envp = NULL; | ^~~~ readdb.c: In function ‘readdb_get_link’: readdb.c:4752:12: warning: variable ‘loaded_new’ set but not used [-Wunused-but-set-variable] 4752 | Boolean loaded_new = FALSE; | ^~~~~~~~~~ readdb.c:4751:24: warning: variable ‘last_used’ set but not used [-Wunused-but-set-variable] 4751 | ReadDBFILEPtr last, last_used, rdfp_var; | ^~~~~~~~~ readdb.c: In function ‘readdb_check_oid’: readdb.c:4896:45: warning: comparisons like ‘X<=Y<=Z’ do not have their mathematical meaning [-Wparentheses] 4896 | if (rdfp_var->start <= oid <= rdfp_var->stop) | ~~~~~~~~~~~~~~~~^~~~~~ readdb.c: In function ‘readdb_seqid2fasta’: readdb.c:5236:22: warning: unused variable ‘dummy_gi’ [-Wunused-variable] 5236 | Int4 dummy_gi = 0; /* Not used, should have been handled above. */ | ^~~~~~~~ readdb.c:5180:13: warning: unused variable ‘chptr’ [-Wunused-variable] 5180 | CharPtr chptr = NULL; | ^~~~~ readdb.c: In function ‘FDBuildOldStyleDefline’: readdb.c:6366:33: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 6366 | MemSet(defline, '\0', sizeof(defline)); | ^ readdb.c: In function ‘PrintDbInformationWithRID’: readdb.c:7571:14: warning: comparison between pointer and zero character constant [-Wpointer-compare] 7571 | if (rdfp == FALSE) | ^~ readdb.c:7571:9: note: did you mean to dereference the pointer? 7571 | if (rdfp == FALSE) | ^ readdb.c: In function ‘FDBLoadMembershipsTable’: readdb.c:8265:21: warning: variable ‘fn_name’ set but not used [-Wunused-but-set-variable] 8265 | const char* fn_name = NULL; | ^~~~~~~ readdb.c: In function ‘SeqIdE2Index’: readdb.c:8613:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 8613 | if ((tsip->version > 0) && (tsip->release == NULL)) | ^~ readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 8615 | break; | ^~~~~ readdb.c:8618:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 8618 | if (tsip->version > 0) | ^~ readdb.c:8620:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 8620 | break; | ^~~~~ readdb.c:8577:13: warning: unused variable ‘tmp’ [-Wunused-variable] 8577 | CharPtr tmp, ptr=NULL; | ^~~ readdb.c:8576:11: warning: unused variable ‘tmptype’ [-Wunused-variable] 8576 | Uint1 tmptype; | ^~~~~~~ readdb.c: In function ‘SeqIdSetE2Index’: readdb.c:8881:14: warning: variable ‘oldanp’ set but not used [-Wunused-but-set-variable] 8881 | SeqIdPtr oldanp; | ^~~~~~ readdb.c: In function ‘FDBAddSequence2’: readdb.c:9804:30: warning: the comparison will always evaluate as ‘true’ for the address of ‘div’ will never be NULL [-Waddress] 9804 | srp->div ? srp->div : "N/A", (long) SequenceLen, | ^ ../include/readdb.h:1073:13: note: ‘div’ declared here 1073 | char div[4]; | ^~~ readdb.c:9853:49: warning: the comparison will always evaluate as ‘true’ for the address of ‘div’ will never be NULL [-Waddress] 9853 | (long) direc.owner, pc->div ? pc->div : "N/A", | ^ ../include/readdb.h:1073:13: note: ‘div’ declared here 1073 | char div[4]; | ^~~ readdb.c: In function ‘FindDBbyGI’: readdb.c:11397:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 11397 | if (gi > cih->maxgi) | ^~ readdb.c:11400:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 11400 | cigi = cih->ci + gi; | ^~~~ readdb.c: In function ‘Fastacmd_PrintTaxonomyInfo’: readdb.c:11875:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 11875 | if ( gi && (rdfp->gi_target != 0) && (gi->data.intvalue != rdfp->gi_target) ) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:191:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ readdb.c:11878:9: note: in expansion of macro ‘MemSet’ 11878 | MemSet(buf, 0, sizeof(buf)); | ^~~~~~ readdb.c: In function ‘Fastacmd_Search_ex’: readdb.c:12080:22: warning: variable ‘guess_gi’ set but not used [-Wunused-but-set-variable] 12080 | Int4 guess_gi = -1; | ^~~~~~~~ readdb.c: In function ‘DumpOneSequence’: readdb.c:12407:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12407 | fprintf(fp, "%d\n", gi->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld readdb.c:12417:21: warning: unused variable ‘numeric_id’ [-Wunused-variable] 12417 | Boolean numeric_id = GetAccessionVersionFromSeqId(accn, &gi, &id, TRUE); | ^~~~~~~~~~ In file included from ../include/sqnutils.h:51, from readdb.c:2067: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ readdb.c:12829:1: warning: ‘readdb_preload_index’ defined but not used [-Wunused-function] 12829 | readdb_preload_index (ReadDBFILEPtr rdfp, Int4 first_db_seq, | ^~~~~~~~~~~~~~~~~~~~ In file included from readdb.c:2060: ../include/ncbisami.h:191:14: warning: ‘OneBit’ defined but not used [-Wunused-variable] 191 | static Uint1 OneBit[] = {0x80 , 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1}; | ^~~~~~ ../include/ncbisami.h:183:14: warning: ‘PowersOfTwo’ defined but not used [-Wunused-variable] 183 | static Uint4 PowersOfTwo[] = {01,02,04,010,020,040,0100,0200,0400,01000, | ^~~~~~~~~~~ readdb.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: readdb.c,v 6.549 2016/09/02 15:04:59 ucko Exp $"; | ^~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3084:53: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3084 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:3084:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3090:57: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3090 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:3090:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:2994:57: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2994 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:2994:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘Int4ListReadFromFile’: readdb.c:2656:31: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2656 | sprintf(file_name, "%s%s%s", blast_dir, DIRDELIMSTR, FileNameFind(fname)); | ^ In function ‘sprintf’, inlined from ‘Int4ListReadFromFileEx’ at readdb.c:2656:5, inlined from ‘Int4ListReadFromFile’ at readdb.c:2764:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2277:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2277 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2277:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2296:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2296 | sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2296:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2252:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2252 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2252:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2252:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2252 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2252:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2259:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2259 | sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2259:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_get_taxonomy_names’: readdb.c:5679:28: warning: ‘ufp_last’ may be used uninitialized [-Wmaybe-uninitialized] 5679 | ufp_last->next = ufp; | ~~~~~~~~~~~~~~~^~~~~ readdb.c:5627:23: note: ‘ufp_last’ was declared here 5627 | UserFieldPtr ufp, ufp_last; | ^~~~~~~~ readdb.c: In function ‘readdb_get_descriptor’: ../include/ncbimem.h:192:21: warning: ‘new_defline_length’ may be used uninitialized [-Wmaybe-uninitialized] 192 | #define Nlm_MemCpy memcpy readdb.c:6622:26: note: ‘new_defline_length’ was declared here 6622 | Int4 defline_length, new_defline_length; | ^~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3600:33: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3600 | sprintf(buffer1, "%s%s%s", buffer, DIRDELIMSTR, filename); | ^ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3600:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3671:25: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3671 | sprintf(buffer, "%s.%cin", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3671:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3811:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3811 | sprintf(buffer, "%s.%cnd", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3811:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3812:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3812 | sprintf(buffer1, "%s.%cni", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3812:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3825:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3825 | sprintf(buffer, "%s.%csd", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3825:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3826:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3826 | sprintf(buffer1, "%s.%csi", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3826:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3845:29: warning: ‘.ppd’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 3845 | sprintf(buffer, "%s.ppd", rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3845:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3846:29: warning: ‘.ppi’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 3846 | sprintf(buffer1, "%s.ppi", rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3846:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘GetAccList’: readdb.c:11821:29: warning: ‘AccListLast’ may be used uninitialized [-Wmaybe-uninitialized] 11821 | AccListLast->next = AccListTmp; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ readdb.c:11705:32: note: ‘AccListLast’ was declared here 11705 | FCMDAccListPtr AccListTmp, AccListLast; | ^~~~~~~~~~~ readdb.c: In function ‘FD_ConstructMultivolumeDBList’: readdb.c:12690:31: warning: ‘%03ld’ directive writing between 3 and 10 bytes into a region of size 9 [-Wformat-overflow=] 12690 | sprintf(numstr, ".%03ld ", (long) i); | ^~~~~ readdb.c:12690:29: note: directive argument in the range [100, 2147483646] 12690 | sprintf(numstr, ".%03ld ", (long) i); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘FD_ConstructMultivolumeDBList’ at readdb.c:12690:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisam.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbisam.c:198: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisam.c: In function ‘ISAMMakeStringIndex’: ncbisam.c:842:22: warning: unused variable ‘file_pos’ [-Wunused-variable] 842 | Int4 file_pos = ftell(data->db_fd); | ^~~~~~~~ ncbisam.c: In function ‘ISAMInitSearch’: ncbisam.c:1399:10: warning: variable ‘reserved2’ set but not used [-Wunused-but-set-variable] 1399 | Int4 reserved2; | ^~~~~~~~~ ncbisam.c: At top level: ncbisam.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $"; | ^~~~~ In file included from ../include/ncbierr.h:105, from ../include/ncbimsg.h:78, from ../include/ncbi.h:60: In function ‘ISAMMakeNumericIndex’, inlined from ‘ISAMMakeIndex’ at ncbisam.c:1146:16: ../include/ncbimisc.h:342:41: warning: ‘KeyInfo’ may be used uninitialized [-Wmaybe-uninitialized] 342 | #define Nlm_SwapUint4(value) Nlm_SwitchUint4(value) | ^~~~~~~~~~~~~~~~~~~~~~ ncbisam.c: In function ‘ISAMMakeIndex’: ncbisam.c:983:14: note: ‘KeyInfo’ was declared here 983 | Uint4Ptr KeyInfo, KeySamples; | ^~~~~~~ In function ‘ISAMMakeNumericIndex’, inlined from ‘ISAMMakeIndex’ at ncbisam.c:1146:16: ../include/ncbimisc.h:342:41: warning: ‘KeyDataInfo’ may be used uninitialized [-Wmaybe-uninitialized] 342 | #define Nlm_SwapUint4(value) Nlm_SwitchUint4(value) | ^~~~~~~~~~~~~~~~~~~~~~ ncbisam.c: In function ‘ISAMMakeIndex’: ncbisam.c:984:21: note: ‘KeyDataInfo’ was declared here 984 | NISAMKeyDataPtr KeyDataInfo, KeyDataSamples; | ^~~~~~~~~~~ In function ‘ISAMMakeNumericIndex’, inlined from ‘ISAMMakeIndex’ at ncbisam.c:1146:16: ncbisam.c:1060:27: warning: ‘KeySamples’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | KeySamples[SampleCount] = KeyInfo[i]; | ^ ncbisam.c: In function ‘ISAMMakeIndex’: ncbisam.c:983:23: note: ‘KeySamples’ was declared here 983 | Uint4Ptr KeyInfo, KeySamples; | ^~~~~~~~~~ In function ‘ISAMMakeNumericIndex’, inlined from ‘ISAMMakeIndex’ at ncbisam.c:1146:16: ncbisam.c:1062:31: warning: ‘KeyDataSamples’ may be used uninitialized [-Wmaybe-uninitialized] 1062 | KeyDataSamples[SampleCount] = KeyDataInfo[i]; | ^ ncbisam.c: In function ‘ISAMMakeIndex’: ncbisam.c:984:34: note: ‘KeyDataSamples’ was declared here 984 | NISAMKeyDataPtr KeyDataInfo, KeyDataSamples; | ^~~~~~~~~~~~~~ ncbisam.c: In function ‘ISAMCreateDatabase’: ../include/ncbierr.h:246:23: warning: ‘field_in’ may be used uninitialized [-Wmaybe-uninitialized] 246 | #define ErrLogPrintf Nlm_ErrLogPrintf ncbisam.c:1177:37: note: ‘field_in’ was declared here 1177 | unsigned long uid_in, uid_last, field_in; | ^~~~~~~~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: warning: ‘prevterm’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1181:13: note: ‘prevterm’ was declared here 1181 | CharPtr prevterm; | ^~~~~~~~ ncbisam.c: In function ‘NISAMSearch’: ncbisam.c:1681:11: warning: ‘SampleNum’ may be used uninitialized [-Wmaybe-uninitialized] 1681 | if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) { | ^ ncbisam.c:1618:27: note: ‘SampleNum’ was declared here 1618 | Int4 Start = 0, Stop, SampleNum; | ^~~~~~~~~ ncbisam.c:1750:36: warning: ‘KeyPage’ may be used uninitialized [-Wmaybe-uninitialized] 1750 | Key = SwapUint4(KeyPage[current]); | ^ ncbisam.c:1619:24: note: ‘KeyPage’ was declared here 1619 | Int4 NumElements, *KeyPage, *KeyPageStart; | ^~~~~~~ ../include/ncbimem.h:232:23: warning: ‘KeyPageStart’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1619:34: note: ‘KeyPageStart’ was declared here 1619 | Int4 NumElements, *KeyPage, *KeyPageStart; | ^~~~~~~~~~~~ ../include/ncbimem.h:232:23: warning: ‘KeyDataPageStart’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1622:55: note: ‘KeyDataPageStart’ was declared here 1622 | NISAMKeyDataPtr KeyDataPage=NULL, KeyDataSamples, KeyDataPageStart; | ^~~~~~~~~~~~~~~~ ncbisam.c: In function ‘SISAMSearch’: ncbisam.c:2373:8: warning: ‘SampleNum’ may be used uninitialized [-Wmaybe-uninitialized] 2373 | if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) { | ^ ncbisam.c:2280:29: note: ‘SampleNum’ was declared here 2280 | Int4 Diff, Start, Stop, SampleNum, Length, Pos; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbisort.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbisort.h:62, from ../include/ncbisrti.h:60, from ncbisort.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisort.c: In function ‘SORTFracCompare’: ncbisort.c:699:12: warning: type defaults to ‘int’ in declaration of ‘tmpa’ [-Wimplicit-int] 699 | register tmpa = UCHAR(*a), tmpb = UCHAR(*b); | ^~~~ ncbisort.c:699:30: warning: type defaults to ‘int’ in declaration of ‘tmpb’ [-Wimplicit-int] 699 | register tmpa = UCHAR(*a), tmpb = UCHAR(*b); | ^~~~ ../include/ncbisrti.h: At top level: ../include/ncbisrti.h:213:13: warning: ‘inthandler’ declared ‘static’ but never defined [-Wunused-function] 213 | static void inthandler(int i); | ^~~~~~~~~~ ncbisort.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: ncbisort.c,v 6.9 2012/08/22 23:02:39 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salign.h:10, from salign.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salign.c: In function ‘BandAlignTwoSeqLocsFunc’: salign.c:173:13: warning: variable ‘is_prot’ set but not used [-Wunused-but-set-variable] 173 | Boolean is_prot; | ^~~~~~~ salign.c: In function ‘SortBlastHits’: salign.c:391:15: warning: variable ‘totalvalmax’ set but not used [-Wunused-but-set-variable] 391 | totalvalmax = INT4_MAX, | ^~~~~~~~~~~ salign.c: In function ‘link_solution’: salign.c:1188:15: warning: unused variable ‘first’ [-Wunused-variable] 1188 | Boolean first = TRUE; | ^~~~~ salign.c: At top level: salign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $"; | ^~~~~ salign.c: In function ‘SortBlastHits’: salign.c:411:35: warning: ‘salpdup’ may be used uninitialized [-Wmaybe-uninitialized] 411 | for (salptmp=salpdup; salptmp!=NULL; salptmp=salptmp->next) | ^ salign.c:380:15: note: ‘salpdup’ was declared here 380 | SeqAlignPtr salpdup, | ^~~~~~~ salign.c: In function ‘TranslateSeqLoc.constprop.0’: salign.c:660:10: warning: ‘slpp’ may be used uninitialized [-Wmaybe-uninitialized] 660 | return slpp; | ^~~~ salign.c:633:17: note: ‘slpp’ was declared here 633 | SeqLocPtr slpp; | ^~~~ In function ‘find_maxsolution’, inlined from ‘get_solutions’ at salign.c:1313:3, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1270:38: warning: ‘start1’ may be used uninitialized [-Wmaybe-uninitialized] 1270 | intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1229:22: note: ‘start1’ was declared here 1229 | Int4 start, start1, stop; | ^~~~~~ In function ‘find_maxsolution’, inlined from ‘get_solutions’ at salign.c:1313:3, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1270:38: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 1270 | intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1229:30: note: ‘stop’ was declared here 1229 | Int4 start, start1, stop; | ^~~~ In function ‘get_solutions’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1348:38: warning: ‘start1’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1301:22: note: ‘start1’ was declared here 1301 | Int4 start, start1, stop; | ^~~~~~ In function ‘get_solutions’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1348:38: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1301:30: note: ‘stop’ was declared here 1301 | Int4 start, start1, stop; | ^~~~ In function ‘seqalign_reverse_sorting’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1489:25: salign.c:1433:17: warning: ‘tail’ may be used uninitialized [-Wmaybe-uninitialized] 1433 | tail->next = salptmp; | ~~~~~~~~~~~^~~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1408:15: note: ‘tail’ was declared here 1408 | tail, | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF salptool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from salptool.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salptool.c: In function ‘MergeTwoDspBySIM4’: salptool.c:285:17: warning: variable ‘has_overlap’ set but not used [-Wunused-but-set-variable] 285 | Boolean has_overlap; | ^~~~~~~~~~~ salptool.c:281:14: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 281 | Int4 gap=0,gap_1, gap_2; | ^~~ salptool.c: In function ‘extend_dsp_ends’: salptool.c:1329:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1329 | else | ^~~~ salptool.c:1331:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1331 | if(extend_len > 0) | ^~ salptool.c:1346:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1346 | else | ^~~~ salptool.c:1348:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1348 | if(extend_len > 0) | ^~ salptool.c:1363:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1363 | else | ^~~~ salptool.c:1365:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1365 | if(extend_len > 0) | ^~ salptool.c:1380:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1380 | else | ^~~~ salptool.c:1382:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1382 | if(extend_len > 0) | ^~ In file included from ../include/sqnutils.h:51, from salptool.c:12: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salptool.c:14: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salptool.c:1518:24: warning: ‘OrderBestHits’ defined but not used [-Wunused-function] 1518 | static int LIBCALLBACK OrderBestHits(Pointer ptr1, Pointer ptr2) | ^~~~~~~~~~~~~ salptool.c:1468:13: warning: ‘showtextalign_fromalign’ defined but not used [-Wunused-function] 1468 | static void showtextalign_fromalign (SeqAlignPtr salp, CharPtr path, FILE *fp) | ^~~~~~~~~~~~~~~~~~~~~~~ salptool.c:1453:13: warning: ‘getlengthforid’ defined but not used [-Wunused-function] 1453 | static Int4 getlengthforid (SeqIdPtr sip) | ^~~~~~~~~~~~~~ salptool.c:1267:16: warning: ‘need_recompute’ defined but not used [-Wunused-function] 1267 | static Boolean need_recompute(SeqAlignPtr align, Int4 m_len, Int4 s_len) | ^~~~~~~~~~~~~~ salptool.c:838:13: warning: ‘SeqLocTrimPolyATail’ defined but not used [-Wunused-function] 838 | static void SeqLocTrimPolyATail(SeqLocPtr loc_2, BioseqPtr bsp_2) { | ^~~~~~~~~~~~~~~~~~~ salptool.c:46:13: warning: ‘SeqAnnotWrite’ defined but not used [-Wunused-function] 46 | static void SeqAnnotWrite(SeqAlignPtr align) | ^~~~~~~~~~~~~ salptool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: salptool.c,v 6.57 2008/07/07 18:52:31 bollin Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from urkutil.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkpcc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkpcc.h:54, from urkpcc.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkpcc.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkptpf.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from urkptpf.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkptpf.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkptpf.c,v 6.33 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkepi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkepi.h:54, from urkepi.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkepi.c: In function ‘PredictEpiI0’: urkepi.c:214:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 214 | epip->epiarray[*seq] += 1; | ^~~~ urkepi.c:239:59: warning: array subscript has type ‘char’ [-Wchar-subscripts] 239 | episcore = DownArrayScore (episcore, epip->epiarray[*seq]); | ^~~~ urkepi.c:240:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 240 | epip->epiarray[*seq] += 1; | ^~~~ urkepi.c:241:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 241 | episcore = UpArrayScore (episcore, epip->epiarray[*seq]); | ^~~~ urkepi.c:263:59: warning: array subscript has type ‘char’ [-Wchar-subscripts] 263 | episcore = DownArrayScore (episcore, epip->epiarray[*(seq-window)]); | ^~~~~~~~~~~~~ urkepi.c:264:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 264 | epip->epiarray[*(seq-window)] -= 1; | ^~~~~~~~~~~~~ urkepi.c:265:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 265 | episcore = UpArrayScore (episcore, epip->epiarray[*(seq-window)]); | ^~~~~~~~~~~~~ urkepi.c: In function ‘OptimizeEpiComp’: urkepi.c:605:18: warning: array subscript has type ‘char’ [-Wchar-subscripts] 605 | bin[seq[i]] += 1; | ~~~^~~ urkepi.c:621:18: warning: array subscript has type ‘char’ [-Wchar-subscripts] 621 | bin[seq[i]] += 1; | ~~~^~~ urkepi.c:651:19: warning: array subscript has type ‘char’ [-Wchar-subscripts] 651 | if (fbin[seq[i]] > expect) | ~~~^~~ urkepi.c:657:19: warning: array subscript has type ‘char’ [-Wchar-subscripts] 657 | if (fbin[seq[i]] > expect) | ~~~^~~ urkepi.c: In function ‘OptimizeEpiHP’: urkepi.c:782:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 782 | epip->epiarray[seq[j]] += 1; | ~~~^~~ urkepi.c:797:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 797 | epip->epiarray[seq[j]] += 1; | ~~~^~~ urkepi.c:837:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 837 | epip->epiarray[seq[n]] -= 1; | ~~~^~~ urkepi.c: In function ‘OptimizeEpiProbFunc’: urkepi.c:982:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 982 | epip->epiarray[seq[n]] += 1; | ~~~^~~ urkepi.c:994:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 994 | epip->epiarray[seq[n]] += 1; | ~~~^~~ urkepi.c: At top level: urkepi.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkepi.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ In function ‘OptimizeEpiProbFunc’, inlined from ‘FilterEpi’ at urkepi.c:1190:5: urkepi.c:1052:20: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized] 1052 | cfap->left = left; | ~~~~~~~~~~~^~~~~~ urkepi.c: In function ‘FilterEpi’: urkepi.c:936:50: note: ‘left’ was declared here 936 | Int4 i, n, j, k, start, stop, loop, fact, left, right; | ^~~~ In function ‘OptimizeEpiProbFunc’, inlined from ‘FilterEpi’ at urkepi.c:1190:5: urkepi.c:1053:21: warning: ‘right’ may be used uninitialized [-Wmaybe-uninitialized] 1053 | cfap->right = right; | ~~~~~~~~~~~~^~~~~~~ urkepi.c: In function ‘FilterEpi’: urkepi.c:936:56: note: ‘right’ was declared here 936 | Int4 i, n, j, k, start, stop, loop, fact, left, right; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkfltr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkfltr.h:51, from urkfltr.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkfltr.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkdust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkdust.h:51, from urkdust.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkdust.c: In function ‘DustMe_h’: urkdust.c:196:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 196 | (dcvp->curlevel <= newlevel) && dcvp->curend == loop+1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ urkdust.c: In function ‘DustForGraph’: urkdust.c:776:17: warning: variable ‘drphead’ set but not used [-Wunused-but-set-variable] 776 | DustRegionPtr drphead; | ^~~~~~~ urkdust.c: At top level: urkdust.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urksigu.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urksigu.h:57, from urksigu.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urksigu.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seg.c seg.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ seg.c: In function ‘getprob’: seg.c:935:15: warning: ‘ans2’ may be used uninitialized [-Wmaybe-uninitialized] 935 | ans = ans1 + ans2 - totseq; | ~~~~~^~~~~~ seg.c:916:23: note: ‘ans2’ was declared here 916 | FloatHi ans, ans1, ans2, totseq; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkbias.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from urkbias.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkbias.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkcnsrt.h:60, from urkcnsrt.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkcnsrt.c:1203:13: warning: ‘ScanFrame’ defined but not used [-Wunused-function] 1203 | static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame, | ^~~~~~~~~ urkcnsrt.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ urkcnsrt.c: In function ‘Scan3Frames’: urkcnsrt.c:1385:19: warning: ‘length’ may be used uninitialized [-Wmaybe-uninitialized] 1385 | for (i = n; i < length; i++) | ~~^~~~~~~~ urkcnsrt.c:1312:34: note: ‘length’ was declared here 1312 | Int4 i, n, start, stop, length, chunk; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF urktree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urktree.h:51, from urktree.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urktree.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urktree.c,v 6.6 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pseed3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pseed3.c:176: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pseed3.c: In function ‘SeedPruneHitsFromSeedReturn’: pseed3.c:230:17: warning: variable ‘curSegs’ set but not used [-Wunused-but-set-variable] 230 | DenseSegPtr curSegs, testSegs; /*Used to extract ids from curSeqAlign, testSeqAlign*/ | ^~~~~~~ pseed3.c: In function ‘seedEngineCore’: pseed3.c:507:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 507 | while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) { | ^~~~~~~ pseed3.c: In function ‘output_hits’: pseed3.c:1202:10: warning: variable ‘posBaseIndex’ set but not used [-Wunused-but-set-variable] 1202 | Int4 posBaseIndex; /*loop index for copying pos results arrays*/ | ^~~~~~~~~~~~ pseed3.c: In function ‘init_order’: pseed3.c:1483:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1483 | seedSearch->order[seedSearch->pchars[i]] = i; | ^ pseed3.c:1483:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1483 | seedSearch->order[seedSearch->pchars[i]] = i; | ~~~~~~~~~~~~~~~~~~^~~ pseed3.c:1487:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1487 | seedSearch->charMultiple[i] = 0; | ^ pseed3.c:1489:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1489 | if (seedSearch->standardProb[i] > seedepsilon) { | ^ pseed3.c:1490:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1490 | matrixRow = matrix[i]; | ^ pseed3.c:1493:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1493 | if (seedSearch->standardProb[j] > seedepsilon) | ^ pseed3.c:1494:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1494 | rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]); | ^ pseed3.c:1494:93: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1494 | rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]); | ^ pseed3.c:1496:35: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1496 | seedSearch->charMultiple[i] = rowSum; | ^ pseed3.c: At top level: pseed3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pseed3.c,v 6.54 2008/10/31 18:51:07 madden Exp $"; | ^~~~~ pseed3.c: In function ‘seedParallelFill’: pseed3.c:712:68: warning: iteration 100 invokes undefined behavior [-Waggressive-loop-optimizations] 712 | returnData->seedSearch->name_space[i] = seedSearch->name_space[i]; | ~~~~~~~~~~~~~~~~~~~~~~^~~ pseed3.c:711:18: note: within this loop 711 | for( i = 0; i <= BUF_SIZE; i++) x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pattern1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pattern1.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pattern1.c: In function ‘init_pattern’: pattern1.c:286:77: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | positionProbability = seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c:303:78: warning: array subscript has type ‘char’ [-Wchar-subscripts] 303 | positionProbability += seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c:317:78: warning: array subscript has type ‘char’ [-Wchar-subscripts] 317 | positionProbability -= seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c: In function ‘find_hitsS_DNA’: pattern1.c:534:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 534 | if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { | ^~~ pattern1.c:547:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 547 | if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { | ^~~ pattern1.c: At top level: pattern1.c:744:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 744 | static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch) | ^~~ pattern1.c: In function ‘and’: pattern1.c:750:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 750 | if (result[i] = (a[i] & b[i])) | ^~~~~~ pattern1.c: In function ‘align’: pattern1.c:1102:14: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1102 | if (leftd >= 1) | ^ pattern1.c: In function ‘pat_output’: pattern1.c:1637:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1637 | else | ^~~~ pattern1.c:1639:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1639 | ValNodeCopyStr(info_vnp, 0, buffer); | ^~~~~~~~~~~~~~ pattern1.c: At top level: pattern1.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pattern1.c,v 6.22 2006/08/04 21:11:17 papadopo Exp $"; | ^~~~~ pattern1.c: In function ‘align’: pattern1.c:1158:15: warning: ‘CDrow’ may be used uninitialized [-Wmaybe-uninitialized] 1158 | score = (CDrow-1)->CC; | ~~~~~~^~~~~~~~~~~~~~~ pattern1.c:1049:25: note: ‘CDrow’ was declared here 1049 | register dp_ptr CDrow; /*points to a row of CD*/ | ^~~~~ pattern1.c: In function ‘get_patLL’: pattern1.c:1393:19: warning: ‘pos’ may be used uninitialized [-Wmaybe-uninitialized] 1393 | for (j = 0; j < pos; j+= wordIndex) { | ~~^~~~~ pattern1.c:1363:10: note: ‘pos’ was declared here 1363 | Int4 pos; /*keeps track of how many intermediate hits*/ | ^~~ pattern1.c: In function ‘get_patL’: pattern1.c:1348:10: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | *end = wordIndex*BITS_PACKED_PER_WORD+j; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:1311:10: note: ‘j’ was declared here 1311 | Int4 j; /*index over bits in a word*/ | ^ In function ‘longpacking2’, inlined from ‘init_pattern’ at pattern1.c:357:7: pattern1.c:859:10: warning: ‘tj’ may be used uninitialized [-Wmaybe-uninitialized] 859 | if (placeIndex==numPlacesInPattern || inputPatternMasked[placeIndex] < 0 | ^ pattern1.c: In function ‘init_pattern’: pattern1.c:192:11: note: ‘tj’ was declared here 192 | Int4 tj; /*temporary copy of j*/ | ^~ pattern1.c: In function ‘align_of_pattern’: pattern1.c:1506:30: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 1506 | local_score += ALIGN_B(querySeq-1, dbSeq-1, hitArray1[wordIndex+1], hitArray2[wordIndex+1], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1507 | BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:1425:14: note: ‘data’ was declared here 1425 | data_dp *data; /*stores dynaic program info*/ | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF impatool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from impatool.c:73: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ impatool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $"; | ^~~~~ In file included from ../include/ncbi.h:59: impatool.c: In function ‘IMPALAPrintHelp’: ../include/ncbimem.h:232:23: warning: ‘ret_buffer’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree impatool.c:288:17: note: ‘ret_buffer’ was declared here 288 | CharPtr ret_buffer; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF posit2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from posit2.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ posit2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mbalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/mbalign.h:4, from mbalign.c:176: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mbalign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF vecscrn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vecscrn.h:74, from vecscrn.c:103: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vecscrn.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: vecscrn.c,v 6.137 2005/12/27 14:46:44 madden Exp $"; | ^~~~~ vecscrn.c: In function ‘VSPrintOverviewFromSeqLocs’: vecscrn.c:1078:24: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1078 | while (tmp) | ^~~ vecscrn.c:993:75: note: ‘tmp’ was declared here 993 | SeqLocPtr seqloc1=NULL, seqloc2=NULL, seqloc3=NULL, seqloc4=NULL, tmp; | ^~~ vecscrn.c: In function ‘VSPrintListFromSeqLocs’: vecscrn.c:1188:24: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1188 | while (tmp) | ^~~ vecscrn.c:1152:75: note: ‘tmp’ was declared here 1152 | SeqLocPtr seqloc1=NULL, seqloc2=NULL, seqloc3=NULL, seqloc4=NULL, tmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF mblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mblast.c:710: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mblast.c: In function ‘BioseqMegaBlastEngineCore’: mblast.c:961:19: warning: statement with no effect [-Wunused-value] 961 | stop_timer("BioseqBlastEngineCore: before do_the_blast_run()"); | ^ mblast.c:987:12: warning: statement with no effect [-Wunused-value] 987 | stop_timer("MegaBlastEngineCore: after do_the_blast_run()"); | ^ mblast.c:942:21: warning: variable ‘seqalign’ set but not used [-Wunused-but-set-variable] 942 | SeqAlignPtr seqalign, PNTR seqalignp; | ^~~~~~~~ mblast.c: In function ‘MegaBlastSetUpSearchInternalByLoc’: mblast.c:1167:16: warning: variable ‘avglen’ set but not used [-Wunused-but-set-variable] 1167 | Nlm_FloatHi avglen; | ^~~~~~ mblast.c: In function ‘MegaBlastPackAlignmentsByQuery’: mblast.c:1829:14: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 1829 | SeqLocPtr slp; | ^~~ mblast.c: In function ‘MegaBlastWordFinder_disc_1b’: mblast.c:2372:32: warning: variable ‘mask’ set but not used [-Wunused-but-set-variable] 2372 | register Int4 s_off, ecode, mask, q_off, extra_code; | ^~~~ mblast.c: At top level: mblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: mblast.c,v 6.215 2006/09/21 13:42:37 madden Exp $"; | ^~~~~ mblast.c: In function ‘MegaBlastWordFinder_disc’: mblast.c:2250:53: warning: ‘ecode2’ may be used uninitialized [-Wmaybe-uninitialized] 2250 | (((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) { | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c:2024:17: note: ‘ecode2’ was declared here 2024 | Int4 ecode1, ecode2; | ^~~~~~ mblast.c:2117:51: warning: ‘ecode1’ may be used uninitialized [-Wmaybe-uninitialized] 2117 | (((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0) | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c:2024:9: note: ‘ecode1’ was declared here 2024 | Int4 ecode1, ecode2; | ^~~~~~ In function ‘MegaBlastWordFinder_disc_1b’, inlined from ‘MegaBlastWordFinder’ at mblast.c:2749:17: mblast.c:2620:54: warning: ‘ecode2’ may be used uninitialized [-Wmaybe-uninitialized] 2620 | (((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) { | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c: In function ‘MegaBlastWordFinder’: mblast.c:2373:17: note: ‘ecode2’ was declared here 2373 | Int4 ecode1, ecode2; | ^~~~~~ In function ‘MegaBlastWordFinder_disc_1b’, inlined from ‘MegaBlastWordFinder’ at mblast.c:2749:17: mblast.c:2475:52: warning: ‘ecode1’ may be used uninitialized [-Wmaybe-uninitialized] 2475 | (((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0) | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c: In function ‘MegaBlastWordFinder’: mblast.c:2373:9: note: ‘ecode1’ was declared here 2373 | Int4 ecode1, ecode2; | ^~~~~~ mblast.c: In function ‘MegaBlastGapInfoToSeqAlign’: mblast.c:3575:11: warning: ‘seqalign’ may be used uninitialized [-Wmaybe-uninitialized] 3575 | return seqalign; | ^~~~~~~~ mblast.c:3504:16: note: ‘seqalign’ was declared here 3504 | SeqAlignPtr seqalign, seqalign_var, sap; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF rpsutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/rpsutil.h:128, from rpsutil.c:281: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rpsutil.c: In function ‘getAuxInformation’: rpsutil.c:399:30: warning: the comparison will always evaluate as ‘true’ for the address of ‘underlyingMatrixName’ will never be NULL [-Waddress] 399 | if (underlyingMatrixName != NULL) | ^~ rpsutil.c:382:10: note: ‘underlyingMatrixName’ declared here 382 | Char underlyingMatrixName[PATH_MAX]; /*name of matrix to read*/ | ^~~~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSBlastSearchLight’: rpsutil.c:1838:10: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1838 | Int2 status; | ^~~~~~ rpsutil.c: In function ‘SaveUntilChar’: rpsutil.c:2190:13: warning: comparison between pointer and zero character constant [-Wpointer-compare] 2190 | if (ptr != NULLB) | ^~ rpsutil.c:2190:9: note: did you mean to dereference the pointer? 2190 | if (ptr != NULLB) | ^ rpsutil.c: In function ‘RPSBgetCddHits’: rpsutil.c:2210:21: warning: variable ‘found_score’ set but not used [-Wunused-but-set-variable] 2210 | Boolean found_score = FALSE; | ^~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from rpsutil.c:282: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘getAuxInformation’: rpsutil.c:398:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 398 | fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:404:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 404 | fscanf(matrixAuxiliaryFile,"%d\n", gap_open); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:405:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 405 | fscanf(matrixAuxiliaryFile,"%d\n", gap_extend); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf(matrixAuxiliaryFile, "%le", &Kungapped); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:407:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 407 | fscanf(matrixAuxiliaryFile, "%le", &Hungapped); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:408:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 408 | fscanf(matrixAuxiliaryFile, "%d", &maxLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:409:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 409 | fscanf(matrixAuxiliaryFile, "%d", &dbLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:410:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 410 | fscanf(matrixAuxiliaryFile, "%lf", &privateScalingFactor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:415:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 415 | fscanf(matrixAuxiliaryFile, "%d", &maxLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:416:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 416 | fscanf(matrixAuxiliaryFile, "%le", &(rpsinfo->karlinK[index])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c: At top level: rpsutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: rpsutil.c,v 6.76 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:451:28: warning: ‘.rps’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 451 | sprintf(rps_matrix, "%s.rps", rpsinfo->rdfp->full_filename); | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:451:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:452:28: warning: ‘.loo’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 452 | sprintf(rps_lookup, "%s.loo", rpsinfo->rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:452:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:453:25: warning: ‘.aux’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 453 | sprintf(rps_aux, "%s.aux", rpsinfo->rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:453:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSAlignTraceBack’: rpsutil.c:1433:24: warning: ‘rev_subject_length’ may be used uninitialized [-Wmaybe-uninitialized] 1433 | seqalign = BlastGetGapAlgnTbck (search, 0, TRUE, FALSE, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1434 | subject, subject_length, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1435 | rev_subject, rev_subject_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:1295:41: note: ‘rev_subject_length’ was declared here 1295 | Int4 index, index1, subject_length, rev_subject_length; | ^~~~~~~~~~~~~~~~~~ rpsutil.c:1444:32: warning: ‘posMatrix’ may be used uninitialized [-Wmaybe-uninitialized] 1444 | search->sbp->posMatrix = posMatrix; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ rpsutil.c:1296:18: note: ‘posMatrix’ was declared here 1296 | Int4Ptr PNTR posMatrix; | ^~~~~~~~~ rpsutil.c: In function ‘RPSCalcEValue’: rpsutil.c:1269:30: warning: ‘posMatrix’ may be used uninitialized [-Wmaybe-uninitialized] 1269 | search->sbp->posMatrix = posMatrix; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ rpsutil.c:1188:16: note: ‘posMatrix’ was declared here 1188 | Int4Ptr PNTR posMatrix; | ^~~~~~~~~ In file included from ../include/ncbi.h:62: rpsutil.c: In function ‘RPSBgetCddHits’: ../include/ncbistr.h:284:25: warning: ‘dbname’ may be used uninitialized [-Wmaybe-uninitialized] 284 | #define Nlm_StrCmp strcmp rpsutil.c:2212:21: note: ‘dbname’ was declared here 2212 | CharPtr dbname; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF kappa.c kappa.c: In function ‘Kappa_SequenceGetProteinRange’: kappa.c:1399:7: warning: unused variable ‘i’ [-Wunused-variable] 1399 | int i; | ^ kappa.c: At top level: kappa.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: kappa.c,v 6.94 2013/11/04 15:42:10 boratyng Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF xmlblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/xmlblast.h:89, from xmlblast.c:171: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ xmlblast.c: In function ‘PSIXmlInit’: xmlblast.c:1239:13: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 1239 | Boolean retval = FALSE; | ^~~~~~ xmlblast.c: At top level: xmlblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: xmlblast.c,v 6.41 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ xmlblast.c: In function ‘BXMLGetSeqLineForStdSeg’: xmlblast.c:373:28: warning: ‘genetic_code2’ may be used uninitialized [-Wmaybe-uninitialized] 373 | CharPtr genetic_code1, genetic_code2; | ^~~~~~~~~~~~~ xmlblast.c: In function ‘BXMLSeqAlignToHits’: xmlblast.c:867:36: warning: ‘hspp’ may be used uninitialized [-Wmaybe-uninitialized] 867 | if((hspp->next = BXMLGetHspFromSeqAlign(sap2, is_aa, chain, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 868 | is_ooframe, mask_loc)) == NULL) | ~~~~~~~~~~~~~~~~~~~~~~ xmlblast.c:799:12: note: ‘hspp’ was declared here 799 | HspPtr hspp; | ^~~~ xmlblast.c: In function ‘SeqAlignToHits’: xmlblast.c:1646:24: warning: ‘hspp’ may be used uninitialized [-Wmaybe-uninitialized] 1646 | hspp->next = GetHspFromSeqAlign(sap2, ungapped, &hsp_count); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlblast.c:1618:11: note: ‘hspp’ was declared here 1618 | HspPtr hspp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF bxmlobj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from bxmlobj.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bxmlobj.c: In function ‘BlastOutputAsnRead’: bxmlobj.c:96:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 96 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘ParametersAsnRead’: bxmlobj.c:361:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 361 | AsnReadFunc func; | ^~~~ bxmlobj.c:360:12: warning: unused variable ‘isError’ [-Wunused-variable] 360 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: In function ‘IterationAsnRead’: bxmlobj.c:613:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 613 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘StatisticsAsnRead’: bxmlobj.c:829:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 829 | AsnReadFunc func; | ^~~~ bxmlobj.c:828:12: warning: unused variable ‘isError’ [-Wunused-variable] 828 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: In function ‘HitAsnRead’: bxmlobj.c:1039:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1039 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘HspAsnRead’: bxmlobj.c:1244:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1244 | AsnReadFunc func; | ^~~~ bxmlobj.c:1243:12: warning: unused variable ‘isError’ [-Wunused-variable] 1243 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: At top level: bxmlobj.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bxmlobj.c,v 6.11 2006/09/18 15:20:39 bealer Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dotseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/tofasta.h:47, from ../include/dotseq.h:63, from dotseq.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dotseq.c:96:36: warning: missing braces around initializer [-Wmissing-braces] 96 | static Int4 DOTblosum62[24][24] = { | ^ 97 | 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4, | { } 98 | -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4, | { } 99 | -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4, | { } 100 | -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4, | { } 101 | 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4, | { } 102 | -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4, | { } 103 | -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4, | { } 104 | 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4, | { } 105 | -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4, | { } 106 | -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4, | { } 107 | -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4, | { } 108 | -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4, | { } 109 | -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4, | { } 110 | -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4, | { } 111 | -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4, | { } 112 | 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4, | { } 113 | 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4, | { } 114 | -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4, | { } 115 | -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4, | { } 116 | 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4, | { } 117 | -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4, | { } 118 | -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4, | { } 119 | 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4, | { } 120 | -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1 | { 121 | }; | } dotseq.c: In function ‘DOT_BuildPLookup’: dotseq.c:887:31: warning: variable ‘found_ambig’ set but not used [-Wunused-but-set-variable] 887 | Boolean EXACTMATCH, found_ambig, saved_index = FALSE; | ^~~~~~~~~~~ dotseq.c:885:19: warning: unused variable ‘threshold’ [-Wunused-variable] 885 | Int4 threshold=13; /* one-hit heuristics T must be at least 13*/ | ^~~~~~~~~ dotseq.c:883:19: warning: unused variable ‘index’ [-Wunused-variable] 883 | Int4 index = 0; | ^~~~~ dotseq.c: In function ‘DOT_ComputeHits’: dotseq.c:1043:47: warning: variable ‘q_end’ set but not used [-Wunused-but-set-variable] 1043 | Uint1Ptr s, subject0, s_end, q_end; | ^~~~~ dotseq.c:1041:19: warning: unused variable ‘saved_index’ [-Wunused-variable] 1041 | Boolean saved_index = FALSE; | ^~~~~~~~~~~ dotseq.c:1039:19: warning: unused variable ‘threshold’ [-Wunused-variable] 1039 | Int4 threshold=13; | ^~~~~~~~~ dotseq.c: In function ‘DOT_SPI_FindBestAlnByDotPlot’: dotseq.c:2016:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 2016 | Uint1 strand; | ^~~~~~ dotseq.c:2015:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2015 | Int4 start2; | ^~~~~~ dotseq.c:2014:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2014 | Int4 start1; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from dotseq.c:87: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dotseq.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: dotseq.c,v 6.14 2006/07/13 17:16:20 bollin Exp $"; | ^~~~~ In function ‘DOT_ScoreCount’, inlined from ‘DOT_BuildHitList’ at dotseq.c:1327:5: dotseq.c:1260:16: warning: ‘hitlist’ may be used uninitialized [-Wmaybe-uninitialized] 1260 | score=hitlist[0]->score; | ~~~~~~~^~~ dotseq.c: In function ‘DOT_BuildHitList’: dotseq.c:1309:19: note: ‘hitlist’ was declared here 1309 | DOTDiagPtr PNTR hitlist; | ^~~~~~~ In function ‘DOT_ScoreCount’, inlined from ‘DOT_BuildHitList’ at dotseq.c:1327:5: dotseq.c:1264:11: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 1264 | while (i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF spidey.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/spidey.h:102, from spidey.c:263: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ spidey.c: In function ‘SPI_PrintResult’: spidey.c:1740:21: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 1740 | Int4 offset; | ^~~~~~ spidey.c: In function ‘SPI_AlnSinglemRNAToPieces’: spidey.c:2854:19: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 2854 | if (spot->from == spot->to == 0) | ~~~~~~~~~~~^~~~~~~~~~~ spidey.c: In function ‘SPI_FillInLastmRNAHoles’: spidey.c:6299:21: warning: variable ‘internal’ set but not used [-Wunused-but-set-variable] 6299 | Boolean internal; | ^~~~~~~~ spidey.c: In function ‘SPI_FindBestAlnByDotPlot’: spidey.c:6445:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 6445 | Uint1 strand; | ^~~~~~ spidey.c:6444:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 6444 | Int4 start2; | ^~~~~~ spidey.c:6443:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 6443 | Int4 start1; | ^~~~~~ spidey.c: In function ‘SPI_ConnectAlnPieces’: spidey.c:7814:30: warning: variable ‘tmparray’ set but not used [-Wunused-but-set-variable] 7814 | SPI_FragPtr PNTR tmparray; | ^~~~~~~~ spidey.c:7800:25: warning: variable ‘sfpprev’ set but not used [-Wunused-but-set-variable] 7800 | SPI_FragPtr sfpprev; | ^~~~~~~ spidey.c: In function ‘SPI_AdjustSplicesInPieces’: spidey.c:8448:23: warning: variable ‘minus’ set but not used [-Wunused-but-set-variable] 8448 | Boolean minus; | ^~~~~ spidey.c: In function ‘SPI_CheckMrnaOrder’: spidey.c:10296:35: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10296 | if ((ival->strand == Seq_strand_plus == ival2->strand spidey.c:10300:38: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10300 | || (ival->strand == Seq_strand_minus == ival2->strand spidey.c:10313:35: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10313 | if ((ival->strand == Seq_strand_plus == ival2->strand spidey.c:10315:38: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10315 | || (ival->strand == Seq_strand_plus == ival2->strand In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/spidey.h:103: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ spidey.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: spidey.c,v 6.74 2016/09/02 14:57:38 ucko Exp $"; | ^~~~~ spidey.c: In function ‘SPI_GetProteinFrommRNA’: spidey.c:9765:14: warning: ‘c1start’ may be used uninitialized [-Wmaybe-uninitialized] 9765 | tmp += c1start; | ^~ spidey.c:9727:18: note: ‘c1start’ was declared here 9727 | Int4 c1start; | ^~~~~~~ spidey.c:9771:14: warning: ‘c2start’ may be used uninitialized [-Wmaybe-uninitialized] 9771 | tmp += c2start; | ^~ spidey.c:9728:18: note: ‘c2start’ was declared here 9728 | Int4 c2start; | ^~~~~~~ spidey.c:9777:14: warning: ‘c3start’ may be used uninitialized [-Wmaybe-uninitialized] 9777 | tmp += c3start; | ^~ spidey.c:9729:18: note: ‘c3start’ was declared here 9729 | Int4 c3start; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF motif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/motif.h:45, from motif.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ motif.c: In function ‘MOT_FindPolyA’: motif.c:86:18: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 86 | Uint1 buf[MOT_WINSIZE]; | ^~~ motif.c: In function ‘MOT_FindKozak’: motif.c:216:18: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 216 | Uint1 buf[MOT_WINSIZE]; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/motif.h:48: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ motif.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blfmtutl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blfmtutl.c:175: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blfmtutl.c: In function ‘CBStatisticsGetReference’: blfmtutl.c:593:11: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 593 | } else | ^~~~ blfmtutl.c:595:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 595 | add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE); | ^~~~~~~~~~~~~~~~~~~~~~ blfmtutl.c: In function ‘BlastPrintTabularResults’: blfmtutl.c:1281:16: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1281 | for (index=1; ssp->next; index++) | ^~~ blfmtutl.c:1283:20: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1283 | num_gap_opens = index / 2; | ^~~~~~~~~~~~~ blfmtutl.c: At top level: blfmtutl.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blfmtutl.c,v 1.44 2012/10/10 14:05:50 fongah2 Exp $"; | ^~~~~ blfmtutl.c: In function ‘BlastPrintTabularResults’: blfmtutl.c:1076:11: warning: ‘query_id’ may be used uninitialized [-Wmaybe-uninitialized] 1076 | if (SeqIdComp(query_id, old_query_id) != SIC_YES) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blfmtutl.c:1039:13: note: ‘query_id’ was declared here 1039 | SeqIdPtr query_id, old_query_id = NULL, subject_id, old_subject_id = NULL; | ^~~~~~~~ blfmtutl.c:1117:13: warning: ‘alignments_count’ may be used uninitialized [-Wmaybe-uninitialized] 1117 | if (--alignments_count < 0) | ^ blfmtutl.c:1048:9: note: ‘alignments_count’ was declared here 1048 | Int4 alignments_count; | ^~~~~~~~~~~~~~~~ blfmtutl.c:1350:21: warning: ‘q_start’ may be used uninitialized [-Wmaybe-uninitialized] 1350 | q_start += q_shift; | ~~~~~~~~^~~~~~~~~~ blfmtutl.c:1035:9: note: ‘q_start’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~~~ blfmtutl.c:1351:19: warning: ‘q_end’ may be used uninitialized [-Wmaybe-uninitialized] 1351 | q_end += q_shift; | ~~~~~~^~~~~~~~~~ blfmtutl.c:1035:18: note: ‘q_end’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~ blfmtutl.c:1352:21: warning: ‘s_start’ may be used uninitialized [-Wmaybe-uninitialized] 1352 | s_start += s_shift; | ~~~~~~~~^~~~~~~~~~ blfmtutl.c:1035:25: note: ‘s_start’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~~~ blfmtutl.c:1353:19: warning: ‘s_end’ may be used uninitialized [-Wmaybe-uninitialized] 1353 | s_end += s_shift; | ~~~~~~^~~~~~~~~~ blfmtutl.c:1035:34: note: ‘s_end’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~ blfmtutl.c: In function ‘BlastSetUserErrorString’: blfmtutl.c:1448:21: warning: ‘title’ may be used uninitialized [-Wmaybe-uninitialized] 1448 | else if (title) | ^ blfmtutl.c:1413:33: note: ‘title’ was declared here 1413 | CharPtr buf_start, ptr, title; | ^~~~~ rm -f libncbitool.a ar cru libncbitool.a csim.o db_slist.o dust.o blast_dust.o falign.o g_any.o sim2.o sim3.o sim4.o simutil.o slist.o sec.o tfuns.o toasn3.o toporg.o pobutil.o stsutil.o suggadj.o suggest.o suggslp.o blast.o blastutl.o blastool.o blastconcat.o splutil.o gapxdrop.o bandalg0.o bandalg1.o bandalg2.o bandalg3.o bandalg4.o bandalg5.o bandalgn.o blastkar.o actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o pseed3.o pattern1.o impatool.o posit2.o mbalign.o vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o dotseq.o spidey.o motif.o blfmtutl.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbitool.a ../lib ranlib ../lib/libncbitool.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF compo_heap.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF smith_waterman.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF redo_alignment.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c rm -f libblastcompadj.a ar cru libblastcompadj.a matrix_frequency_data.o compo_mode_condition.o composition_adjustment.o nlm_linear_algebra.o optimize_target_freq.o compo_heap.o smith_waterman.o redo_alignment.o unified_pvalues.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblastcompadj.a ../lib ranlib ../lib/libblastcompadj.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontg.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontmb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontmb.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pictogif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from pictogif.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gdfontl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontl.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gdfonts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfonts.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -DWIN_GIF -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbidrwg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidrwg.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidrwg.c: In function ‘Nlm_ClearRgn’: ncbidrwg.c:6081:16: warning: variable ‘ntool’ set but not used [-Wunused-but-set-variable] 6081 | Nlm_RgnTool ntool; | ^~~~~ ncbidrwg.c: In function ‘Nlm_DiffRgn’: ncbidrwg.c:6273:16: warning: variable ‘ntool3’ set but not used [-Wunused-but-set-variable] 6273 | Nlm_RgnTool ntool3; | ^~~~~~ ncbidrwg.c:6272:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6272 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6271:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6271 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_XorRgn’: ncbidrwg.c:6324:16: warning: variable ‘ntool3’ set but not used [-Wunused-but-set-variable] 6324 | Nlm_RgnTool ntool3; | ^~~~~~ ncbidrwg.c:6323:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6323 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6322:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6322 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_EqualRgn’: ncbidrwg.c:6353:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6353 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6352:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6352 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_EmptyRgn’: ncbidrwg.c:6381:17: warning: variable ‘ntool’ set but not used [-Wunused-but-set-variable] 6381 | Nlm_RgnTool ntool; | ^~~~~ ncbidrwg.c: In function ‘Nlm_CopyPixmap’: ncbidrwg.c:7040:25: warning: variable ‘height’ set but not used [-Wunused-but-set-variable] 7040 | Nlm_Int2 height; | ^~~~~~ ncbidrwg.c:7039:25: warning: variable ‘width’ set but not used [-Wunused-but-set-variable] 7039 | Nlm_Int2 width; | ^~~~~ ncbidrwg.c: In function ‘Nlm_GetColorRGB’: ncbidrwg.c:1373:10: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1373 | return (Nlm_Uint4)i; | ^~~~~~~~~~~~ ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ rm -f libvibgif.a ar cru libvibgif.a gdfontg.o gdfontmb.o gdfontt.o pictogif.o gdfontl.o gdfonts.o ncbidrwg.o drawing.o mapping.o picture.o ncbimain.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibgif.a ../lib ranlib ../lib/libvibgif.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF algorend.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/viewer3d.h:125, from algorend.c:584: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ algorend.c: In function ‘ColorFromSS’: algorend.c:893:10: warning: unused variable ‘rsult’ [-Wunused-variable] 893 | Int2 rsult = 0; | ^~~~~ algorend.c: In function ‘Cn3D_RenWire’: algorend.c:1400:10: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1400 | PMLD pmldThis = NULL; | ^~~~~~~~ algorend.c:1399:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1399 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ algorend.c:1398:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1398 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘Cn3D_ColSeqCons’: algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1795 | pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i); | ^ algorend.c: In function ‘RenderObject’: algorend.c:3135:25: warning: variable ‘fZTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3135:19: warning: variable ‘fYTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3135:13: warning: variable ‘fXTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3134:29: warning: variable ‘fZFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3134:21: warning: variable ‘fYFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3134:13: warning: variable ‘fXFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c: In function ‘RenderLabel’: algorend.c:3393:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 3393 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘RenderBond’: algorend.c:3554:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3554 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderHalfWormBond’: algorend.c:3673:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3673 | PMSD pmsdParent; | ^~~~~~~~~~ algorend.c:3671:24: warning: variable ‘pmad2’ set but not used [-Wunused-but-set-variable] 3671 | PMAD pmad0, pmad1, pmad2, pmad3; | ^~~~~ algorend.c: In function ‘RenderAnAtom’: algorend.c:3758:10: warning: unused variable ‘pmadFrom’ [-Wunused-variable] 3758 | PMAD pmadFrom = NULL; | ^~~~~~~~ algorend.c:3757:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3757 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderAllAtom’: algorend.c:3829:9: warning: variable ‘iMenu’ set but not used [-Wunused-but-set-variable] 3829 | int iMenu; | ^~~~~ algorend.c:3815:11: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 3815 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c:3811:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 3811 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderGraph’: algorend.c:4498:10: warning: unused variable ‘bReservedThis’ [-Wunused-variable] 4498 | Byte bReservedThis = 0; | ^~~~~~~~~~~~~ algorend.c: In function ‘LabelChainTermini’: algorend.c:4772:14: warning: unused variable ‘pmbdThis’ [-Wunused-variable] 4772 | PMBD pmbdThis = NULL; | ^~~~~~~~ algorend.c:4771:15: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 4771 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderMolecule’: algorend.c:4871:11: warning: variable ‘pdnmmThis’ set but not used [-Wunused-but-set-variable] 4871 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘fnARLoop’: algorend.c:5556:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 5556 | Int2 iTest; | ^~~~~ algorend.c: In function ‘AlgorithmicRendering’: algorend.c:5684:10: warning: unused variable ‘i’ [-Wunused-variable] 5684 | Int2 i = 0; | ^ algorend.c:5683:10: warning: unused variable ‘Cn3d_LayerNow_sofar’ [-Wunused-variable] 5683 | Int2 Cn3d_LayerNow_sofar = 0; | ^~~~~~~~~~~~~~~~~~~ algorend.c: In function ‘Do3DOrigin’: algorend.c:5756:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 5756 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c:5751:13: warning: variable ‘fTo’ set but not used [-Wunused-but-set-variable] 5751 | FloatLo fTo[3]; | ^~~ algorend.c:5750:13: warning: variable ‘fFrom’ set but not used [-Wunused-but-set-variable] 5750 | FloatLo fFrom[3]; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from algorend.c:598: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ algorend.c:2265:13: warning: ‘LabelGroupOnOffProc’ defined but not used [-Wunused-function] 2265 | static void LabelGroupOnOffProc(GrouP g) | ^~~~~~~~~~~~~~~~~~~ algorend.c:717:16: warning: ‘Cn3d_CopyToNode’ defined but not used [-Wunused-variable] 717 | static Boolean Cn3d_CopyToNode = FALSE; | ^~~~~~~~~~~~~~~ In file included from ../include/viewer3d.h:129: algorend.c: In function ‘RenderLabel’: ../include/pictur3d.h:235:27: warning: ‘iX’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:10: note: ‘iX’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ ../include/pictur3d.h:235:27: warning: ‘iY’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:14: note: ‘iY’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ ../include/pictur3d.h:235:27: warning: ‘iZ’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:18: note: ‘iZ’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3442:41: warning: ‘fXCen’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3391:13: note: ‘fXCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3443:41: warning: ‘fYCen’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3391:20: note: ‘fYCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3444:41: warning: ‘fZCen’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3391:27: note: ‘fZCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3442:41: warning: ‘fXTo’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3390:13: note: ‘fXTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3443:41: warning: ‘fYTo’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3390:19: note: ‘fYTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3444:41: warning: ‘fZTo’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3390:25: note: ‘fZTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3442:22: warning: ‘fXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:13: note: ‘fXFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3443:22: warning: ‘fYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:21: note: ‘fYFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3444:22: warning: ‘fZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:29: note: ‘fZFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c: In function ‘MasterChangeRenderProc.isra.0’: algorend.c:1295:29: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 1295 | pars->PBBRender = k; | ~~~~~~~~~~~~~~~~^~~ algorend.c:1138:16: note: ‘k’ was declared here 1138 | Int2 i, j, k; | ^ algorend.c: In function ‘RenderObject’: ../include/pictur3d.h:234:27: warning: ‘iXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:10: note: ‘iXFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:18: note: ‘iYFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:26: note: ‘iZFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iXTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:10: note: ‘iXTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:234:27: warning: ‘iYTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:16: note: ‘iYTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:234:27: warning: ‘iZTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:22: note: ‘iZTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c: In function ‘Do3DOrigin’: ../include/pictur3d.h:232:27: warning: ‘iXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:10: note: ‘iXFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:18: note: ‘iYFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:26: note: ‘iZFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iXTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:10: note: ‘iXTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:232:27: warning: ‘iYTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:16: note: ‘iYTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:232:27: warning: ‘iZTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:22: note: ‘iZTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmsel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsel.c:60: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dopen.c:394: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dopen.c: In function ‘Cn3D_OpenStart’: cn3dopen.c:722:10: warning: unused variable ‘iBioseq’ [-Wunused-variable] 722 | Int4 iBioseq = 0; | ^~~~~~~ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:1000:19: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1000 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dopen.c:989:25: warning: unused variable ‘pbsasThis’ [-Wunused-variable] 989 | BiostrucAlignSeqPtr pbsasThis = NULL; | ^~~~~~~~~ cn3dopen.c: In function ‘Cn3D_NetOpenBiostruc’: cn3dopen.c:1310:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 1310 | ButtoN b; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dopen.c:412: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from cn3dopen.c:413: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ cn3dopen.c:431:15: warning: ‘Cn3D_bOpenBrowse’ defined but not used [-Wunused-variable] 431 | static ButtoN Cn3D_bOpenBrowse; | ^~~~~~~~~~~~~~~~ cn3dopen.c:430:15: warning: ‘Cn3D_wOpen’ defined but not used [-Wunused-variable] 430 | static WindoW Cn3D_wOpen; | ^~~~~~~~~~ In function ‘Cn3D_ShredCBlast’, inlined from ‘MMDB_ReadMime’ at cn3dopen.c:1058:23: cn3dopen.c:527:8: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 527 | if (salp) { | ^ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:513:15: note: ‘salp’ was declared here 513 | SeqAlign *salp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dsave.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dsave.c:157: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportAsnNow’: cn3dsave.c:375:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 375 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dsave.c:372:24: warning: variable ‘pbsfThis’ set but not used [-Wunused-but-set-variable] 372 | BiostrucFeaturePtr pbsfThis; | ^~~~~~~~ cn3dsave.c:366:10: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 366 | PMSD pmsdSlave = NULL, pmsdMaster = NULL; | ^~~~~~~~~ cn3dsave.c:362:27: warning: variable ‘FirstSlave’ set but not used [-Wunused-but-set-variable] 362 | Boolean iCn3d = TRUE, FirstSlave = FALSE; | ^~~~~~~~~~ cn3dsave.c:357:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 357 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveBiostruc’: cn3dsave.c:524:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 524 | ButtoN b; | ^ cn3dsave.c:523:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 523 | GrouP gMS; | ^~~ cn3dsave.c:518:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 518 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportDictNow’: cn3dsave.c:598:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 598 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c:596:10: warning: unused variable ‘iCount’ [-Wunused-variable] 596 | Int4 iCount = 0; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveDictionary’: cn3dsave.c:629:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 629 | ButtoN b; | ^ cn3dsave.c:624:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 624 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_SaveSub’: cn3dsave.c:688:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 688 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dsave.c:171: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dsave.c:184:15: warning: ‘Cn3D_bFeatOn’ defined but not used [-Wunused-variable] 184 | static ButtoN Cn3D_bFeatOn; | ^~~~~~~~~~~~ In file included from cn3dsave.c:165: ../include/asnmime.h:119:21: warning: ‘amp’ defined but not used [-Wunused-variable] 119 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnmime.h:118:19: warning: ‘at’ defined but not used [-Wunused-variable] 118 | static AsnTypePtr at = atx; | ^~ ../include/asnmime.h:117:23: warning: ‘avn’ defined but not used [-Wunused-variable] 117 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/asnmime.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnmime.h12"; | ^~~~~~~~~~~ cn3dsave.c: In function ‘Cn3D_GetSubSet’: cn3dsave.c:289:24: warning: ‘isep’ may be used uninitialized [-Wmaybe-uninitialized] 289 | isep->next = SeqEntryNew(); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ cn3dsave.c:261:28: note: ‘isep’ was declared here 261 | SeqEntry *sep = NULL, *isep; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dxprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dxprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportPDB’: cn3dxprt.c:209:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 209 | ButtoN b; | ^ cn3dxprt.c:208:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 208 | GrouP gMS; | ^~~ cn3dxprt.c:203:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 203 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportKin’: cn3dxprt.c:381:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 381 | ButtoN b; | ^ cn3dxprt.c:380:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 380 | GrouP gMS; | ^~~ cn3dxprt.c:375:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 375 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportSub’: cn3dxprt.c:513:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 513 | IteM i; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dwin.c:647: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces] 733 | { | ^ 734 | 255, 255, 255, /* default 0 */ | { } 735 | 255, 20, 147, /* hotpink 1 */ | { } 736 | 255, 0, 255, /* magenta 2 */ | { } 737 | 155, 48, 255, /* purple 3 */ | { } 738 | 0, 0, 255, /* blue 4 */ | { } 739 | 30, 144, 255, /* sky 5 */ | { } 740 | 0, 255, 255, /* cyan 6 */ | { } 741 | 0, 255, 127, /* sea 7 */ | { } 742 | 0, 255, 0, /* green 8 */ | { } 743 | 255, 255, 0, /* yellow 9 */ | { } 744 | 255, 165, 0, /* gold 10 */ | { } 745 | 255, 69, 0, /* orange 11 */ | { } 746 | 255, 0, 0, /* red 12 */ | { } 747 | 255, 114, 86, /* pink 13 */ | { } 748 | 255, 174, 185, /* pinktint 14 */ | { } 749 | 255, 255, 255, /* white 15 */ | { } 750 | 0, 0, 0, /* black 16 */ | { } 751 | 176, 226, 255, /* bluetint 17 */ | { } 752 | 154, 255, 154, /* greentint 18 */ | { } 753 | 255, 236, 139, /* yellowtint 19 */ | { } 754 | 125, 125, 125, /* gray 20 */ | { } 755 | 139, 87, 66, /* brown 21 */ | { } 756 | 255, 0, 0, /* perm colors 22: red */ | { } 757 | 0, 255, 0, /* perm colors 23: green */ | { } 758 | 255, 0, 255, /* perm colors 24: magenta */ | { } 759 | 30, 144, 255, /* perm colors 25: sky */ | { } 760 | 155, 48, 255, /* perm colors 26: purple */ | { } 761 | 0, 255, 0, /* SS colors 27: helix, green */ | { } 762 | 255, 165, 0, /* SS colors 28: strand, gold */ | { } 763 | 255, 69, 0, /* SS colors 29: turn, orange */ | { } 764 | 0, 255, 255, /* SS colors 30: coil, cyan */ | { } 765 | 255, 255, 0, /* highlight colors 31: yellow */ | { } 766 | 0, 0, 0, /* background colors 32: black */ | { } 767 | 160, 82, 45, /* sienna 33 */ | { } 768 | 240, 230, 140, /* khaki 34 */ | { } 769 | 171, 130, 255, /* light purple 35 */ | { } 770 | 255, 200, 0, /* orange yellow 36 */ | { } 771 | 117, 128, 160, /* 37 */ | { } 772 | 5, 53, 239, /* 38 */ | { } 773 | 27, 62, 255, /* 39 */ | { } 774 | 84, 110, 203, /* 40 */ | { } 775 | 216, 77, 84, /* 41 */ | { } 776 | 125, 128, 135, /* 42 */ | { } 777 | 237, 29, 61, /* 43 */ | { } 778 | 184, 118, 120, /* 44 */ | { } 779 | 155, 9, 0, /* 45 */ | { } 780 | 155, 119, 107, /* 46 */ | { } 781 | 80, 110, 196, /* 47 */ | { } 782 | 122, 127, 157, /* 48 */ | { } 783 | 50, 85, 241, /* 49 */ | { } 784 | 201, 93, 91, /* 50 */ | { } 785 | 254, 0, 5, /* 51 */ | { } 786 | 155, 137, 133, /* 52 */ | { } 787 | 3, 53, 246 /* 53 */ | { 788 | }; | } cn3dwin.c: In function ‘Viewer3DGroups’: cn3dwin.c:1728:10: warning: unused variable ‘groups’ [-Wunused-variable] 1728 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Viewer3DViewer’: cn3dwin.c:1784:10: warning: unused variable ‘groups’ [-Wunused-variable] 1784 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_AlignEdit’: cn3dwin.c:1936:10: warning: unused variable ‘iCount’ [-Wunused-variable] 1936 | Int2 iCount = 0; | ^~~~~~ cn3dwin.c:1935:10: warning: variable ‘pmmdThis’ set but not used [-Wunused-but-set-variable] 1935 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dwin.c:1933:17: warning: unused variable ‘salp’ [-Wunused-variable] 1933 | SeqAlignPtr salp = NULL; | ^~~~ cn3dwin.c:1931:29: warning: variable ‘pmsdSlave’ set but not used [-Wunused-but-set-variable] 1931 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dwin.c:1930:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 1930 | PDNMS pdnmsSlave = NULL; | ^~~~~~~~~~ cn3dwin.c: In function ‘Cn3D_Menus’: cn3dwin.c:2131:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2131 | (Nlm_VoidPtr) i, NULL); | ^ In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from cn3dwin.c:665: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dwin.c:1626:13: warning: ‘HLmolecule_MA’ defined but not used [-Wunused-function] 1626 | static void HLmolecule_MA(MAPtr ma, | ^~~~~~~~~~~~~ cn3dwin.c:1428:13: warning: ‘HLatom_MA’ defined but not used [-Wunused-function] 1428 | static void HLatom_MA(MAPtr ma, | ^~~~~~~~~ cn3dwin.c:929:13: warning: ‘Cn3D_MoveCB’ defined but not used [-Wunused-function] 929 | static void Cn3D_MoveCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:922:13: warning: ‘Cn3D_ZoomCB’ defined but not used [-Wunused-function] 922 | static void Cn3D_ZoomCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:688:13: warning: ‘Cn3D_iModelCtrl’ defined but not used [-Wunused-variable] 688 | static IteM Cn3D_iModelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:682:13: warning: ‘Cn3D_iLabelCtrl’ defined but not used [-Wunused-variable] 682 | static IteM Cn3D_iLabelCtrl = NULL; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dentr.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsg.c:254: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmsg.c: In function ‘SeqStrucMediaMsgFunc’: cn3dmsg.c:593:19: warning: variable ‘omudp’ set but not used [-Wunused-but-set-variable] 593 | OMUserDataPtr omudp = NULL; | ^~~~~ In file included from ../include/sqnutils.h:51, from cn3dmsg.c:267: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmsg.c:271: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmatn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmatn.c:173: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmatn.c: In function ‘FindMM’: cn3dmatn.c:217:29: warning: unused variable ‘pdnmsThisSlave’ [-Wunused-variable] 217 | PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL; | ^~~~~~~~~~~~~~ cn3dmatn.c: In function ‘DoMediaHL’: cn3dmatn.c:249:10: warning: variable ‘MainAtom’ set but not used [-Wunused-but-set-variable] 249 | Byte MainAtom = 0; | ^~~~~~~~ cn3dmatn.c:247:10: warning: unused variable ‘paldThis’ [-Wunused-variable] 247 | PALD paldThis = NULL; | ^~~~~~~~ cn3dmatn.c:246:11: warning: unused variable ‘pvnalThis’ [-Wunused-variable] 246 | PVNAL pvnalThis = NULL; | ^~~~~~~~~ cn3dmatn.c:245:10: warning: unused variable ‘pmadThis’ [-Wunused-variable] 245 | PMAD pmadThis = NULL; | ^~~~~~~~ cn3dmatn.c:244:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 244 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ cn3dmatn.c: In function ‘Cn3DCheckAndDoHighlight’: cn3dmatn.c:372:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 372 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmatn.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmodl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dmodl.c:302: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckNoSingleHighlight’: cn3dmodl.c:353:11: warning: unused variable ‘pdnmgThis’ [-Wunused-variable] 353 | PDNMG pdnmgThis = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckHighlighted’: cn3dmodl.c:364:29: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 364 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ReSetVisibleStatus’: cn3dmodl.c:508:10: warning: unused variable ‘pmgd’ [-Wunused-variable] 508 | PMGD pmgd = NULL; | ^~~~ cn3dmodl.c:507:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 507 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:506:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 506 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘fnAlignList’: cn3dmodl.c:996:25: warning: unused variable ‘itemtype’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:996:11: warning: unused variable ‘entityID’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:995:14: warning: unused variable ‘sipThis’ [-Wunused-variable] 995 | SeqIdPtr sipThis = NULL; | ^~~~~~~ cn3dmodl.c:993:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 993 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SynchronizeModVisibleStatus’: cn3dmodl.c:1065:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 1065 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:1064:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 1064 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SetResidueVisibilities’: cn3dmodl.c:1201:11: warning: unused variable ‘pvnmoThis’ [-Wunused-variable] 1201 | PVNMO pvnmoThis = NULL; | ^~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmodl.c:319: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dmodl.c:323: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:413:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 413 | sprintf(MolName, "%4s %2s %2d", | ^~ cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767] 413 | sprintf(MolName, "%4s %2s %2d", | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:413:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 32 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:410:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 410 | sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName, | ^~ In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:410:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 24 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dshim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dshim.c:131: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dmesh.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmesh.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:103:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 103 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmesh.c: In function ‘Cn3D_OpenMesh’: cn3dmesh.c:151:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 151 | ButtoN b; | ^ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | &(Mesh.NumTri)); | ~~~~~~~~~~~~~~~ cn3dmesh.c:119:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | &(Mesh.Vertices[i].Vertex[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 | &(Mesh.Vertices[i].Vertex[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 | &(Mesh.Vertices[i].Vertex[2]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 123 | &(Mesh.Vertices[i].Normal[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 124 | &(Mesh.Vertices[i].Normal[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | &(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:129:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 | &Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:133:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 | &Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 | &Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 | &Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 | &lDummy); | ~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF cn3dstyl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dstyl.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dstyl.c: In function ‘GetThisSpecialAlgorRenderSet’: cn3dstyl.c:459:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 459 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘GetSpecialAlgorRenderSet’: cn3dstyl.c:641:10: warning: unused variable ‘parsThis’ [-Wunused-variable] 641 | PARS parsThis = NULL; | ^~~~~~~~ cn3dstyl.c:640:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 640 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ChangeSpecialLabelsProc’: cn3dstyl.c:866:44: warning: unused variable ‘PDBOn’ [-Wunused-variable] 866 | Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn = | ^~~~~ cn3dstyl.c: In function ‘lFeatureEditedAction’: cn3dstyl.c:1136:10: warning: unused variable ‘val’ [-Wunused-variable] 1136 | Int4 val = 0; | ^~~ cn3dstyl.c: In function ‘bFeatureMoveAction’: cn3dstyl.c:1153:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1153 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘bFeatureEditAction’: cn3dstyl.c:1176:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1176 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ModelControls’: cn3dstyl.c:1364:19: warning: variable ‘ppt13’ set but not used [-Wunused-but-set-variable] 1364 | PrompT ppt12, ppt13, ppt14; | ^~~~~ cn3dstyl.c:1362:36: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:12: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c: In function ‘GetBiostrucFeatureLocationForHihglightedResidues’: cn3dstyl.c:1728:30: warning: variable ‘SingleInterval’ set but not used [-Wunused-but-set-variable] 1728 | Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound = | ^~~~~~~~~~~~~~ cn3dstyl.c:1725:20: warning: variable ‘iMolCurrent’ set but not used [-Wunused-but-set-variable] 1725 | Int2 iMol = 0, iMolCurrent = 0; | ^~~~~~~~~~~ cn3dstyl.c: In function ‘MakeBiostrucFeatureSetForUserDefinedFeature’: cn3dstyl.c:2122:60: warning: unused variable ‘bsfsp_tail’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c:2122:41: warning: unused variable ‘bsfsp_head’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c: In function ‘GetUserDefinedFeature’: cn3dstyl.c:2196:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 2196 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘Cn3DIndexUserDefinedFeature’: cn3dstyl.c:2551:23: warning: variable ‘sfpThis’ set but not used [-Wunused-but-set-variable] 2551 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c:2549:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 2549 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dstyl.c:2548:11: warning: unused variable ‘pdnmmHead’ [-Wunused-variable] 2548 | PDNMM pdnmmHead = NULL; | ^~~~~~~~~ cn3dstyl.c:2547:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 2547 | PMSD pmsdThis = NULL; | ^~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dstyl.c:89: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:456:30: warning: ‘GetThisSpecialAlgorRenderSet’ defined but not used [-Wunused-function] 456 | static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:149:15: warning: ‘bResetFeatureTitle’ defined but not used [-Wunused-variable] 149 | static ButtoN bResetFeatureTitle; | ^~~~~~~~~~~~~~~~~~ cn3dstyl.c:144:14: warning: ‘Cn3D_pupModelStyleItem’ defined but not used [-Wunused-variable] 144 | static PopuP Cn3D_pupModelStyleItem; | ^~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c: In function ‘CopyLocation’: cn3dstyl.c:496:27: warning: ‘rsipNewHead’ may be used uninitialized [-Wmaybe-uninitialized] 496 | rspNew->data.ptrvalue = (VoidPtr) rsipNewHead; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:478:61: note: ‘rsipNewHead’ was declared here 478 | ResidueIntervalPntrPtr rsipNew = NULL, rsipPrev = NULL, rsipNewHead, | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqcons.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from seqcons.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from seqcons.c:115: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from seqcons.c:116: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ seqcons.c:263:19: warning: ‘CSC_Blosum62Fields’ defined but not used [-Wunused-const-variable=] 263 | static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] = | ^~~~~~~~~~~~~~~~~~ seqcons.c: In function ‘CSC_Algorithm_ByBlosum62’: seqcons.c:398:12: warning: ‘maxScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:30: note: ‘maxScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ seqcons.c:398:12: warning: ‘minScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:40: note: ‘minScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ rm -f libncbicn3d.a ar cru libncbicn3d.a algorend.o cn3dmsel.o cn3dopen.o cn3dsave.o cn3dxprt.o cn3dwin.o cn3dentr.o cn3dmsg.o cn3dmatn.o cn3dmodl.o cn3dshim.o cn3dmesh.o cn3dstyl.o seqcons.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicn3d.a ../lib ranlib ../lib/libncbicn3d.a mv algorend.o algorend.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL algorend.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/shim3d.h:153, from algorend.c:582: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ algorend.c: In function ‘Cn3D_SetOGLFont’: algorend.c:791:24: warning: unused variable ‘currentUnderlined’ [-Wunused-variable] 791 | currentUnderlined = FALSE; | ^~~~~~~~~~~~~~~~~ algorend.c:790:45: warning: unused variable ‘currentItalic’ [-Wunused-variable] 790 | static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE, | ^~~~~~~~~~~~~ algorend.c:790:24: warning: unused variable ‘currentBold’ [-Wunused-variable] 790 | static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE, | ^~~~~~~~~~~ algorend.c:789:40: warning: unused variable ‘currentSize’ [-Wunused-variable] 789 | static Nlm_Int2 currentIndex = -1, currentSize = -1; | ^~~~~~~~~~~ algorend.c:789:21: warning: unused variable ‘currentIndex’ [-Wunused-variable] 789 | static Nlm_Int2 currentIndex = -1, currentSize = -1; | ^~~~~~~~~~~~ algorend.c: In function ‘ColorFromSS’: algorend.c:893:10: warning: unused variable ‘rsult’ [-Wunused-variable] 893 | Int2 rsult = 0; | ^~~~~ algorend.c: In function ‘Cn3D_RenWire’: algorend.c:1400:10: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1400 | PMLD pmldThis = NULL; | ^~~~~~~~ algorend.c:1399:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1399 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ algorend.c:1398:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1398 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘Cn3D_ColSeqCons’: algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1795 | pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i); | ^ algorend.c: In function ‘MasterChangeLabelsProc’: algorend.c:2075:44: warning: unused variable ‘TopOn’ [-Wunused-variable] 2075 | Boolean NumOn, NameOn, PDBOn, WhiteOn, TopOn; | ^~~~~ algorend.c:2073:13: warning: unused variable ‘k’ [-Wunused-variable] 2073 | Int2 i, k, nameval; | ^ algorend.c: In function ‘ResetLabelCtrls’: algorend.c:2272:25: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2272 | Int2 i, val, style, size, termStyle; | ^~~~ algorend.c: In function ‘LabelControls’: algorend.c:2434:19: warning: variable ‘ppt11’ set but not used [-Wunused-but-set-variable] 2434 | PrompT ppt10, ppt11; | ^~~~~ algorend.c:2431:36: warning: unused variable ‘ppt7’ [-Wunused-variable] 2431 | PrompT ppt1, ppt2, ppt3, ppt4, ppt7, ppt8, ppt9; | ^~~~ algorend.c: In function ‘Cn3D_SetQualityFromAppParams’: algorend.c:2649:9: warning: unused variable ‘i’ [-Wunused-variable] 2649 | int i; | ^ algorend.c: In function ‘OGL_Quality’: algorend.c:2769:23: warning: unused variable ‘q’ [-Wunused-variable] 2769 | Nlm_PrompT bp, p, q; | ^ algorend.c:2769:20: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 2769 | Nlm_PrompT bp, p, q; | ^ algorend.c:2769:16: warning: variable ‘bp’ set but not used [-Wunused-but-set-variable] 2769 | Nlm_PrompT bp, p, q; | ^~ algorend.c: In function ‘RenderControls’: algorend.c:2893:12: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 2893 | PrompT ppt5; | ^~~~ algorend.c: In function ‘RenderObject’: algorend.c:3138:10: warning: unused variable ‘iCylRadius’ [-Wunused-variable] 3138 | Int4 iCylRadius; | ^~~~~~~~~~ algorend.c:3137:22: warning: unused variable ‘iZTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3137:16: warning: unused variable ‘iYTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3137:10: warning: unused variable ‘iXTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3136:26: warning: unused variable ‘iZFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3136:18: warning: unused variable ‘iYFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3136:10: warning: unused variable ‘iXFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3133:10: warning: unused variable ‘i’ [-Wunused-variable] 3133 | Int4 i = 0; | ^ algorend.c: In function ‘RenderLabel’: algorend.c:3394:10: warning: variable ‘paldPrim’ set but not used [-Wunused-but-set-variable] 3394 | PALD paldPrim = NULL; | ^~~~~~~~ algorend.c:3393:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 3393 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c:3389:18: warning: unused variable ‘iZ’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3389:14: warning: unused variable ‘iY’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3389:10: warning: unused variable ‘iX’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c: In function ‘RenderBond’: algorend.c:3554:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3554 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderHalfWormBond’: algorend.c:3673:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3673 | PMSD pmsdParent; | ^~~~~~~~~~ algorend.c:3671:24: warning: variable ‘pmad2’ set but not used [-Wunused-but-set-variable] 3671 | PMAD pmad0, pmad1, pmad2, pmad3; | ^~~~~ algorend.c: In function ‘RenderAnAtom’: algorend.c:3758:10: warning: unused variable ‘pmadFrom’ [-Wunused-variable] 3758 | PMAD pmadFrom = NULL; | ^~~~~~~~ algorend.c: In function ‘RenderAllAtom’: algorend.c:3829:9: warning: variable ‘iMenu’ set but not used [-Wunused-but-set-variable] 3829 | int iMenu; | ^~~~~ algorend.c:3815:11: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 3815 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c:3811:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 3811 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderGraph’: algorend.c:4498:10: warning: unused variable ‘bReservedThis’ [-Wunused-variable] 4498 | Byte bReservedThis = 0; | ^~~~~~~~~~~~~ algorend.c: In function ‘LabelChainTermini’: algorend.c:4772:14: warning: unused variable ‘pmbdThis’ [-Wunused-variable] 4772 | PMBD pmbdThis = NULL; | ^~~~~~~~ algorend.c:4771:15: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 4771 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderMolecule’: algorend.c:4871:11: warning: variable ‘pdnmmThis’ set but not used [-Wunused-but-set-variable] 4871 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘fnARLoop’: algorend.c:5556:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 5556 | Int2 iTest; | ^~~~~ algorend.c: In function ‘AlgorithmicRendering’: algorend.c:5684:10: warning: unused variable ‘i’ [-Wunused-variable] 5684 | Int2 i = 0; | ^ algorend.c:5683:10: warning: unused variable ‘Cn3d_LayerNow_sofar’ [-Wunused-variable] 5683 | Int2 Cn3d_LayerNow_sofar = 0; | ^~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from algorend.c:598: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ algorend.c:2265:13: warning: ‘LabelGroupOnOffProc’ defined but not used [-Wunused-function] 2265 | static void LabelGroupOnOffProc(GrouP g) | ^~~~~~~~~~~~~~~~~~~ algorend.c:717:16: warning: ‘Cn3d_CopyToNode’ defined but not used [-Wunused-variable] 717 | static Boolean Cn3d_CopyToNode = FALSE; | ^~~~~~~~~~~~~~~ algorend.c: In function ‘MasterChangeRenderProc’: algorend.c:1295:29: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 1295 | pars->PBBRender = k; | ~~~~~~~~~~~~~~~~^~~ algorend.c:1138:16: note: ‘k’ was declared here 1138 | Int2 i, j, k; | ^ algorend.c: In function ‘RenderLabel’: algorend.c:3442:41: warning: ‘fXCen’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3391:13: note: ‘fXCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3443:41: warning: ‘fYCen’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3391:20: note: ‘fYCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3444:41: warning: ‘fZCen’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3391:27: note: ‘fZCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3437:30: warning: ‘fXTo’ may be used uninitialized [-Wmaybe-uninitialized] 3437 | fXCen = fXTo + (fXTo - fXFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:13: note: ‘fXTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3438:30: warning: ‘fYTo’ may be used uninitialized [-Wmaybe-uninitialized] 3438 | fYCen = fYTo + (fYTo - fYFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:19: note: ‘fYTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3439:30: warning: ‘fZTo’ may be used uninitialized [-Wmaybe-uninitialized] 3439 | fZCen = fZTo + (fZTo - fZFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:25: note: ‘fZTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3437:30: warning: ‘fXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3437 | fXCen = fXTo + (fXTo - fXFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:13: note: ‘fXFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3438:30: warning: ‘fYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3438 | fYCen = fYTo + (fYTo - fYFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:21: note: ‘fYFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3439:30: warning: ‘fZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3439 | fZCen = fZTo + (fZTo - fZFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:29: note: ‘fZFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ mv algorend.o algorend.glo mv algorend.tmp algorend.o mv cn3dmsel.o cn3dmsel.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsel.c:60: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv cn3dmsel.o cn3dmsel.glo mv cn3dmsel.tmp cn3dmsel.o mv cn3dopen.o cn3dopen.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dopen.c:394: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dopen.c: In function ‘Cn3D_OpenStart’: cn3dopen.c:722:10: warning: unused variable ‘iBioseq’ [-Wunused-variable] 722 | Int4 iBioseq = 0; | ^~~~~~~ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:1000:19: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1000 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dopen.c:989:25: warning: unused variable ‘pbsasThis’ [-Wunused-variable] 989 | BiostrucAlignSeqPtr pbsasThis = NULL; | ^~~~~~~~~ cn3dopen.c: In function ‘Cn3D_NetOpenBiostruc’: cn3dopen.c:1310:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 1310 | ButtoN b; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dopen.c:412: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from cn3dopen.c:413: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ cn3dopen.c:431:15: warning: ‘Cn3D_bOpenBrowse’ defined but not used [-Wunused-variable] 431 | static ButtoN Cn3D_bOpenBrowse; | ^~~~~~~~~~~~~~~~ cn3dopen.c:430:15: warning: ‘Cn3D_wOpen’ defined but not used [-Wunused-variable] 430 | static WindoW Cn3D_wOpen; | ^~~~~~~~~~ In function ‘Cn3D_ShredCBlast’, inlined from ‘MMDB_ReadMime’ at cn3dopen.c:1058:23: cn3dopen.c:527:8: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 527 | if (salp) { | ^ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:513:15: note: ‘salp’ was declared here 513 | SeqAlign *salp; | ^~~~ mv cn3dopen.o cn3dopen.glo mv cn3dopen.tmp cn3dopen.o mv cn3dsave.o cn3dsave.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dsave.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dsave.c:157: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dsave.c: In function ‘Cn3D_AddMatrix’: cn3dsave.c:206:41: warning: unused variable ‘bsfsp_new’ [-Wunused-variable] 206 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_new = NULL; | ^~~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportAsnNow’: cn3dsave.c:375:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 375 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dsave.c:372:24: warning: variable ‘pbsfThis’ set but not used [-Wunused-but-set-variable] 372 | BiostrucFeaturePtr pbsfThis; | ^~~~~~~~ cn3dsave.c:366:10: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 366 | PMSD pmsdSlave = NULL, pmsdMaster = NULL; | ^~~~~~~~~ cn3dsave.c:362:27: warning: variable ‘FirstSlave’ set but not used [-Wunused-but-set-variable] 362 | Boolean iCn3d = TRUE, FirstSlave = FALSE; | ^~~~~~~~~~ cn3dsave.c:357:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 357 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveBiostruc’: cn3dsave.c:524:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 524 | ButtoN b; | ^ cn3dsave.c:523:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 523 | GrouP gMS; | ^~~ cn3dsave.c:518:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 518 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportDictNow’: cn3dsave.c:598:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 598 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c:596:10: warning: unused variable ‘iCount’ [-Wunused-variable] 596 | Int4 iCount = 0; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveDictionary’: cn3dsave.c:629:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 629 | ButtoN b; | ^ cn3dsave.c:624:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 624 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_SaveSub’: cn3dsave.c:688:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 688 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dsave.c:171: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dsave.c:184:15: warning: ‘Cn3D_bFeatOn’ defined but not used [-Wunused-variable] 184 | static ButtoN Cn3D_bFeatOn; | ^~~~~~~~~~~~ In file included from cn3dsave.c:165: ../include/asnmime.h:119:21: warning: ‘amp’ defined but not used [-Wunused-variable] 119 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnmime.h:118:19: warning: ‘at’ defined but not used [-Wunused-variable] 118 | static AsnTypePtr at = atx; | ^~ ../include/asnmime.h:117:23: warning: ‘avn’ defined but not used [-Wunused-variable] 117 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/asnmime.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnmime.h12"; | ^~~~~~~~~~~ cn3dsave.c: In function ‘Cn3D_GetSubSet’: cn3dsave.c:289:24: warning: ‘isep’ may be used uninitialized [-Wmaybe-uninitialized] 289 | isep->next = SeqEntryNew(); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ cn3dsave.c:261:28: note: ‘isep’ was declared here 261 | SeqEntry *sep = NULL, *isep; | ^~~~ mv cn3dsave.o cn3dsave.glo mv cn3dsave.tmp cn3dsave.o mv cn3dxprt.o cn3dxprt.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dxprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dxprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportPDB’: cn3dxprt.c:209:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 209 | ButtoN b; | ^ cn3dxprt.c:208:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 208 | GrouP gMS; | ^~~ cn3dxprt.c:203:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 203 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportKin’: cn3dxprt.c:381:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 381 | ButtoN b; | ^ cn3dxprt.c:380:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 380 | GrouP gMS; | ^~~ cn3dxprt.c:375:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 375 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportSub’: cn3dxprt.c:513:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 513 | IteM i; | ^ mv cn3dxprt.o cn3dxprt.glo mv cn3dxprt.tmp cn3dxprt.o mv cn3dwin.o cn3dwin.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dwin.c:647: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces] 733 | { | ^ 734 | 255, 255, 255, /* default 0 */ | { } 735 | 255, 20, 147, /* hotpink 1 */ | { } 736 | 255, 0, 255, /* magenta 2 */ | { } 737 | 155, 48, 255, /* purple 3 */ | { } 738 | 0, 0, 255, /* blue 4 */ | { } 739 | 30, 144, 255, /* sky 5 */ | { } 740 | 0, 255, 255, /* cyan 6 */ | { } 741 | 0, 255, 127, /* sea 7 */ | { } 742 | 0, 255, 0, /* green 8 */ | { } 743 | 255, 255, 0, /* yellow 9 */ | { } 744 | 255, 165, 0, /* gold 10 */ | { } 745 | 255, 69, 0, /* orange 11 */ | { } 746 | 255, 0, 0, /* red 12 */ | { } 747 | 255, 114, 86, /* pink 13 */ | { } 748 | 255, 174, 185, /* pinktint 14 */ | { } 749 | 255, 255, 255, /* white 15 */ | { } 750 | 0, 0, 0, /* black 16 */ | { } 751 | 176, 226, 255, /* bluetint 17 */ | { } 752 | 154, 255, 154, /* greentint 18 */ | { } 753 | 255, 236, 139, /* yellowtint 19 */ | { } 754 | 125, 125, 125, /* gray 20 */ | { } 755 | 139, 87, 66, /* brown 21 */ | { } 756 | 255, 0, 0, /* perm colors 22: red */ | { } 757 | 0, 255, 0, /* perm colors 23: green */ | { } 758 | 255, 0, 255, /* perm colors 24: magenta */ | { } 759 | 30, 144, 255, /* perm colors 25: sky */ | { } 760 | 155, 48, 255, /* perm colors 26: purple */ | { } 761 | 0, 255, 0, /* SS colors 27: helix, green */ | { } 762 | 255, 165, 0, /* SS colors 28: strand, gold */ | { } 763 | 255, 69, 0, /* SS colors 29: turn, orange */ | { } 764 | 0, 255, 255, /* SS colors 30: coil, cyan */ | { } 765 | 255, 255, 0, /* highlight colors 31: yellow */ | { } 766 | 0, 0, 0, /* background colors 32: black */ | { } 767 | 160, 82, 45, /* sienna 33 */ | { } 768 | 240, 230, 140, /* khaki 34 */ | { } 769 | 171, 130, 255, /* light purple 35 */ | { } 770 | 255, 200, 0, /* orange yellow 36 */ | { } 771 | 117, 128, 160, /* 37 */ | { } 772 | 5, 53, 239, /* 38 */ | { } 773 | 27, 62, 255, /* 39 */ | { } 774 | 84, 110, 203, /* 40 */ | { } 775 | 216, 77, 84, /* 41 */ | { } 776 | 125, 128, 135, /* 42 */ | { } 777 | 237, 29, 61, /* 43 */ | { } 778 | 184, 118, 120, /* 44 */ | { } 779 | 155, 9, 0, /* 45 */ | { } 780 | 155, 119, 107, /* 46 */ | { } 781 | 80, 110, 196, /* 47 */ | { } 782 | 122, 127, 157, /* 48 */ | { } 783 | 50, 85, 241, /* 49 */ | { } 784 | 201, 93, 91, /* 50 */ | { } 785 | 254, 0, 5, /* 51 */ | { } 786 | 155, 137, 133, /* 52 */ | { } 787 | 3, 53, 246 /* 53 */ | { 788 | }; | } cn3dwin.c: In function ‘Cn3D_Default_HLColor’: cn3dwin.c:982:27: warning: variable ‘colorB’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c:982:19: warning: variable ‘colorG’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c:982:11: warning: variable ‘colorR’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_RedrawEx’: cn3dwin.c:1251:19: warning: unused variable ‘iColor’ [-Wunused-variable] 1251 | DDV_ColorCell iColor; | ^~~~~~ cn3dwin.c: In function ‘fnPreCHLresidue’: cn3dwin.c:1543:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1543 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dwin.c: In function ‘Viewer3DGroups’: cn3dwin.c:1728:10: warning: unused variable ‘groups’ [-Wunused-variable] 1728 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_AlignEdit’: cn3dwin.c:1936:10: warning: unused variable ‘iCount’ [-Wunused-variable] 1936 | Int2 iCount = 0; | ^~~~~~ cn3dwin.c:1935:10: warning: variable ‘pmmdThis’ set but not used [-Wunused-but-set-variable] 1935 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dwin.c:1933:17: warning: unused variable ‘salp’ [-Wunused-variable] 1933 | SeqAlignPtr salp = NULL; | ^~~~ cn3dwin.c:1931:29: warning: variable ‘pmsdSlave’ set but not used [-Wunused-but-set-variable] 1931 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dwin.c:1930:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 1930 | PDNMS pdnmsSlave = NULL; | ^~~~~~~~~~ cn3dwin.c: In function ‘Cn3D_Menus’: cn3dwin.c:2131:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2131 | (Nlm_VoidPtr) i, NULL); | ^ cn3dwin.c: In function ‘Cn3DWin’: cn3dwin.c:2364:5: warning: implicit declaration of function ‘Nlm_SetOGLContext’; did you mean ‘Nlm_InitAppContext’? [-Wimplicit-function-declaration] 2364 | Nlm_SetOGLContext(NULL, NULL, NULL, NULL); | ^~~~~~~~~~~~~~~~~ | Nlm_InitAppContext In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from cn3dwin.c:665: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dwin.c:1626:13: warning: ‘HLmolecule_MA’ defined but not used [-Wunused-function] 1626 | static void HLmolecule_MA(MAPtr ma, | ^~~~~~~~~~~~~ cn3dwin.c:1428:13: warning: ‘HLatom_MA’ defined but not used [-Wunused-function] 1428 | static void HLatom_MA(MAPtr ma, | ^~~~~~~~~ cn3dwin.c:1349:25: warning: ‘DoHighlightSeg’ defined but not used [-Wunused-function] 1349 | static void LIBCALLBACK DoHighlightSeg(PFB pfbThis, | ^~~~~~~~~~~~~~ cn3dwin.c:979:13: warning: ‘Cn3D_Default_HLColor’ defined but not used [-Wunused-function] 979 | static void Cn3D_Default_HLColor(IteM i) | ^~~~~~~~~~~~~~~~~~~~ cn3dwin.c:953:13: warning: ‘Cn3D_BgColor’ defined but not used [-Wunused-function] 953 | static void Cn3D_BgColor(IteM i) | ^~~~~~~~~~~~ cn3dwin.c:936:13: warning: ‘Cn3D_Default_BgColor’ defined but not used [-Wunused-function] 936 | static void Cn3D_Default_BgColor(IteM i) | ^~~~~~~~~~~~~~~~~~~~ cn3dwin.c:929:13: warning: ‘Cn3D_MoveCB’ defined but not used [-Wunused-function] 929 | static void Cn3D_MoveCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:922:13: warning: ‘Cn3D_ZoomCB’ defined but not used [-Wunused-function] 922 | static void Cn3D_ZoomCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:719:14: warning: ‘Cn3D_gViewCtrl’ defined but not used [-Wunused-variable] 719 | static GrouP Cn3D_gViewCtrl; | ^~~~~~~~~~~~~~ cn3dwin.c:713:14: warning: ‘Cn3D_gViewer’ defined but not used [-Wunused-variable] 713 | static GrouP Cn3D_gViewer; | ^~~~~~~~~~~~ cn3dwin.c:688:13: warning: ‘Cn3D_iModelCtrl’ defined but not used [-Wunused-variable] 688 | static IteM Cn3D_iModelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:682:13: warning: ‘Cn3D_iLabelCtrl’ defined but not used [-Wunused-variable] 682 | static IteM Cn3D_iLabelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:676:14: warning: ‘Cn3D_Vy’ defined but not used [-Wunused-variable] 676 | static Uint2 Cn3D_Vy, Cn3D_Rx; | ^~~~~~~ mv cn3dwin.o cn3dwin.glo mv cn3dwin.tmp cn3dwin.o mv cn3dentr.o cn3dentr.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dentr.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv cn3dentr.o cn3dentr.glo mv cn3dentr.tmp cn3dentr.o mv cn3dmsg.o cn3dmsg.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsg.c:254: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmsg.c: In function ‘SeqStrucMediaMsgFunc’: cn3dmsg.c:593:19: warning: variable ‘omudp’ set but not used [-Wunused-but-set-variable] 593 | OMUserDataPtr omudp = NULL; | ^~~~~ In file included from ../include/sqnutils.h:51, from cn3dmsg.c:267: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmsg.c:271: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv cn3dmsg.o cn3dmsg.glo mv cn3dmsg.tmp cn3dmsg.o mv cn3dmatn.o cn3dmatn.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmatn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmatn.c:173: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmatn.c: In function ‘FindMM’: cn3dmatn.c:217:29: warning: unused variable ‘pdnmsThisSlave’ [-Wunused-variable] 217 | PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL; | ^~~~~~~~~~~~~~ cn3dmatn.c: In function ‘DoMediaHL’: cn3dmatn.c:249:10: warning: variable ‘MainAtom’ set but not used [-Wunused-but-set-variable] 249 | Byte MainAtom = 0; | ^~~~~~~~ cn3dmatn.c:247:10: warning: unused variable ‘paldThis’ [-Wunused-variable] 247 | PALD paldThis = NULL; | ^~~~~~~~ cn3dmatn.c:246:11: warning: unused variable ‘pvnalThis’ [-Wunused-variable] 246 | PVNAL pvnalThis = NULL; | ^~~~~~~~~ cn3dmatn.c:245:10: warning: unused variable ‘pmadThis’ [-Wunused-variable] 245 | PMAD pmadThis = NULL; | ^~~~~~~~ cn3dmatn.c:244:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 244 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ cn3dmatn.c: In function ‘Cn3DCheckAndDoHighlight’: cn3dmatn.c:372:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 372 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmatn.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ mv cn3dmatn.o cn3dmatn.glo mv cn3dmatn.tmp cn3dmatn.o mv cn3dmodl.o cn3dmodl.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmodl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dmodl.c:302: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckNoSingleHighlight’: cn3dmodl.c:353:11: warning: unused variable ‘pdnmgThis’ [-Wunused-variable] 353 | PDNMG pdnmgThis = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckHighlighted’: cn3dmodl.c:364:29: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 364 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ReSetVisibleStatus’: cn3dmodl.c:508:10: warning: unused variable ‘pmgd’ [-Wunused-variable] 508 | PMGD pmgd = NULL; | ^~~~ cn3dmodl.c:507:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 507 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:506:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 506 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘fnAlignList’: cn3dmodl.c:996:25: warning: unused variable ‘itemtype’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:996:11: warning: unused variable ‘entityID’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:995:14: warning: unused variable ‘sipThis’ [-Wunused-variable] 995 | SeqIdPtr sipThis = NULL; | ^~~~~~~ cn3dmodl.c:993:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 993 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SynchronizeModVisibleStatus’: cn3dmodl.c:1065:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 1065 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:1064:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 1064 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SetResidueVisibilities’: cn3dmodl.c:1201:11: warning: unused variable ‘pvnmoThis’ [-Wunused-variable] 1201 | PVNMO pvnmoThis = NULL; | ^~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmodl.c:319: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dmodl.c:323: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:413:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 413 | sprintf(MolName, "%4s %2s %2d", | ^~ cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767] 413 | sprintf(MolName, "%4s %2s %2d", | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:413:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 32 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:410:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 410 | sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName, | ^~ In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:410:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 24 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mv cn3dmodl.o cn3dmodl.glo mv cn3dmodl.tmp cn3dmodl.o mv cn3dshim.o cn3dshim.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dshim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dshim.c:131: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dshim.c: In function ‘Cn3D_Size’: cn3dshim.c:413:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 413 | PMSD pmsdThis; | ^~~~~~~~ cn3dshim.c:412:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 412 | PDNMS pdnmsSlave; | ^~~~~~~~~~ cn3dshim.c: In function ‘Cn3D_SizeCB’: cn3dshim.c:399:36: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations] 399 | BoundBox->x[i + 1]) BoundBox->x[i + 1] = | ~~~~~~~~~~~^~~~~~~ cn3dshim.c:395:31: note: within this loop 395 | for (i = 0; i < 6; i += 2) { /* check to see if the atom lies outside the bound box */ | ~~^~~ cn3dshim.c:391:36: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 391 | BoundBox->x[i] = pflvDataThis[i / (int) 2]; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dshim.c:390:31: note: within this loop 390 | for (i = 0; i < 6; i++) { | ~~^~~ mv cn3dshim.o cn3dshim.glo mv cn3dshim.tmp cn3dshim.o mv cn3dmesh.o cn3dmesh.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmesh.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmesh.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:103:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 103 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmesh.c: In function ‘Cn3D_OpenMesh’: cn3dmesh.c:151:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 151 | ButtoN b; | ^ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | &(Mesh.NumTri)); | ~~~~~~~~~~~~~~~ cn3dmesh.c:119:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | &(Mesh.Vertices[i].Vertex[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 | &(Mesh.Vertices[i].Vertex[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 | &(Mesh.Vertices[i].Vertex[2]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 123 | &(Mesh.Vertices[i].Normal[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 124 | &(Mesh.Vertices[i].Normal[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | &(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:129:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 | &Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:133:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 | &Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 | &Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 | &Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 | &lDummy); | ~~~~~~~~ mv cn3dmesh.o cn3dmesh.glo mv cn3dmesh.tmp cn3dmesh.o mv cn3dstyl.o cn3dstyl.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dstyl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dstyl.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dstyl.c: In function ‘GetThisSpecialAlgorRenderSet’: cn3dstyl.c:459:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 459 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘GetSpecialAlgorRenderSet’: cn3dstyl.c:641:10: warning: unused variable ‘parsThis’ [-Wunused-variable] 641 | PARS parsThis = NULL; | ^~~~~~~~ cn3dstyl.c:640:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 640 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ChangeSpecialLabelsProc’: cn3dstyl.c:867:16: warning: unused variable ‘TopOn’ [-Wunused-variable] 867 | FALSE, TopOn = FALSE; | ^~~~~ cn3dstyl.c:866:44: warning: unused variable ‘PDBOn’ [-Wunused-variable] 866 | Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn = | ^~~~~ cn3dstyl.c:864:17: warning: unused variable ‘k’ [-Wunused-variable] 864 | Int2 i = 0, k = 0, nameval = 0; | ^ cn3dstyl.c: In function ‘ModelSetLabelCtrls’: cn3dstyl.c:1059:37: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 1059 | Int2 i = 0, val = 0, style = 0, size = 0; | ^~~~ cn3dstyl.c: In function ‘lFeatureEditedAction’: cn3dstyl.c:1136:10: warning: unused variable ‘val’ [-Wunused-variable] 1136 | Int4 val = 0; | ^~~ cn3dstyl.c: In function ‘bFeatureMoveAction’: cn3dstyl.c:1153:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1153 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘bFeatureEditAction’: cn3dstyl.c:1176:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1176 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ModelControls’: cn3dstyl.c:1364:19: warning: variable ‘ppt13’ set but not used [-Wunused-but-set-variable] 1364 | PrompT ppt12, ppt13, ppt14; | ^~~~~ cn3dstyl.c:1363:9: warning: unused variable ‘ppt11’ [-Wunused-variable] 1363 | ppt11; | ^~~~~ cn3dstyl.c:1362:60: warning: unused variable ‘ppt9’ [-Wunused-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:36: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:12: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c: In function ‘GetBiostrucFeatureLocationForHihglightedResidues’: cn3dstyl.c:1728:30: warning: variable ‘SingleInterval’ set but not used [-Wunused-but-set-variable] 1728 | Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound = | ^~~~~~~~~~~~~~ cn3dstyl.c:1725:20: warning: variable ‘iMolCurrent’ set but not used [-Wunused-but-set-variable] 1725 | Int2 iMol = 0, iMolCurrent = 0; | ^~~~~~~~~~~ cn3dstyl.c: In function ‘MakeBiostrucFeatureSetForUserDefinedFeature’: cn3dstyl.c:2122:60: warning: unused variable ‘bsfsp_tail’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c:2122:41: warning: unused variable ‘bsfsp_head’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c: In function ‘GetUserDefinedFeature’: cn3dstyl.c:2196:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 2196 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘Cn3DIndexUserDefinedFeature’: cn3dstyl.c:2551:23: warning: variable ‘sfpThis’ set but not used [-Wunused-but-set-variable] 2551 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c:2549:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 2549 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dstyl.c:2548:11: warning: unused variable ‘pdnmmHead’ [-Wunused-variable] 2548 | PDNMM pdnmmHead = NULL; | ^~~~~~~~~ cn3dstyl.c:2547:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 2547 | PMSD pmsdThis = NULL; | ^~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dstyl.c:89: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:456:30: warning: ‘GetThisSpecialAlgorRenderSet’ defined but not used [-Wunused-function] 456 | static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:149:15: warning: ‘bResetFeatureTitle’ defined but not used [-Wunused-variable] 149 | static ButtoN bResetFeatureTitle; | ^~~~~~~~~~~~~~~~~~ cn3dstyl.c:144:14: warning: ‘Cn3D_pupModelStyleItem’ defined but not used [-Wunused-variable] 144 | static PopuP Cn3D_pupModelStyleItem; | ^~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c: In function ‘CopyLocation’: cn3dstyl.c:496:27: warning: ‘rsipNewHead’ may be used uninitialized [-Wmaybe-uninitialized] 496 | rspNew->data.ptrvalue = (VoidPtr) rsipNewHead; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:478:61: note: ‘rsipNewHead’ was declared here 478 | ResidueIntervalPntrPtr rsipNew = NULL, rsipPrev = NULL, rsipNewHead, | ^~~~~~~~~~~ mv cn3dstyl.o cn3dstyl.glo mv cn3dstyl.tmp cn3dstyl.o mv seqcons.o seqcons.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF -D_OPENGL seqcons.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from seqcons.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from seqcons.c:115: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from seqcons.c:116: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ seqcons.c:263:19: warning: ‘CSC_Blosum62Fields’ defined but not used [-Wunused-const-variable=] 263 | static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] = | ^~~~~~~~~~~~~~~~~~ seqcons.c: In function ‘CSC_Algorithm_ByBlosum62’: seqcons.c:398:12: warning: ‘maxScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:30: note: ‘maxScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ seqcons.c:398:12: warning: ‘minScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:40: note: ‘minScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ mv seqcons.o seqcons.glo mv seqcons.tmp seqcons.o rm -f libncbicn3dOGL.a ar cru libncbicn3dOGL.a algorend.glo cn3dmsel.glo cn3dopen.glo cn3dsave.glo cn3dxprt.glo cn3dwin.glo cn3dentr.glo cn3dmsg.glo cn3dmatn.glo cn3dmodl.glo cn3dshim.glo cn3dmesh.glo cn3dstyl.glo seqcons.glo ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicn3dOGL.a ../lib ranlib ../lib/libncbicn3dOGL.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_engine.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_extend.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_filter.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hits.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_itree.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_lookup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_message.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seg.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_sw.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_setup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_stat.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_traceback.c blast_traceback.c: In function ‘BLAST_ComputeTraceback_MT’: blast_traceback.c:1500: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 1500 | #pragma omp parallel for default(none) num_threads(actual_num_threads) schedule(guided) if (actual_num_threads > 1) \ | blast_traceback.c:1524: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1524 | #pragma omp critical(retval) | blast_traceback.c:1530: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 1530 | #pragma omp flush(has_been_interrupted) | blast_traceback.c:1561: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1561 | #pragma omp critical(tback_gen_code) | blast_traceback.c:1591: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1591 | #pragma omp critical(retval) | blast_traceback.c:1631: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1631 | #pragma omp critical(tback_gen_code) | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_util.c blast_util.c: In function ‘BlastProgram2Number’: blast_util.c:306:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 306 | else if (strcasecmp("mapper", program) == 0) | ^~ blast_util.c:309:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 309 | return 0; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gapinfo.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF greedy_align.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF link_hsps.c link_hsps.c: In function ‘s_FwdCompareHSPs’: link_hsps.c:133:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 133 | else if (h1->context > h2->context) | ^~ link_hsps.c:136:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 136 | if (h1->query.offset < h2->query.offset) | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF na_ungapped.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_math.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbi_std.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF pattern.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_extend.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_lookup.c phi_lookup.c: In function ‘SPHIPatternSearchBlkNew’: phi_lookup.c:634:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 634 | localPattern[posIndex-1] = 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~ phi_lookup.c:411:11: note: at offset [-2147483648, -1] into destination object ‘localPattern’ of size 330 411 | Uint1 localPattern[PHI_MAX_PATTERN_LENGTH]; /*local variable to hold for each position whether | ^~~~~~~~~~~~ phi_lookup.c:634:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 634 | localPattern[posIndex-1] = 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~ phi_lookup.c:411:11: note: at offset -1 into destination object ‘localPattern’ of size 330 411 | Uint1 localPattern[PHI_MAX_PATTERN_LENGTH]; /*local variable to hold for each position whether | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF lookup_util.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_encoding.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_kappa.c blast_kappa.c: In function ‘Blast_RedoAlignmentCore_MT’: blast_kappa.c:3407: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3407 | #pragma omp parallel \ | blast_kappa.c:3426: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 3426 | #pragma omp for schedule(static) | blast_kappa.c:3428: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3428 | #pragma omp flush(interrupt) | blast_kappa.c:3489: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3489 | #pragma omp critical(intrpt) | blast_kappa.c:3491: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3491 | #pragma omp flush(interrupt) | blast_kappa.c:3504: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3504 | #pragma omp critical(intrpt) | blast_kappa.c:3506: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3506 | #pragma omp flush(interrupt) | blast_kappa.c:3722: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3722 | #pragma omp critical(intrpt) | blast_kappa.c:3724: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3724 | #pragma omp flush(interrupt) | blast_kappa.c:3730: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 3730 | #pragma omp barrier | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_parameters.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_posit.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_program.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_query_info.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tune.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c blast_nalookup.c: In function ‘s_NaHashLookupScanSubjectForWordCounts’: blast_nalookup.c:1850: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 1850 | #pragma omp parallel for if (num_threads > 1) num_threads(num_threads) \ | blast_nalookup.c:1858: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1858 | #pragma omp critical (get_sequence_for_word_counts) | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_aascan.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_nascan.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF split_query.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF index_ungapped.c In function ‘ir_fp_entry_destroy’, inlined from ‘ir_fp_entry_destroy’ at index_ungapped.c:45:22, inlined from ‘ir_fp_entry_create’ at index_ungapped.c:67:35, inlined from ‘ir_locate’ at index_ungapped.c:136:28: index_ungapped.c:48:16: warning: ‘result_38->entries’ may be used uninitialized [-Wmaybe-uninitialized] 48 | free( e->entries ); | ~^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_hspstream_mt_utils.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_traceback_mt_priv.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF boost_erf.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF jumper.c rm -f libblast.a ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblast.a ../lib ranlib ../lib/libblast.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_tabular.h:42, from ../include/algo/blast/api/blast_api.h:47, from blast_api.c:38: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:149:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fscanf(auxfile, "%s", buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:151:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fscanf(auxfile, "%d", &info->aux_info.gap_open_penalty); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:152:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fscanf(auxfile, "%d", &info->aux_info.gap_extend_penalty); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:153:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | fscanf(auxfile, "%le", &info->aux_info.ungapped_k); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:154:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 154 | fscanf(auxfile, "%le", &info->aux_info.ungapped_h); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:155:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(auxfile, "%d", &info->aux_info.max_db_seq_length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:156:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(auxfile, "%d", &info->aux_info.db_length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:157:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(auxfile, "%lf", &info->aux_info.scale_factor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:161:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 161 | fscanf(auxfile, "%d", &seq_size); /* not used */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:162:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fscanf(auxfile, "%le", &info->aux_info.karlin_k[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:502:39: warning: ‘%s’ directive writing up to 2 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 502 | sprintf(buf_full, "%s%s%s%s", buf_path, | ^~ 503 | alphabet_type, DIRDELIMSTR, matrix_name); | ~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:502:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4099) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:484:35: warning: ‘data’ directive writing 4 bytes into a region of size between 0 and 4095 [-Wformat-overflow=] 484 | sprintf(buf_path_2, "%s%sdata%s", buf_path, DIRDELIMSTR, DIRDELIMSTR); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:484:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 4102 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:470:35: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 470 | sprintf(buf_path_2, "%s%s", buf_path, DIRDELIMSTR); | ^ In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:470:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4097 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:104:25: warning: ‘.loo’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 104 | sprintf(filename, "%s.loo", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:104:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:123:25: warning: ‘.rps’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 123 | sprintf(filename, "%s.rps", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:123:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:144:25: warning: ‘.aux’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 144 | sprintf(filename, "%s.aux", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:144:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_input.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from blast_input.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_input.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast_input.c,v 1.32 2008/06/09 17:28:41 madden Exp $"; | ^~~~~ blast_input.c: In function ‘BLAST_GetQuerySeqLoc’: blast_input.c:98:21: warning: ‘%ld’ directive writing between 1 and 7 bytes into a region of size 4 [-Wformat-overflow=] 98 | sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES)); | ^~~ blast_input.c:98:20: note: directive argument in the range [-131080, 131080] 98 | sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES)); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BLAST_GetQuerySeqLoc’ at blast_input.c:98:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 8 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_format.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_format.h:45, from blast_format.c:38: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_format.c: In function ‘s_MBXmlInit’: blast_format.c:255:13: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 255 | Boolean retval = FALSE; | ^~~~~~ blast_format.c: In function ‘s_LoadMatrix’: blast_format.c:673:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 673 | ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j]; | ~~~~~~^~~ blast_format.c:673:38: warning: array subscript has type ‘char’ [-Wchar-subscripts] 673 | ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j]; | ~~~~~~^~~ blast_format.c: At top level: blast_format.c:35:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 35 | static char const rcsid[] = "$Id: blast_format.c,v 1.120 2012/10/10 14:07:01 fongah2 Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/ncbithr.h:87, from blast_mtlock.c:39: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_mtlock.c:35:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 35 | static char const rcsid[] = | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_options_api.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_prelim.c blast_prelim.c: In function ‘Blast_PrelimSearchThreadRun’: blast_prelim.c:100:9: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 100 | Int2 status = 0; | ^~~~~~ blast_prelim.c: At top level: blast_prelim.c:34:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 34 | static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_returns.c blast_returns.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from blast_seq.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_seq.c: In function ‘s_SeqLocFillSequenceBuffer’: blast_seq.c:529:10: warning: variable ‘seq_code’ set but not used [-Wunused-but-set-variable] 529 | Uint1 seq_code, strand; | ^~~~~~~~ blast_seq.c: At top level: blast_seq.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from ../include/algo/blast/api/blast_seqalign.h:42, from blast_seqalign.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_seqalign.c: In function ‘s_HSPListToSeqAlignUngapped’: blast_seqalign.c:343:26: warning: variable ‘hspset_cnt_old’ set but not used [-Wunused-but-set-variable] 343 | Int4 hsp_cnt, index2, hspset_cnt_old; | ^~~~~~~~~~~~~~ blast_seqalign.c: At top level: blast_seqalign.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_tabular.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_tabular.h:42, from blast_tabular.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_tabular.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF repeats_filter.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from ../include/algo/blast/api/repeats_filter.h:41, from repeats_filter.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ repeats_filter.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c seqsrc_multiseq.c:33:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 33 | static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from ../include/algo/blast/api/seqsrc_readdb.h:38, from seqsrc_readdb.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqsrc_readdb.c: In function ‘s_ReaddbGetNextChunk’: seqsrc_readdb.c:375:11: warning: variable ‘real_readdb_entries’ set but not used [-Wunused-but-set-variable] 375 | Uint4 real_readdb_entries; | ^~~~~~~~~~~~~~~~~~~ seqsrc_readdb.c: At top level: seqsrc_readdb.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.60 2011/05/26 20:59:45 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF twoseq_api.c twoseq_api.c: In function ‘s_TwoSeqBasicFillOptions’: twoseq_api.c:100:10: warning: unused variable ‘status’ [-Wunused-variable] 100 | Int2 status = 0; | ^~~~~~ In file included from ../include/sqnutils.h:51, from ../include/algo/blast/api/twoseq_api.h:41, from twoseq_api.c:45: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF dust_filter.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from ../include/algo/blast/api/dust_filter.h:41, from dust_filter.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dust_filter.c: In function ‘s_GetFilteringLocations’: dust_filter.c:171:32: warning: unused variable ‘filter_slp_rev’ [-Wunused-variable] 171 | BlastSeqLoc* filter_slp_rev = NULL; | ^~~~~~~~~~~~~~ dust_filter.c: At top level: dust_filter.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: dust_filter.c,v 1.12 2007/12/19 22:05:56 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF blast_message_api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from blast_message_api.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -D_PNG -I../include -DWIN_MOTIF hspfilter_queue.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/ncbithr.h:87, from hspfilter_queue.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ hspfilter_queue.c: In function ‘s_BlastHSPQueueInit’: hspfilter_queue.c:65:24: warning: unused variable ‘q_data’ [-Wunused-variable] 65 | BlastHSPQueueData * q_data = data; | ^~~~~~ hspfilter_queue.c: In function ‘s_BlastHSPQueueNew’: hspfilter_queue.c:157:24: warning: assignment to ‘BlastHSPWriterInitFn’ {aka ‘int (*)(void *, void *)’} from incompatible pointer type ‘int (*)(void *, BlastHSPResults *)’ [-Wincompatible-pointer-types] 157 | writer->InitFnPtr = &s_BlastHSPQueueInit; | ^ hspfilter_queue.c:158:24: warning: assignment to ‘BlastHSPWriterFinalFn’ {aka ‘int (*)(void *, void *)’} from incompatible pointer type ‘int (*)(void *, BlastHSPResults *)’ [-Wincompatible-pointer-types] 158 | writer->FinalFnPtr = &s_BlastHSPQueueFinal; | ^ hspfilter_queue.c: In function ‘BlastHSPQueueInfoNew’: hspfilter_queue.c:189:26: warning: assignment to ‘BlastHSPWriterNewFn’ {aka ‘BlastHSPWriter * (*)(void *, BlastQueryInfo *, BLAST_SequenceBlk *)’} from incompatible pointer type ‘BlastHSPWriter * (*)(void *, BlastQueryInfo *)’ [-Wincompatible-pointer-types] 189 | writer_info->NewFnPtr = &s_BlastHSPQueueNew; | ^ hspfilter_queue.c: At top level: hspfilter_queue.c:36:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 36 | static char const rcsid[] = | ^~~~~ rm -f libblastapi.a ar cru libblastapi.a blast_api.o blast_input.o blast_format.o blast_mtlock.o blast_options_api.o blast_prelim.o blast_returns.o blast_seq.o blast_seqalign.o blast_tabular.o repeats_filter.o seqsrc_multiseq.o seqsrc_readdb.o twoseq_api.o dust_filter.o blast_message_api.o hspfilter_queue.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblastapi.a ../lib ranlib ../lib/libblastapi.a x86_64-linux-gnu-gcc -o asntool -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -DWIN_MOTIF -L../shlib asntool.c asncode.c ../lib/libncbi.a -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asntool.c:64: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asncode.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asncode.c: In function ‘AsnCodeGenEnumDefines’: asncode.c:736:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 736 | sprintf (iter->buf, "%s %d\n", AsnCodeCleanName (avtp->name, lclbuf, | ~^ | | | int | %ld 737 | CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength), avtp->intvalue); | ~~~~~~~~~~~~~~ | | | Nlm_Int8 {aka long int} asncode.c: In function ‘AsnCode_SETOF_base_or_user’: asncode.c:1518:20: warning: variable ‘real_type’ set but not used [-Wunused-but-set-variable] 1518 | Int2 real_type; | ^~~~~~~~~ asncode.c:1517:20: warning: variable ‘valslot’ set but not used [-Wunused-but-set-variable] 1517 | CharPtr valslot; | ^~~~~~~ asncode.c: In function ‘userobj_and_basetype_SETOF’: asncode.c:2472:20: warning: variable ‘valslot’ set but not used [-Wunused-but-set-variable] 2472 | CharPtr valslot; | ^~~~~~~ asncode.c: In function ‘AsnCodeIsReallyChoice’: asncode.c:3201:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 3201 | if (now_atp) | ^ asncode.c: At top level: asncode.c:3533:38: warning: argument 2 of type ‘char[100]’ with mismatched bound [-Warray-parameter=] 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ~~~~~^~~~~~~~~~~~ asncode.c:269:58: note: previously declared as ‘char *’ 269 | CharPtr AsnCodeCleanName PROTO ((CharPtr name, char PNTR buf, int wash_or_buf, int maxlen)); | ~~~~~~~~~~^~~ ../include/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’ 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ asncode.c: In function ‘AsnCodeFunctionWriteFuncChoiceStart’: asncode.c:3623:20: warning: variable ‘obj_use’ set but not used [-Wunused-but-set-variable] 3623 | CharPtr obj_use = which_node->obj_name; | ^~~~~~~ asncode.c: In function ‘AsnCodeIter’: asncode.c:4238:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 4238 | if (iter->atp != NULL) | ^ asncode.c: In function ‘AsnCode’: asncode.c:4317:48: warning: variable ‘objnamety’ set but not used [-Wunused-but-set-variable] 4317 | CharPtr objnameuc = NULL, objnamemc = NULL, objnamety = NULL; | ^~~~~~~~~ asncode.c: At top level: asncode.c:291:17: warning: ‘defbyte’ defined but not used [-Wunused-variable] 291 | static CharPtr defbyte = "ASNCODE_BYTEVAL_SLOT"; | ^~~~~~~ asncode.c:290:17: warning: ‘defbool’ defined but not used [-Wunused-variable] 290 | static CharPtr defbool = "ASNCODE_BOOLVAL_SLOT"; | ^~~~~~~ asncode.c:289:17: warning: ‘defreal’ defined but not used [-Wunused-variable] 289 | static CharPtr defreal = "ASNCODE_REALVAL_SLOT"; | ^~~~~~~ asncode.c:288:17: warning: ‘defbigint’ defined but not used [-Wunused-variable] 288 | static CharPtr defbigint = "ASNCODE_BIGINTVAL_SLOT"; | ^~~~~~~~~ asncode.c:286:17: warning: ‘defptr’ defined but not used [-Wunused-variable] 286 | static CharPtr defptr = "ASNCODE_PTRVAL_SLOT"; | ^~~~~~ asncode.c: In function ‘AsnCodePush’: asncode.c:4054:25: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4054 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4055 | CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4054:25: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ asncode.c:4068:25: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4068 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4069 | CLEAN_FOR_OBJ_NAME, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4068:25: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ asncode.c:4080:22: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4080 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4081 | CLEAN_FOR_ASN_TYPE, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4080:22: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘ErrMsgRoot_fopen’ at ncbierr.c:955:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 4096 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ cp -p asntool ../bin make[3]: Leaving directory '/<>/build' /usr/bin/make -C build -f makenet.unx LCL=lnx CC="x86_64-linux-gnu-gcc" LDFLAGS1="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS NCBI_LINKINGLIBDIR="../shlib" \ CFLAGS1="-c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC" \ LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now" \ NETENTREZVERSION="2.02c2ASN1SPEC6" \ BLIB31=libvibnet.a OGLLIBS="-lGLU -lGL -lpng " all libncbimla.a libnetblast.a libncbitxc2.a libncbiid1.a shlib make[3]: Entering directory '/<>/build' ./ln-if-absent ../connect/test/*.c . ./ln-if-absent ../network/entrez/client/*.h ../include ./ln-if-absent ../network/entrez/client/*.c . ./ln-if-absent ../network/medarch/client/*.h ../include ./ln-if-absent ../network/medarch/client/*.c . ./ln-if-absent ../network/taxonomy/client/*.h ../include set: No match. make[3]: [makenet.unx:480: copy] Error 1 (ignored) ./ln-if-absent ../network/taxonomy/client/*.c . set: No match. make[3]: [makenet.unx:481: copy] Error 1 (ignored) ./ln-if-absent ../network/taxon1/common/*.h ../include ./ln-if-absent ../network/taxon1/common/*.c . ./ln-if-absent ../network/taxon1/taxon2/*.h ../include ./ln-if-absent ../network/taxon1/taxon2/*.c . ./ln-if-absent ../network/id0arch/client/*.h ../include set: No match. make[3]: [makenet.unx:486: copy] Error 1 (ignored) ./ln-if-absent ../network/id0arch/client/*.c . set: No match. make[3]: [makenet.unx:487: copy] Error 1 (ignored) ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id1arch/*.c . ./ln-if-absent ../network/id2arch/*.h ../include ./ln-if-absent ../network/id2arch/*.c . ./ln-if-absent ../network/spell/client/*.h ../include ./ln-if-absent ../network/spell/client/*.c . ./ln-if-absent ../network/suggest/client/*.h ../include ./ln-if-absent ../network/suggest/client/*.c . ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/blast3/client/*.c . ./ln-if-absent ../tools/taxblast.h ../include ./ln-if-absent ../tools/taxblast.c . ./ln-if-absent /*.c . set: No match. make[3]: [makenet.unx:500: copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.c . set: No match. make[3]: [makenet.unx:501: copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.h ../include set: No match. make[3]: [makenet.unx:502: copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.c . set: No match. make[3]: [makenet.unx:503: copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.h ../include set: No match. make[3]: [makenet.unx:504: copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.c . set: No match. make[3]: [makenet.unx:505: copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.h ../include set: No match. make[3]: [makenet.unx:506: copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.c . set: No match. make[3]: [makenet.unx:507: copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.h ../include set: No match. make[3]: [makenet.unx:508: copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.c . set: No match. make[3]: [makenet.unx:509: copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.h ../include set: No match. make[3]: [makenet.unx:510: copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.c . set: No match. make[3]: [makenet.unx:511: copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.h ../include set: No match. make[3]: [makenet.unx:512: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.c . set: No match. make[3]: [makenet.unx:513: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.h ../include set: No match. make[3]: [makenet.unx:514: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.c . set: No match. make[3]: [makenet.unx:515: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.h ../include set: No match. make[3]: [makenet.unx:516: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.c . set: No match. make[3]: [makenet.unx:517: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.h ../include set: No match. make[3]: [makenet.unx:518: copy] Error 1 (ignored) ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/nsclilib/*.c . ./ln-if-absent ../network/vibnet/*.c . ./ln-if-absent ../network/vibnet/*.h ../include ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../network/wwwblast/Src/*.c . ./ln-if-absent ../cdromlib/accentr.c . ./ln-if-absent ../cdromlib/accutils.c . ./ln-if-absent ../sequin/*.* . ./ln-if-absent ../demo/entrez.c . ./ln-if-absent ../demo/seqget.c . ./ln-if-absent ../demo/entrcmd.c . ./ln-if-absent ../demo/batch.c . ./ln-if-absent ../demo/qbatch.c . ./ln-if-absent ../demo/elecpcr.c . ./ln-if-absent ../demo/asn2fast.c . ./ln-if-absent ../demo/asn2asn.c . ./ln-if-absent ../demo/cleanasn.c . ./ln-if-absent ../demo/cspeedtest.c . ./ln-if-absent ../demo/sqn2agp.c . ./ln-if-absent ../demo/sugint.c . ./ln-if-absent ../demo/fetchent.c . ./ln-if-absent ../demo/udvmain.c . ./ln-if-absent ../demo/rtestval.c . ./ln-if-absent ../demo/aceread_tst.c . ./ln-if-absent ../demo/asn2ff.c . ./ln-if-absent ../demo/asn2gb.c . ./ln-if-absent ../demo/asn2fsa.c . ./ln-if-absent ../demo/asn2all.c . ./ln-if-absent ../demo/gene2xml.c . ./ln-if-absent ../demo/asnval.c . ./ln-if-absent ../demo/asndisc.c . ./ln-if-absent ../demo/asnbarval.c . ./ln-if-absent ../demo/aceread_tst.c . ./ln-if-absent ../demo/asnmacro.c . ./ln-if-absent ../demo/asnstrip.c . ./ln-if-absent ../demo/tbl2asn.c . ./ln-if-absent ../demo/raw2delt.c . ./ln-if-absent ../demo/flint.c . ./ln-if-absent ../demo/xlint.c . ./ln-if-absent ../demo/diffshift.c . ./ln-if-absent ../demo/gbseqget.c . ./ln-if-absent ../demo/insdseqget.c . ./ln-if-absent ../demo/nps2gps.c . ./ln-if-absent ../demo/testent2.c . ./ln-if-absent ../demo/trna2sap.c . ./ln-if-absent ../demo/trna2tbl.c . ./ln-if-absent ../demo/entrez2.c . ./ln-if-absent ../demo/condense.c . ./ln-if-absent ../demo/spideymain.c . ./ln-if-absent ../demo/dotmain.c . ./ln-if-absent ../demo/ingenmain.c . ./ln-if-absent ../demo/bl2seq.c . ./ln-if-absent ../demo/blastall.c . ./ln-if-absent ../demo/blast_driver.c . ./ln-if-absent ../demo/src_chk.c . ./ln-if-absent ../demo/tbl_chk.c . ./ln-if-absent ../demo/export_cmt.c . ./ln-if-absent ../internal/parser/flat2asn.c . make[3]: [makenet.unx:577: copy] Error 1 (ignored) ./ln-if-absent ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c ../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c ../demo/cnsrt.c ../demo/cnsgn.c ../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c ../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c . ./ln-if-absent ../network/entrez/server/*.* . set: No match. make[3]: [makenet.unx:579: copy] Error 1 (ignored) ./ln-if-absent ../network/suggest/server/*.* . chmod -R ug+rw,o+r . echo Waiting...go Waiting...go x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_lib_.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from ni_lib_.c:76: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_debug.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ni_debug.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_service.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ni_service.c:125: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ni_service.c: In function ‘s_GenericGetService’: ni_service.c:201:19: warning: unused variable ‘c’ [-Wunused-variable] 201 | CONNECTOR c; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_error.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from ../include/ni_error.h:76, from ni_error.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rm -f libnetcli.a ar cru libnetcli.a ni_lib_.o ni_debug.o ni_service.o ni_error.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetcli.a ../lib ranlib ../lib/libnetcli.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from netentr.c:161: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netentr.c: In function ‘s_NetEntTLEvalCount’: netentr.c:798:5: warning: "/*" within comment [-Wcomment] 798 | /*MsgSetReadTimeout(Entrez_ni, 60);*/ | netentr.c: In function ‘s_NetDocSumListGet’: netentr.c:856:18: warning: variable ‘amp’ set but not used [-Wunused-but-set-variable] 856 | AsnModulePtr amp; | ^~~ netentr.c: In function ‘s_NetTermListByTerm’: netentr.c:1212:9: warning: variable ‘terms_to_read’ set but not used [-Wunused-but-set-variable] 1212 | int terms_to_read; | ^~~~~~~~~~~~~ netentr.c:1200:14: warning: unused variable ‘asnout’ [-Wunused-variable] 1200 | AsnIoPtr asnout = Entrez_asnout; | ^~~~~~ netentr.c: In function ‘s_NetTermListByPage’: netentr.c:1343:14: warning: unused variable ‘asnout’ [-Wunused-variable] 1343 | AsnIoPtr asnout = Entrez_asnout; | ^~~~~~ netentr.c: In function ‘NetEntTLEval’: netentr.c:675:12: warning: ‘lsp’ may be used uninitialized [-Wmaybe-uninitialized] 675 | return lsp; | ^~~ netentr.c:660:16: note: ‘lsp’ was declared here 660 | LinkSetPtr lsp; | ^~~ In function ‘s_NetEntTLEvalCount’, inlined from ‘NetEntTLEvalCount’ at netentr.c:829:18: netentr.c:800:8: warning: ‘atp’ may be used uninitialized [-Wmaybe-uninitialized] 800 | if (atp == ENTREZ_BACK_eval_count) | ^ netentr.c: In function ‘NetEntTLEvalCount’: netentr.c:782:16: note: ‘atp’ was declared here 782 | AsnTypePtr atp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from netlib.c:82: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netlib.c: In function ‘BoolExprAsnWrite’: netlib.c:307:16: warning: unused variable ‘n’ [-Wunused-variable] 307 | static int n = 0; | ^ netlib.c: At top level: netlib.c:96:16: warning: ‘loaded’ defined but not used [-Wunused-variable] 96 | static Boolean loaded = FALSE; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objneten.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnneten.h:9, from objneten.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objneten.c: In function ‘NetEntAsnLoad’: objneten.c:106:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 106 | if (loaded) | ^~ objneten.c:108:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 108 | loaded = TRUE; | ^~~~~~ objneten.c: In function ‘EntrezNeighborTextAsnRead’: objneten.c:2938:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2938 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘ChildLinkAsnRead’: objneten.c:3148:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3148 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘EntrezHierarchyAsnRead’: objneten.c:3442:15: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3442 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘EntrezBlastreqAsnRead’: objneten.c:3705:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3705 | AsnReadFunc func; | ^~~~ objneten.c:3704:12: warning: unused variable ‘isError’ [-Wunused-variable] 3704 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘EntrezExtraInfoAsnRead’: objneten.c:3911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3911 | AsnReadFunc func; | ^~~~ objneten.c:3910:12: warning: unused variable ‘isError’ [-Wunused-variable] 3910 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘ClusterArticlesAsnRead’: objneten.c:4262:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4262 | AsnReadFunc func; | ^~~~ objneten.c:4261:12: warning: unused variable ‘isError’ [-Wunused-variable] 4261 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘ClusterRespAsnRead’: objneten.c:4455:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4455 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘DateConstraintsAsnRead’: objneten.c:4622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4622 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘DateVectorAsnRead’: objneten.c:4785:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4785 | AsnReadFunc func; | ^~~~ objneten.c:4784:12: warning: unused variable ‘isError’ [-Wunused-variable] 4784 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘GetByFidAsnRead’: objneten.c:4963:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4963 | AsnReadFunc func; | ^~~~ objneten.c:4962:12: warning: unused variable ‘isError’ [-Wunused-variable] 4962 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘GetFeatIdsAsnRead’: objneten.c:5133:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5133 | AsnReadFunc func; | ^~~~ objneten.c:5132:12: warning: unused variable ‘isError’ [-Wunused-variable] 5132 | Boolean isError = FALSE; | ^~~~~~~ rm -f libnetentr.a ar cru libnetentr.a netentr.o netlib.o objneten.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetentr.a ../lib ranlib ../lib/libnetentr.a ./ln-if-absent accentr.c Naccentr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NETENT_ Naccentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from Naccentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ Naccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces] 357 | Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = { | ^ 358 | 8, 6, 3, 3, | { } 359 | 8, 6, 3, 3, | { } 360 | 8, 6, 3, 3, | { } 361 | 8, 6, 3, 3, | { } 362 | 9, 7, 4, 3, | { } 363 | 9, 8, 5, 3, | { } 364 | 10, 9, 5, 3, | { } 365 | 10, 10, 5, 3, | { } 366 | 11, 10, 5, 3, | { } 367 | 11, 11, 5, 3, | { } 368 | 12, 11, 5, 3, | { } 369 | 12, 11, 5, 3, | { } 370 | 12, 11, 5, 3 | { 371 | }; | } Naccentr.c: In function ‘EntrezDocSumListGet’: Naccentr.c:1409:14: warning: variable ‘actual’ set but not used [-Wunused-but-set-variable] 1409 | Int2 actual; | ^~~~~~ Naccentr.c: In function ‘EntrezGIForSeqIdFunc’: Naccentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ Naccentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ Naccentr.c: In function ‘EntrezMedlineEntryGet’: Naccentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at Naccentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Naccentr.c: In function ‘EntrezSeqEntryGet’: Naccentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at Naccentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbiNacc.a ar cru libncbiNacc.a Naccentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiNacc.a ../lib ranlib ../lib/libncbiNacc.a ./ln-if-absent accentr.c Caccentr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NET_AND_CD_ Caccentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from Caccentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ Caccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces] 357 | Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = { | ^ 358 | 8, 6, 3, 3, | { } 359 | 8, 6, 3, 3, | { } 360 | 8, 6, 3, 3, | { } 361 | 8, 6, 3, 3, | { } 362 | 9, 7, 4, 3, | { } 363 | 9, 8, 5, 3, | { } 364 | 10, 9, 5, 3, | { } 365 | 10, 10, 5, 3, | { } 366 | 11, 10, 5, 3, | { } 367 | 11, 11, 5, 3, | { } 368 | 12, 11, 5, 3, | { } 369 | 12, 11, 5, 3, | { } 370 | 12, 11, 5, 3 | { 371 | }; | } Caccentr.c: In function ‘EntrezDocSumListGet’: Caccentr.c:1409:14: warning: variable ‘actual’ set but not used [-Wunused-but-set-variable] 1409 | Int2 actual; | ^~~~~~ Caccentr.c: In function ‘EntrezGIForSeqIdFunc’: Caccentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ Caccentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ Caccentr.c: In function ‘EntrezMedlineEntryGet’: Caccentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at Caccentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Caccentr.c: In function ‘EntrezSeqEntryGet’: Caccentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at Caccentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbiCacc.a ar cru libncbiCacc.a Caccentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiCacc.a ../lib ranlib ../lib/libncbiCacc.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netcnfg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from netcnfg.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netcnfg.c: In function ‘ShowNetConfigForm’: netcnfg.c:319:23: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 319 | PrompT ppt0, ppt1; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" trmlst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from trmlst.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ trmlst.c: In function ‘FetchFromTermList’: trmlst.c:1048:16: warning: variable ‘numRead’ set but not used [-Wunused-but-set-variable] 1048 | Int2 numRead; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" docsum.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from docsum.c:252: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ docsum.c: In function ‘ImportDocSumForm’: docsum.c:2298:21: warning: unused variable ‘sephead’ [-Wunused-variable] 2298 | SeqEntryPtr sephead = NULL; | ^~~~~~~ docsum.c:2296:21: warning: unused variable ‘is_na’ [-Wunused-variable] 2296 | Boolean is_na = TRUE; | ^~~~~ docsum.c:2290:21: warning: unused variable ‘choice’ [-Wunused-variable] 2290 | Uint1 choice = 0; | ^~~~~~ docsum.c: In function ‘SaveDocsumProject’: docsum.c:3042:16: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 3042 | SummFormPtr sfp; | ^~~ docsum.c: In function ‘LaunchStructureViewer’: docsum.c:4192:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4192 | system (cmmd); | ^~~~~~~~~~~~~ docsum.c: At top level: docsum.c:439:15: warning: ‘checkmark’ defined but not used [-Wunused-variable] 439 | static Uint1 checkmark [] = { | ^~~~~~~~~ docsum.c: In function ‘SetDefaultFailureMessage’: docsum.c:687:48: warning: ‘ in ’ directive writing 4 bytes into a region of size between 3 and 42 [-Wformat-overflow=] 687 | sprintf (tmp, "%sProblem with sequence %s in %s database", prefix, buf, dbname); | ^~~~ docsum.c:687:21: note: assuming directive output of 3 bytes 687 | sprintf (tmp, "%sProblem with sequence %s in %s database", prefix, buf, dbname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SetDefaultFailureMessage’ at docsum.c:687:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 36 or more bytes (assuming 78) into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ docsum.c: In function ‘FetchLocalBioseq’: docsum.c:1223:6: warning: ‘str’ may be used uninitialized [-Wmaybe-uninitialized] 1223 | if (str == NULL) return failed; | ^ docsum.c:1204:17: note: ‘str’ was declared here 1204 | CharPtr str; | ^~~ docsum.c: In function ‘LaunchStructureViewer.isra.0’: docsum.c:4191:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4091 [-Wformat-overflow=] 4191 | sprintf (cmmd, "Cn3D %s &", path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘LaunchStructureViewer.isra.0’ at docsum.c:4191:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 4103 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libvibnet.a ar cru libvibnet.a netcnfg.o trmlst.o docsum.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibnet.a ../lib ranlib ../lib/libvibnet.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -DNLM_OBJ_INCL=\"mapmla.h\" objmla.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmla.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmla.c: In function ‘MlaRequestFree’: objmla.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objmla.c: In function ‘MlaRequestAsnRead’: objmla.c:96:12: warning: unused variable ‘isError’ [-Wunused-variable] 96 | Boolean isError = FALSE; | ^~~~~~~ objmla.c: In function ‘TitleMsgAsnRead’: objmla.c:447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 447 | AsnReadFunc func; | ^~~~ objmla.c:446:12: warning: unused variable ‘isError’ [-Wunused-variable] 446 | Boolean isError = FALSE; | ^~~~~~~ objmla.c: In function ‘TitleMsgListAsnRead’: objmla.c:612:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 612 | AsnReadFunc func; | ^~~~ objmla.c: In function ‘MlaRequestAsnRead’: objmla.c:249:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 249 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla.c:95:10: note: ‘choice’ was declared here 95 | Uint1 choice; | ^~~~~~ objmla.c: In function ‘MlaBackAsnRead’: objmla.c:902:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 902 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla.c:785:10: note: ‘choice’ was declared here 785 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medarch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from medarch.c:122: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medarch.c:758:8: warning: ‘s_MedArchPubSetEntryGetUid’ defined but not used [-Wunused-function] 758 | /*FCN*/s_MedArchPubSetEntryGetUid ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:710:8: warning: ‘s_MedArchPubSetEntryGetPmId’ defined but not used [-Wunused-function] 710 | /*FCN*/s_MedArchPubSetEntryGetPmId ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c: In function ‘MedArchPubSetCreate’: medarch.c:1655:5: warning: ‘startAtp’ may be used uninitialized [-Wmaybe-uninitialized] 1655 | AsnWrite (aip, startAtp, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:1624:16: note: ‘startAtp’ was declared here 1624 | AsnTypePtr startAtp; | ^~~~~~~~ In file included from ../include/ni_types.h:85: ../include/asn.h:494:29: warning: ‘pubSetAtp’ may be used uninitialized [-Wmaybe-uninitialized] 494 | #define AsnStartStruct(x,y) AsnOpenStruct(x, y, NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:1625:16: note: ‘pubSetAtp’ was declared here 1625 | AsnTypePtr pubSetAtp; | ^~~~~~~~~ In function ‘s_MedArchPubSetEntryGet’, inlined from ‘MedArchPubSetCreate’ at medarch.c:1669:19: medarch.c:683:9: warning: ‘pubSetEAtp’ may be used uninitialized [-Wmaybe-uninitialized] 683 | MedlineEntryAsnWrite (lastmep, aip, atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c: In function ‘MedArchPubSetCreate’: medarch.c:1626:16: note: ‘pubSetEAtp’ was declared here 1626 | AsnTypePtr pubSetEAtp; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/medutil.h:79, from medutil.c:58: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medutil.c: In function ‘FixPubEquiv’: medutil.c:1134:16: warning: variable ‘got’ set but not used [-Wunused-but-set-variable] 1134 | Boolean got; | ^~~ rm -f libncbimla.a ar cru libncbimla.a objmla.o medarch.o medutil.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbimla.a ../lib ranlib ../lib/libncbimla.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objblst3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objblst3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objblst3.c: In function ‘BlastSearchAsnRead’: objblst3.c:91:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 91 | AsnReadFunc func; | ^~~~ objblst3.c:90:12: warning: unused variable ‘isError’ [-Wunused-variable] 90 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastRequestFree’: objblst3.c:287:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 287 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastRequestAsnRead’: objblst3.c:337:12: warning: unused variable ‘isError’ [-Wunused-variable] 337 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff2_cutoff2Free’: objblst3.c:999:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 999 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1027:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1027 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘Cutoff2_cutoff2AsnRead’: objblst3.c:1422:12: warning: unused variable ‘isError’ [-Wunused-variable] 1422 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff_cutoffAsnRead’: objblst3.c:1788:12: warning: unused variable ‘isError’ [-Wunused-variable] 1788 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff_cutoffFree’: objblst3.c:1871:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1871 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastMatrixAsnRead’: objblst3.c:1936:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1936 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastDbinfoAsnRead’: objblst3.c:2153:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2153 | AsnReadFunc func; | ^~~~ objblst3.c:2152:12: warning: unused variable ‘isError’ [-Wunused-variable] 2152 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastMaskAsnRead’: objblst3.c:2357:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2357 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastKABlkAsnRead’: objblst3.c:2517:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2517 | AsnReadFunc func; | ^~~~ objblst3.c:2516:12: warning: unused variable ‘isError’ [-Wunused-variable] 2516 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastErrorAsnRead’: objblst3.c:2697:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2697 | AsnReadFunc func; | ^~~~ objblst3.c:2696:12: warning: unused variable ‘isError’ [-Wunused-variable] 2696 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastPhialignAsnRead’: objblst3.c:2861:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2861 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastDbinfoGetAsnRead’: objblst3.c:3022:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3022 | AsnReadFunc func; | ^~~~ objblst3.c:3021:12: warning: unused variable ‘isError’ [-Wunused-variable] 3021 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastSeqIdAsnRead’: objblst3.c:3187:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3187 | AsnReadFunc func; | ^~~~ objblst3.c:3186:12: warning: unused variable ‘isError’ [-Wunused-variable] 3186 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastSequenceAsnRead’: objblst3.c:3364:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3364 | AsnReadFunc func; | ^~~~ objblst3.c:3363:12: warning: unused variable ‘isError’ [-Wunused-variable] 3363 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastPartsAsnRead’: objblst3.c:3532:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3532 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastQueuedAsnRead’: objblst3.c:3694:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3694 | AsnReadFunc func; | ^~~~ objblst3.c:3693:12: warning: unused variable ‘isError’ [-Wunused-variable] 3693 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastProgressAsnRead’: objblst3.c:3846:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3846 | AsnReadFunc func; | ^~~~ objblst3.c:3845:12: warning: unused variable ‘isError’ [-Wunused-variable] 3845 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastDeflineAsnRead’: objblst3.c:4000:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4000 | AsnReadFunc func; | ^~~~ objblst3.c:3999:12: warning: unused variable ‘isError’ [-Wunused-variable] 3999 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastVersionAsnRead’: objblst3.c:4168:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4168 | AsnReadFunc func; | ^~~~ objblst3.c:4167:12: warning: unused variable ‘isError’ [-Wunused-variable] 4167 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘MegaBlastHitAsnRead’: objblst3.c:4335:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4335 | AsnReadFunc func; | ^~~~ objblst3.c:4334:12: warning: unused variable ‘isError’ [-Wunused-variable] 4334 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘MegaBlastResultsAsnRead’: objblst3.c:4546:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4546 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastRequestAsnRead’: objblst3.c:430:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 430 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c:336:10: note: ‘choice’ was declared here 336 | Uint1 choice; | ^~~~~~ objblst3.c: In function ‘BlastResponseAsnRead’: objblst3.c:791:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 791 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c:643:10: note: ‘choice’ was declared here 643 | Uint1 choice; | ^~~~~~ In function ‘Cutoff_cutoffAsnRead’, inlined from ‘BlastParametersAsnRead’ at objblst3.c:1077:30: objblst3.c:1840:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1840 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1787:10: note: ‘choice’ was declared here 1787 | Uint1 choice; | ^~~~~~ In function ‘Cutoff2_cutoff2AsnRead’, inlined from ‘BlastParametersAsnRead’ at objblst3.c:1084:32: objblst3.c:1474:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1474 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1421:10: note: ‘choice’ was declared here 1421 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netblap3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from netblap3.c:359: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netblap3.c: In function ‘BlastNetBioseqFetchFunc’: netblap3.c:1835:23: warning: variable ‘omdp’ set but not used [-Wunused-but-set-variable] 1835 | OMUserDataPtr omdp; | ^~~~ netblap3.c: In function ‘MegaBlastSeqLocNetCore’: netblap3.c:2049:15: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 2049 | Uint2 entityID = 0; | ^~~~~~~~ In file included from ../include/netblap3.h:135, from netblap3.c:364: ../include/objblst3.h: At top level: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ netblap3.c:452:1: warning: ‘BlastResetOldHook’ defined but not used [-Wunused-function] 452 | BlastResetOldHook(void) | ^~~~~~~~~~~~~~~~~ netblap3.c:445:1: warning: ‘BlastGetErrorStatus’ defined but not used [-Wunused-function] 445 | BlastGetErrorStatus(void) | ^~~~~~~~~~~~~~~~~~~ netblap3.c:438:1: warning: ‘BlastSetErrorStatus’ defined but not used [-Wunused-function] 438 | BlastSetErrorStatus(Boolean status) | ^~~~~~~~~~~~~~~~~~~ netblap3.c:430:1: warning: ‘BlastSetErrorHook’ defined but not used [-Wunused-function] 430 | BlastSetErrorHook(void) | ^~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ netblap3.c: In function ‘BlastNetMatrixToBlastMatrix’: netblap3.c:1212:42: warning: ‘index2’ may be used uninitialized [-Wmaybe-uninitialized] 1212 | if (index1 != blast_matrix->rows || index2 != blast_matrix->columns) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ netblap3.c:1181:18: note: ‘index2’ was declared here 1181 | Int4 index1, index2; | ^~~~~~ netblap3.c: In function ‘TraditionalBlastReportEngine’: netblap3.c:2570:12: warning: ‘next_seqalign’ may be used uninitialized [-Wmaybe-uninitialized] 2570 | while (seqalign) { | ^~~~~~~~ netblap3.c:2452:39: note: ‘next_seqalign’ was declared here 2452 | SeqAlignPtr seqalign = NULL, sap, next_seqalign; | ^~~~~~~~~~~~~ rm -f libnetblast.a ar cru libnetblast.a objblst3.o netblap3.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetblast.a ../lib ranlib ../lib/libnetblast.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objtax1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtax1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtax1.c: In function ‘Taxon1ReqFree’: objtax1.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objtax1.c: In function ‘Taxon1ReqAsnRead’: objtax1.c:92:12: warning: unused variable ‘isError’ [-Wunused-variable] 92 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1InfoAsnRead’: objtax1.c:502:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 502 | AsnReadFunc func; | ^~~~ objtax1.c:501:12: warning: unused variable ‘isError’ [-Wunused-variable] 501 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1ErrorAsnRead’: objtax1.c:1131:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1131 | AsnReadFunc func; | ^~~~ objtax1.c:1130:12: warning: unused variable ‘isError’ [-Wunused-variable] 1130 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1NameAsnRead’: objtax1.c:1296:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1296 | AsnReadFunc func; | ^~~~ objtax1.c:1295:12: warning: unused variable ‘isError’ [-Wunused-variable] 1295 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1DataAsnRead’: objtax1.c:1482:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1482 | AsnReadFunc func; | ^~~~ objtax1.c:1481:12: warning: unused variable ‘isError’ [-Wunused-variable] 1481 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon2DataAsnRead’: objtax1.c:1670:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1670 | AsnReadFunc func; | ^~~~ objtax1.c: In function ‘Taxon1ReqAsnRead’: objtax1.c:284:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 284 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax1.c:91:10: note: ‘choice’ was declared here 91 | Uint1 choice; | ^~~~~~ objtax1.c: In function ‘Taxon1RespAsnRead’: objtax1.c:920:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 920 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax1.c:695:10: note: ‘choice’ was declared here 695 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/utilpub.h:4, from taxutil.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ taxutil.c: In function ‘taxname_match’: taxutil.c:85:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if(err) | ^~ taxutil.c:88:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 88 | return -1; | ^~~~~~ taxutil.c:90:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 90 | if(err) | ^~ taxutil.c:93:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 93 | return -1; | ^~~~~~ taxutil.c:97:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 97 | if(err) | ^~ taxutil.c:100:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 100 | return -1; | ^~~~~~ taxutil.c:66:24: warning: unused variable ‘taxstr’ [-Wunused-variable] 66 | CharPtr taxstr = NULL; | ^~~~~~ taxutil.c: In function ‘get_lineage’: taxutil.c:140:42: warning: ‘onp’ may be used uninitialized [-Wmaybe-uninitialized] 140 | return Nlm_StringSave(onp->lineage); | ~~~^~~~~~~~~ taxutil.c:132:20: note: ‘onp’ was declared here 132 | OrgNamePtr onp; | ^~~ taxutil.c: In function ‘get_gcode’: taxutil.c:158:20: warning: ‘onp’ may be used uninitialized [-Wmaybe-uninitialized] 158 | if (onp) { | ^ taxutil.c:150:20: note: ‘onp’ was declared here 150 | OrgNamePtr onp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o tc2dproc.o -DTAXSERVICE tc2proc.c tc2proc.c: In function ‘getIdByOrgRef’: tc2proc.c:407:17: warning: unused variable ‘om_flag’ [-Wunused-variable] 407 | Boolean om_flag= FALSE; | ^~~~~~~ tc2proc.c: In function ‘bldLineage’: tc2proc.c:1095:10: warning: unused variable ‘rank’ [-Wunused-variable] 1095 | Int2 rank= 0; | ^~~~ tc2proc.c: In function ‘storedTaxId’: tc2proc.c:2114:17: warning: unused variable ‘object_id’ [-Wunused-variable] 2114 | ObjectIdPtr object_id; | ^~~~~~~~~ tc2proc.c: In function ‘tax1e_needUpdate’: tc2proc.c:2181:13: warning: unused variable ‘hit_name’ [-Wunused-variable] 2181 | CharPtr hit_name; | ^~~~~~~~ tc2proc.c:2180:13: warning: unused variable ‘need_search_name’ [-Wunused-variable] 2180 | Boolean need_search_name= TRUE; | ^~~~~~~~~~~~~~~~ tc2proc.c:2179:9: warning: unused variable ‘is_species’ [-Wunused-variable] 2179 | int is_species; | ^~~~~~~~~~ tc2proc.c:2176:19: warning: unused variable ‘res’ [-Wunused-variable] 2176 | Taxon1DataPtr res; | ^~~ tc2proc.c: At top level: tc2proc.c:403:13: warning: ‘getIdByOrgRef’ defined but not used [-Wunused-function] 403 | static Int4 getIdByOrgRef(CharPtr sname, OrgNamePtr orNm) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o txcdproc.o -DTAXSERVICE txcdproc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from txcdproc.c:116: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" parttree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/txclient.h:73, from parttree.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ parttree.c: In function ‘tax_ptree_addSubtree’: parttree.c:392:13: warning: unused variable ‘need_remove’ [-Wunused-variable] 392 | Boolean need_remove= FALSE; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxcs.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from taxblast.c:161: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ taxblast.c: In function ‘TXBHtmlReportInternal’: taxblast.c:1359:37: warning: variable ‘linlines’ set but not used [-Wunused-but-set-variable] 1359 | Int2 numtaxa, numorgs, numhits, linlines, longname; | ^~~~~~~~ taxblast.c: In function ‘RDTaxLookupReset’: taxblast.c:2050:1: warning: control reaches end of non-void function [-Wreturn-type] 2050 | } | ^ taxblast.c: At top level: taxblast.c:1967:13: warning: ‘getTotalTaxIdCount’ defined but not used [-Wunused-function] 1967 | static Int4 getTotalTaxIdCount(TreeCursorPtr cursor) | ^~~~~~~~~~~~~~~~~~ taxblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: taxblast.c,v 6.31 2015/07/06 19:25:47 madden Exp $"; | ^~~~~ taxblast.c: In function ‘TXBGetTargetGi’: taxblast.c:504:12: warning: ‘gi’ may be used uninitialized [-Wmaybe-uninitialized] 504 | return gi; | ^~ taxblast.c:462:10: note: ‘gi’ was declared here 462 | Int4 gi; | ^~ In file included from ../include/ncbi.h:62: taxblast.c: In function ‘TXBHtmlReport’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ rm -f libncbitxc2.a ar cru libncbitxc2.a objtax1.o taxutil.o tc2dproc.o txcdproc.o parttree.o taxcs.o taxblast.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbitxc2.a ../lib ranlib ../lib/libncbitxc2.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1gen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from id1gen.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ id1gen.c: In function ‘ID1serverRequestFree’: id1gen.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ id1gen.c: In function ‘ID1serverRequestAsnRead’: id1gen.c:90:12: warning: unused variable ‘isError’ [-Wunused-variable] 90 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1serverMaxcomplexAsnRead’: id1gen.c:348:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 348 | AsnReadFunc func; | ^~~~ id1gen.c:347:12: warning: unused variable ‘isError’ [-Wunused-variable] 347 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1SeqHistAsnRead’: id1gen.c:530:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 530 | AsnReadFunc func; | ^~~~ id1gen.c:529:12: warning: unused variable ‘isError’ [-Wunused-variable] 529 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1SeqEntryInfoAsnRead’: id1gen.c:979:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 979 | AsnReadFunc func; | ^~~~ id1gen.c:978:12: warning: unused variable ‘isError’ [-Wunused-variable] 978 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1blobInfoAsnRead’: id1gen.c:1147:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1147 | AsnReadFunc func; | ^~~~ id1gen.c:1146:12: warning: unused variable ‘isError’ [-Wunused-variable] 1146 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1serverDebugAsnRead’: id1gen.c:1368:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1368 | AsnReadFunc func; | ^~~~ id1gen.c: In function ‘ID1serverBackAsnRead’: id1gen.c:811:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 811 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ id1gen.c:697:10: note: ‘choice’ was declared here 697 | Uint1 choice; | ^~~~~~ id1gen.c: In function ‘ID1serverRequestAsnRead’: id1gen.c:186:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 186 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ id1gen.c:89:10: note: ‘choice’ was declared here 89 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1arch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from id1arch.c:31: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ id1arch.c: In function ‘ID1ArchSeqEntryGet’: id1arch.c:173:14: warning: unused variable ‘retval’ [-Wunused-variable] 173 | Int4 retval = 0; | ^~~~~~ id1arch.c: In function ‘ID1ArchGIGet’: id1arch.c:486:10: warning: unused variable ‘retval’ [-Wunused-variable] 486 | Int4 retval = 0; | ^~~~~~ id1arch.c: In function ‘SeqHistPrintTable’: id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 553 | sprintf(repl_date,"%0.2d/%0.2d/%0.4d", | ^~~~~~~~~~~~~~~~~~~ id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] id1arch.c:563:47: warning: spurious trailing ‘%’ in format [-Wformat=] 563 | fprintf(fp,"%-20d%-20s%",old_gi,repl_date); | ^ id1arch.c:558:65: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 558 | sprintf(repl_date,"%-20s",shp->replace_date->str); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SeqHistPrintTable’ at id1arch.c:558:41, inlined from ‘SeqHistPrintTable’ at id1arch.c:505:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 21 or more bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" accid1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from accid1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ accid1.c: In function ‘s_ID1BioseqFetchFunc’: accid1.c:262:33: warning: unused variable ‘retcode’ [-Wunused-variable] 262 | Int2 retcode=0; | ^~~~~~~ rm -f libncbiid1.a ar cru libncbiid1.a id1gen.o id1arch.o accid1.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiid1.a ../lib ranlib ../lib/libncbiid1.a mkdir ../shlib rm -f ../shlib/*.a ln ../lib/*.a ../shlib cd ../shlib; make -f ../make/makeshlb.unx `ls *.a | sed "s/\.a/.so.6/"` SH1="x86_64-linux-gnu-gcc -o" SH2="-shared *.o" make[4]: Entering directory '/<>/shlib' x86_64-linux-gnu-gcc -shared -Wl,-soname=libblastcompadj.so.6 -o libblastcompadj.so.6.1.20170106 \ -Wl,--whole-archive libblastcompadj.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ -lm x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbi.so.6 -o libncbi.so.6.1.20170106 \ -Wl,--whole-archive libncbi.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ -lm In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ../build/ncbisgml.c:273:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ../build/ncbisgml.c:292:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ../build/ncbisgml.c:348:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ../build/ncbisgml.c:362:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘ErrMsgRoot_fopen’ at ../build/ncbierr.c:955:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 4096 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strcpy’, inlined from ‘SERV_CreateNcbidInfoEx’ at ../build/ncbi_server_info.c:716:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__builtin___strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^ In function ‘strcpy’, inlined from ‘SERV_CreateHttpInfoEx’ at ../build/ncbi_server_info.c:902:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__builtin___strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^ /usr/bin/ld: /tmp/cca9Z2NP.ltrans0.ltrans.o: in function `Nlm_TmpNam': /<>/shlib/../build/ncbifile.c:1211:(.text+0x1093): warning: the use of `tempnam' is dangerous, better use `mkstemp' x86_64-linux-gnu-gcc -shared -Wl,-soname=libblast.so.6 -o libblast.so.6.1.20170106 \ -Wl,--whole-archive libblast.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libblastcompadj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ../build/phi_lookup.c: In function ‘SPHIPatternSearchBlkNew’: ../build/phi_lookup.c:634:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 634 | localPattern[posIndex-1] = 1; | ^ ../build/phi_lookup.c:411:11: note: at offset [-2147483648, -1] into destination object ‘localPattern’ of size 330 411 | Uint1 localPattern[PHI_MAX_PATTERN_LENGTH]; /*local variable to hold for each position whether | ^ ln -s libblast.so.6.1.20170106 libblast.so.6 ln -s libblast.so.6.1.20170106 libblast.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbiobj.so.6 -o libncbiobj.so.6.1.20170106 \ -Wl,--whole-archive libncbiobj.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbi.so.6.1.20170106 -lm ../build/asn2gnb2.c:3409:14: warning: type of ‘PrintDate’ does not match original declaration [-Wlto-type-mismatch] 3409 | string = PrintDate (spb->created); | ^ ../build/wprint.c:169:20: note: return value type mismatch 169 | NLM_EXTERN CharPtr PrintDate(NCBI_DatePtr date) | ^ ../build/wprint.c:169:20: note: type ‘char *’ should match type ‘int’ ../build/wprint.c:169:20: note: ‘PrintDate’ was previously declared here ../build/wprint.c:169:20: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used ../build/salutil.c:3647:8: warning: type of ‘AlnMgr2IndexSingleChildSeqAlign’ does not match original declaration [-Wlto-type-mismatch] 3647 | AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */ | ^ ../build/alignmgr2.c:921:20: note: return value type mismatch 921 | NLM_EXTERN Boolean AlnMgr2IndexSingleChildSeqAlign(SeqAlignPtr sap) | ^ ../build/alignmgr2.c:921:20: note: type ‘Nlm_Boolean’ should match type ‘int’ ../build/alignmgr2.c:921:20: note: ‘AlnMgr2IndexSingleChildSeqAlign’ was previously declared here ../build/gbparint.c: In function ‘Nlm_gbparselex’: ../build/gbparint.c:1928:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1928 | Nlm_lex_error_MACRO( "Lex list not cleared on entry to Nlm_gbparselex") | ^ lto1: note: destination object is likely at address zero ../build/gbparint.c: In function ‘Nlm_gbparselex_ver’: ../build/gbparint.c:2314:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2314 | Nlm_lex_error_MACRO( "Lex list not cleared on entry to Nlm_gbparselex_ver") | ^ lto1: note: destination object is likely at address zero ../build/maputil.c: In function ‘get_location_for_query’: ../build/maputil.c:1265:1: warning: function may return address of local variable [-Wreturn-local-addr] 1265 | } | ^ ../build/maputil.c:1190:16: note: declared here 1190 | SeqLoc sl; | ^ In function ‘s_AddDeflineFromOrganismLine’, inlined from ‘s_ReadOrgNamesFromText’ at ../build/alnread.c:2949:9: ../build/alnread.c:2876:17: warning: ‘free’ called on pointer ‘clp_173->end’ with nonzero offset 1 [-Wfree-nonheap-object] 2876 | free (defline); | ^ x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbitool.so.6 -o libncbitool.so.6.1.20170106 \ -Wl,--whole-archive libncbitool.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libblastcompadj.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ../build/pseed3.c: In function ‘seedParallelFill’: ../build/pseed3.c:712:68: warning: iteration 100 invokes undefined behavior [-Waggressive-loop-optimizations] 712 | returnData->seedSearch->name_space[i] = seedSearch->name_space[i]; | ^ ../build/pseed3.c:711:18: note: within this loop 711 | for( i = 0; i <= BUF_SIZE; i++) | ^ x86_64-linux-gnu-gcc -shared -Wl,-soname=libblastapi.so.6 -o libblastapi.so.6.1.20170106 \ -Wl,--whole-archive libblastapi.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libblast.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ln -s libblastapi.so.6.1.20170106 libblastapi.so.6 ln -s libblastapi.so.6.1.20170106 libblastapi.so ln -s libblastcompadj.so.6.1.20170106 libblastcompadj.so.6 ln -s libblastcompadj.so.6.1.20170106 libblastcompadj.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libconnssl.so.6 -o libconnssl.so.6.1.20170106 \ -Wl,--whole-archive libconnssl.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbi.so.6.1.20170106 -lgnutls ln -s libconnssl.so.6.1.20170106 libconnssl.so.6 ln -s libconnssl.so.6.1.20170106 libconnssl.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libnetcli.so.6 -o libnetcli.so.6.1.20170106 \ -Wl,--whole-archive libnetcli.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbi.so.6.1.20170106 x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbiid1.so.6 -o libncbiid1.so.6.1.20170106 \ -Wl,--whole-archive libncbiid1.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiobj.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbi.so.6.1.20170106 x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbimmdb.so.6 -o libncbimmdb.so.6.1.20170106 \ -Wl,--whole-archive libncbimmdb.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiid1.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm x86_64-linux-gnu-gcc -shared -Wl,-soname=libvibrantOGL.so.6 -o libvibrantOGL.so.6.1.20170106 \ -Wl,--whole-archive libvibrantOGL.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lGLU -lGL -lpng -lXm -lXmu -lXt -lX11 -lm x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbidesk.so.6 -o libncbidesk.so.6.1.20170106 \ -Wl,--whole-archive libncbidesk.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libblastapi.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libncbitool.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ../build/vsmutil.c: In function ‘ContinueProc’: ../build/vsmutil.c:2256:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2256 | vep->counts [i] = 0; | ^ ../build/vsmutil.c:2255:26: note: within this loop 2255 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ^ ../build/vsmutil.c: In function ‘SetVerbosityAndRepopulate’: ../build/vsmutil.c:2297:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2297 | vep->counts [i] = 0; | ^ ../build/vsmutil.c:2296:26: note: within this loop 2296 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ^ ../build/vsmutil.c: In function ‘RevalidateProc’: ../build/vsmutil.c:2223:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2223 | vep->counts [i] = 0; | ^ ../build/vsmutil.c:2222:26: note: within this loop 2222 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ^ ../build/vsmutil.c: In function ‘ClearValidateWindow’: ../build/vsmutil.c:613:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 613 | vep->counts [sev] = 0; | ^ ../build/vsmutil.c:612:32: note: within this loop 612 | for (sev = SEV_NONE; sev <= SEV_MAX; sev++) { | ^ ../build/vsmutil.c: In function ‘CreateValidateWindowExExEx’: ../build/vsmutil.c:2620:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2620 | vep->counts [i] = 0; | ^ ../build/vsmutil.c:2619:30: note: within this loop 2619 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ^ x86_64-linux-gnu-gcc -shared -Wl,-soname=libddvlib.so.6 -o libddvlib.so.6.1.20170106 \ -Wl,--whole-archive libddvlib.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbidesk.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 ln -s libddvlib.so.6.1.20170106 libddvlib.so.6 ln -s libddvlib.so.6.1.20170106 libddvlib.so ln -s libncbi.so.6.1.20170106 libncbi.so.6 ln -s libncbi.so.6.1.20170106 libncbi.so ln -s libncbiNacc.so.6.1.20170106 libncbiCacc.so.6.1.20170106 ln -s libncbiCacc.so.6.1.20170106 libncbiCacc.so.6 ln -s libncbiCacc.so.6.1.20170106 libncbiCacc.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbicdr.so.6 -o libncbicdr.so.6.1.20170106 \ -Wl,--whole-archive libncbicdr.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 In function ‘strncat’, inlined from ‘CdDevice_FileBuildPath.isra’ at ../build/cdnewlib.c:2679:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 16 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘CdDevice_Init’ at ../build/cdnewlib.c:2751:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ In function ‘strncat’, inlined from ‘CdDevice_Init’ at ../build/cdnewlib.c:2769:6: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbiNacc.so.6 -o libncbiNacc.so.6.1.20170106 \ -Wl,--whole-archive libncbiNacc.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbicdr.so.6.1.20170106 libnetentr.a libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ln -s libncbiNacc.so.6.1.20170106 libncbiNacc.so.6 ln -s libncbiNacc.so.6.1.20170106 libncbiNacc.so ln -s libncbiNacc.so.6.1.20170106 libncbiacc.so.6.1.20170106 ln -s libncbiacc.so.6.1.20170106 libncbiacc.so.6 ln -s libncbiacc.so.6.1.20170106 libncbiacc.so ln -s libncbicdr.so.6.1.20170106 libncbicdr.so.6 ln -s libncbicdr.so.6.1.20170106 libncbicdr.so ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3d.so.6.1.20170106 ln -s libncbicn3d.so.6.1.20170106 libncbicn3d.so.6 ln -s libncbicn3d.so.6.1.20170106 libncbicn3d.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbicn3dOGL.so.6 -o libncbicn3dOGL.so.6.1.20170106 \ -Wl,--whole-archive libncbicn3dOGL.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiNacc.so.6.1.20170106 libddvlib.so.6.1.20170106 libncbidesk.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 -lm In function ‘Cn3D_SizeCB’, inlined from ‘Cn3D_SizeCB’ at ../build/cn3dshim.c:371:25: ../build/cn3dshim.c:391:36: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 391 | BoundBox->x[i] = pflvDataThis[i / (int) 2]; | ^ ../build/cn3dshim.c:390:31: note: within this loop 390 | for (i = 0; i < 6; i++) { | ^ ../build/cn3dshim.c:399:36: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations] 399 | BoundBox->x[i + 1]) BoundBox->x[i + 1] = | ^ ../build/cn3dshim.c:395:31: note: within this loop 395 | for (i = 0; i < 6; i += 2) { /* check to see if the atom lies outside the bound box */ | ^ ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3dOGL.so.6 ln -s libncbicn3dOGL.so.6.1.20170106 libncbicn3dOGL.so ln -s libncbidesk.so.6.1.20170106 libncbidesk.so.6 ln -s libncbidesk.so.6.1.20170106 libncbidesk.so ln -s libncbiid1.so.6.1.20170106 libncbiid1.so.6 ln -s libncbiid1.so.6.1.20170106 libncbiid1.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbimla.so.6 -o libncbimla.so.6.1.20170106 \ -Wl,--whole-archive libncbimla.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiobj.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbi.so.6.1.20170106 ln -s libncbimla.so.6.1.20170106 libncbimla.so.6 ln -s libncbimla.so.6.1.20170106 libncbimla.so ln -s libncbimmdb.so.6.1.20170106 libncbimmdb.so.6 ln -s libncbimmdb.so.6.1.20170106 libncbimmdb.so ln -s libncbiobj.so.6.1.20170106 libncbiobj.so.6 ln -s libncbiobj.so.6.1.20170106 libncbiobj.so ln -s libncbitool.so.6.1.20170106 libncbitool.so.6 ln -s libncbitool.so.6.1.20170106 libncbitool.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libncbitxc2.so.6 -o libncbitxc2.so.6.1.20170106 \ -Wl,--whole-archive libncbitxc2.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbitool.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 -lm ln -s libncbitxc2.so.6.1.20170106 libncbitxc2.so.6 ln -s libncbitxc2.so.6.1.20170106 libncbitxc2.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libnetblast.so.6 -o libnetblast.so.6.1.20170106 \ -Wl,--whole-archive libnetblast.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbitool.so.6.1.20170106 libnetcli.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 ln -s libnetblast.so.6.1.20170106 libnetblast.so.6 ln -s libnetblast.so.6.1.20170106 libnetblast.so ln -s libnetcli.so.6.1.20170106 libnetcli.so.6 ln -s libnetcli.so.6.1.20170106 libnetcli.so ln -s libncbiNacc.so.6.1.20170106 libnetentr.so.6.1.20170106 ln -s libnetentr.so.6.1.20170106 libnetentr.so.6 ln -s libnetentr.so.6.1.20170106 libnetentr.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libvibgif.so.6 -o libvibgif.so.6.1.20170106 \ -Wl,--whole-archive libvibgif.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbi.so.6.1.20170106 -lm ln -s libvibgif.so.6.1.20170106 libvibgif.so.6 ln -s libvibgif.so.6.1.20170106 libvibgif.so x86_64-linux-gnu-gcc -shared -Wl,-soname=libvibnet.so.6 -o libvibnet.so.6.1.20170106 \ -Wl,--whole-archive libvibnet.a -Wl,--no-whole-archive -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now \ libncbiNacc.so.6.1.20170106 libncbidesk.so.6.1.20170106 libncbimmdb.so.6.1.20170106 libvibrantOGL.so.6.1.20170106 libncbitool.so.6.1.20170106 libncbicdr.so.6.1.20170106 libncbiobj.so.6.1.20170106 libncbi.so.6.1.20170106 ln -s libvibnet.so.6.1.20170106 libvibnet.so.6 ln -s libvibnet.so.6.1.20170106 libvibnet.so ln -s libvibrantOGL.so.6.1.20170106 libvibrant.so.6.1.20170106 ln -s libvibrant.so.6.1.20170106 libvibrant.so.6 ln -s libvibrant.so.6.1.20170106 libvibrant.so ln -s libvibrantOGL.so.6.1.20170106 libvibrantOGL.so.6 ln -s libvibrantOGL.so.6.1.20170106 libvibrantOGL.so make[4]: Leaving directory '/<>/shlib' rm -f ../shlib/*.a make[3]: Leaving directory '/<>/build' /usr/bin/make -C build clean make[3]: Entering directory '/<>/build' rm -f *.[acho] *.glo make[3]: Leaving directory '/<>/build' /usr/bin/make -C build all LCL=lnx CC="x86_64-linux-gnu-gcc" LDFLAGS1="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS NCBI_LINKINGLIBDIR="../shlib" \ CFLAGS1="-c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG" \ LIB4=libvibrant.a LIB20=libncbidesk.a LIB28=libvibgif.a \ LIB30=libncbicn3d.a LIB45=libddvlib.a LIB400=libvibrantOGL.a LIB3000=libncbicn3dOGL.a make[3]: Entering directory '/<>/build' chmod -R ug+rw,o+r . ../include ./ln-if-absent ../corelib/tsprintf.h ../include ./ln-if-absent ../corelib/gifgen.h ../include ./ln-if-absent ../corelib/ncbi*.h ../include ./ln-if-absent ../corelib/tree*.h ../include ./ln-if-absent ../corelib/regex.h ../include ./ln-if-absent ../corelib/matrix.h ../include ./ln-if-absent ../corelib/binary.h ../include ./ln-if-absent ../corelib/morefile/*.h ../include ./ln-if-absent ../corelib/morefile/*.c . ./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include ./ln-if-absent ../corelib/ncbilcl.lnx ../include/ncbilcl.h ./ln-if-absent ../corelib/*.c . ./ln-if-absent ../corelib/core*.h . ./ln-if-absent ../asnlib/*.h . rm -f ../include/asn.h mv asn.h ../include ./ln-if-absent ../asnlib/*.c . ./ln-if-absent ../connect/*.c . ./ln-if-absent ../connect/ncbi_ansi_ext.h . ./ln-if-absent ../connect/ncbi_assert.h . ./ln-if-absent ../connect/ncbi_priv.h . ./ln-if-absent ../connect/ncbi_comm.h . ./ln-if-absent ../connect/ncbi_config.h . ./ln-if-absent ../connect/ncbi_connssl.h . ./ln-if-absent ../connect/ncbi_lbos.h . ./ln-if-absent ../connect/ncbi_lbosp.h . ./ln-if-absent ../connect/parson.h . ./ln-if-absent ../connect/ncbi_lbsm.h . make[3]: [makefile:714: copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_lbsm_ipc.h . make[3]: [makefile:715: copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_host_infop.h . ./ln-if-absent ../connect/ncbi_server_infop.h . ./ln-if-absent ../connect/ncbi_servicep.h . ./ln-if-absent ../connect/ncbi_socketp.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/ncbi_local.h . ./ln-if-absent ../connect/ncbi_lb.h . ./ln-if-absent ../connect/ncbi_version.h . ./ln-if-absent ../connect/ncbi_base64.h . ./ln-if-absent ../connect/urlquery.h ../include mkdir ../include/connect mkdir: cannot create directory ‘../include/connect’: File exists make[3]: [makefile:727: copy] Error 1 (ignored) chmod ug+rw,o+r ../include/connect cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect ./ln-if-absent ../util/tables/*.c . mkdir -p ../include/util/tables cp -fp ../util/tables/*.h ../include/util/tables ./ln-if-absent ../util/creaders/*.c . mkdir -p ../include/util/creaders cp -fp ../util/creaders/*.h ../include/util/creaders ./ln-if-absent ../ctools/*.c . ./ln-if-absent ../ctools/*.h . mkdir ../include/ctools mkdir: cannot create directory ‘../include/ctools’: File exists make[3]: [makefile:738: copy] Error 1 (ignored) chmod ug+rw,o+r ../include/ctools cp -fp ../ctools/*.h ../include/ctools ./ln-if-absent ../object/*.c . ./ln-if-absent ../object/*.h ../include ./ln-if-absent ../access/*.c . ./ln-if-absent ../access/*.h ../include ./ln-if-absent ../asnstat/*.h ../include ./ln-if-absent ../api/*.h ../include ./ln-if-absent ../api/*.c . ./ln-if-absent ../api/*.inc . ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../cdromlib/*.c . ./ln-if-absent ../vibrant/*.h ../include ./ln-if-absent ../vibrant/*.c . ./ln-if-absent ../desktop/*.h ../include ./ln-if-absent ../desktop/*.c . ./ln-if-absent ../biostruc/*.h ../include ./ln-if-absent ../biostruc/*.c . ./ln-if-absent ../biostruc/cdd/*.h ../include ./ln-if-absent ../biostruc/cdd/*.c . ./ln-if-absent ../biostruc/cn3d/*.h ../include ./ln-if-absent ../biostruc/cn3d/*.c . ./ln-if-absent ../tools/*.h ../include ./ln-if-absent ../tools/*.c . ./ln-if-absent ../cn3d/*.h ../include ./ln-if-absent ../cn3d/*.c . ./ln-if-absent ../gif/*.c . ./ln-if-absent ../gif/*.h ../include ./ln-if-absent ../ddv/*.h ../include ./ln-if-absent ../ddv/*.c . ./ln-if-absent ../regexp/*.c . ./ln-if-absent ../regexp/*.h ../include ./ln-if-absent ../internal/compr/*.c . set: No match. make[3]: [makefile:771: copy] Error 1 (ignored) ./ln-if-absent ../internal/compr/*.h ../include set: No match. make[3]: [makefile:772: copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.c . set: No match. make[3]: [makefile:773: copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.h ../include set: No match. make[3]: [makefile:774: copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.c . set: No match. make[3]: [makefile:775: copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.h ../include set: No match. make[3]: [makefile:776: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.c . set: No match. make[3]: [makefile:777: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.dat . set: No match. make[3]: [makefile:778: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideochr*.h ../include set: No match. make[3]: [makefile:779: copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideoorgs.h . make[3]: [makefile:780: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.c . set: No match. make[3]: [makefile:781: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.dat . set: No match. make[3]: [makefile:782: copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.h ../include set: No match. make[3]: [makefile:783: copy] Error 1 (ignored) ./ln-if-absent ncbidraw.c ncbidrwg.c ./ln-if-absent ncbithr.c ncbithrs.c ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id2arch/*.h ../include mkdir -p ../include/algo/blast/core ./ln-if-absent ../algo/blast/core/*.c . ./ln-if-absent ../algo/blast/core/*.h . ./ln-if-absent ../algo/blast/core/*.inl . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/composition_adjustment ./ln-if-absent ../algo/blast/composition_adjustment/*.c . cp -fp ../algo/blast/composition_adjustment/*.h \ ../include/algo/blast/composition_adjustment mkdir -p ../include/algo/blast/api ./ln-if-absent ../algo/blast/api/*.c . cp -fp ../algo/blast/api/*.h ../include/algo/blast/api chmod -R ug+rw,o+r . echo Waiting...go Waiting...go x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbithr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ncbithr.c:289: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbithr.c: In function ‘s_TlsDestroyAll’: ncbithr.c:2529:11: warning: variable ‘err_code’ set but not used [-Wunused-but-set-variable] 2529 | int err_code = 0; | ^~~~~~~~ cp -p ncbithr.o ../lib x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbimain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimain.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimain.c:82:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 82 | main(int argc, char *argv[]) | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbibs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbibs.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbibs.c: In function ‘Nlm_BSSeek’: ncbibs.c:448:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 448 | if (sp == bsp->seekptr) /* already in right position */ | ^~ ncbibs.c:451:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 451 | bsp->seekptr = sp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF wwwutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbiwww.h:106, from wwwutils.c:150: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbierr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbierr.c:235: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbierr.c: In function ‘Nlm_ErrGetLogfile’: ncbierr.c:1380:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘logfile’ will never be NULL [-Waddress] 1380 | if (info->logfile != NULL && *info->logfile == '\0') | ^~ ncbierr.c:253:15: note: ‘logfile’ declared here 253 | char logfile[PATH_MAX]; | ^~~~~~~ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘ErrMsgRoot_fopen’ at ncbierr.c:955:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 4096 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbienv.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbienv.c:310: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:62: ncbienv.c: In function ‘Nlm_WorkGetAppParam’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen ncbienv.c: In function ‘Nlm_TransientLookup.constprop.0’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbifile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbifile.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbiprop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbiprop.c:104: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbimath.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbimath.h:69, from ncbimath.c:90: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimath.c: In function ‘general_lngamma’: ncbimath.c:230:12: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 230 | ++y[0]; | ~^~~ ncbimath.c:207:25: note: ‘y’ declared here 207 | Nlm_FloatHi y[POLYGAMMA_ORDER_MAX+1]; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbimem.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimem.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbimisc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbimisc.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbimisc.c: In function ‘Nlm_MD5Final’: ncbimisc.c:2250:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] 2250 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ | ^ ncbimisc.c: In function ‘XmlPathSuffixIs’: ncbimisc.c:2966:58: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2966 | if (StringHasNoText (parentFilter) || parent != NULL && StringICmp (parent->name, parentFilter) == 0) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbimsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corepriv.h:85, from ncbimsg.c:167: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbistr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbistr.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbisgml.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbisgml.c:83: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisgml.c: In function ‘Nlm_Sgml2Ascii’: ncbisgml.c:292:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 292 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ ncbisgml.c:273:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 273 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ncbisgml.c:273:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘Nlm_Sgml2Ascii’ at ncbisgml.c:292:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ ncbisgml.c: In function ‘Nlm_Sgml2AsciiLen’: ncbisgml.c:362:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 362 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ ncbisgml.c:348:33: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-truncation] 348 | strncat(bad,sgml,SGML_ERROR_MSG_LIM); | ^ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ncbisgml.c:348:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘Nlm_Sgml2AsciiLen’ at ncbisgml.c:362:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 100 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbitime.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbitime.c:77: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbilang.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbilang.c:57: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnbufo.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asnbufo.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asndebin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asndebin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asndebin.c: In function ‘AsnBinReadVal’: asndebin.c:565:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 565 | else | ^~~~ asndebin.c:568:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 568 | if (atp == NULL) | ^~ asndebin.c:634:41: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 634 | else /* empty sequence written */ | ^~~~ asndebin.c:636:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 636 | while (atp2 != NULL) | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnenbin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnenbin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asngen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asngen.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asngen.c: In function ‘AsnFindNthPieceOfObject’: asngen.c:540:16: warning: variable ‘aeop’ set but not used [-Wunused-but-set-variable] 540 | AsnExpOptPtr aeop; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnio.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnio.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnio.c: In function ‘AsnIoWriteBlock’: asnio.c:698:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 698 | else /* use alternative write function */ | ^~~~ asnio.c:701:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 701 | if (retval != bytes_to_write) | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnlex.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnlex.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnlex.c: In function ‘AsnTxtReadId’: asnlex.c:198:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 198 | if ((token == END_STRUCT) && ((isa == SEQ_TYPE) || (isa == SET_TYPE))) | ^~ asnlex.c:201:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 201 | if (token != IDENT) | ^~ asnlex.c: In function ‘AsnTxtReadVal’: asnlex.c:345:41: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 345 | else /* empty sequence written */ | ^~~~ asnlex.c:347:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 347 | while (atp2 != NULL) | ^~~~~ asnlex.c: At top level: asnlex.c:1290:13: warning: ‘AsnLexWordUTF8’ defined but not used [-Wunused-function] 1290 | static Int2 AsnLexWordUTF8 (AsnIoPtr aip) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnlext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnlext.c:57: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnout.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnout.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnout.c: In function ‘AsnOutput’: asnout.c:159:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 159 | else | ^~~~ asnout.c:162:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 162 | for (i = 0; i < 12; i++) | ^~~ asnout.c:213:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 213 | if (! loader) | ^~ asnout.c:216:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 216 | attvp = p.root_tmpvalue.next; | ^~~~~ asnout.c:270:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 270 | if (! loader) | ^~ asnout.c:273:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 273 | attp = p.root_tmptype.next; | ^~~~ asnout.c:450:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 450 | if (! loader) | ^~ asnout.c:453:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 453 | i = 1; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asnprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asnprint.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnprint.c: In function ‘GetXMLModuleName’: asnprint.c:102:9: warning: statement with no effect [-Wunused-value] 102 | for (currmod; currmod != NULL; currmod = currmod->next) | ^~~ asnprint.c: In function ‘AsnPrintCloseStruct’: asnprint.c:1774:14: warning: variable ‘isa’ set but not used [-Wunused-but-set-variable] 1774 | Int2 isa; | ^~~ asnprint.c: In function ‘AsnPrintModuleXMLInc’: asnprint.c:2095:17: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 2095 | CharPtr ptr; | ^~~ asnprint.c: In function ‘AsnPrintTreeType’: asnprint.c:2575:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2575 | ptr = (Uint4)(atp); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asntypes.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asntypes.c:111: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asntypes.c: In function ‘AsnEnumTypeStr’: asntypes.c:1383:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1383 | if ((atp->type->isa != ENUM_TYPE) && (atp->type->isa != INTEGER_TYPE)) | ^~ asntypes.c:1386:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1386 | avnp = (AsnValxNodePtr) atp->branch; | ^~~~ asntypes.c: In function ‘AsnTreeLoad’: asntypes.c:1274:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1274 | fscanf(fp, "%d %d %d", &numval, &numtype, &nummod); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1288:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1288 | fscanf(fp, "%d %s %ld %lf %d", &isa, name, &intvalue, &realvalue, &next); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1301:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1301 | fscanf(fp, "%d %s %d %d %d %d %d %d %d %d %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1302 | &isa, name, &tagclass, &tagnumber, bools, bools+1, bools+2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1303 | bools+3, bools+4, &defaultvalue, &type, &branch, &next); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asntypes.c:1333:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1333 | fscanf(fp, "%s %s %d %d", name, fname, &type, &next); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asngenob.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asngenob.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gifgen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from gifgen.c:137: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gifgen.c: In function ‘gdImageSetPixel’: gifgen.c:1027:34: warning: ‘<<’ in boolean context, did you mean ‘<’? [-Wint-in-bool-context] 1027 | (!im->use_pattern || (char)(im->pattern[7-y%8] >> x%8 << 7))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF togif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from togif.c:111: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ togif.c: In function ‘gdImageCreateFromGif’: togif.c:961:12: warning: variable ‘AspectRatio’ set but not used [-Wunused-but-set-variable] 961 | int AspectRatio; | ^~~~~~~~~~~ togif.c:960:12: warning: variable ‘Background’ set but not used [-Wunused-but-set-variable] 960 | int Background; | ^~~~~~~~~~ togif.c:959:12: warning: variable ‘ColorResolution’ set but not used [-Wunused-but-set-variable] 959 | int ColorResolution; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -DNCBI_NOTHREADS_AVAIL -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbithrs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ncbithrs.c:289: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbithrs.c: In function ‘s_TlsDestroyAll’: ncbithrs.c:2529:11: warning: unused variable ‘err_code’ [-Wunused-variable] 2529 | int err_code = 0; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -DHAVE_STRING_H -DREGEX_MALLOC regex.c regex.c: In function ‘re_match_2’: regex.c:3762:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3762 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ regex.c:3762:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3762 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3768:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3768 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3915:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3915 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:3968:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3968 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2509:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2509 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4074:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4074 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ regex.c:2512:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2512 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4074:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4074 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ regex.c:4071:25: warning: variable ‘sdummy’ set but not used [-Wunused-but-set-variable] 4071 | const char *sdummy; | ^~~~~~ regex.c:4070:28: warning: variable ‘pdummy’ set but not used [-Wunused-but-set-variable] 4070 | unsigned char *pdummy; | ^~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:4107:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4107 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2421:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2421 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2342:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2342 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ regex.c:2424:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2424 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2368:11: warning: unused variable ‘destination’ [-Wunused-variable] 2368 | char *destination; \ | ^~~~~~~~~~~ regex.c:4120:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4120 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ regex.c:2509:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2509 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4288:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4288 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ regex.c:2512:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2512 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ regex.c:4288:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4288 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ regex.c: In function ‘regex_compile’: regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:986:42: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 986 | pending_exact = (pending_exact - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:984:34: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 984 | laststart = (laststart - old_buffer) + bufp->buffer; \ | ~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:982:44: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 982 | fixup_alt_jump = (fixup_alt_jump - old_buffer) + bufp->buffer;\ | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ regex.c:980:26: warning: pointer may be used after ‘realloc’ [-Wuse-after-free] 980 | begalt = (begalt - old_buffer) + bufp->buffer; \ | ~~~~~~~~^~~~~~~~~~~~~ regex.c:211:22: note: call to ‘realloc’ here 211 | #define ORIG_REALLOC realloc | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tsprintf.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbiargs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbiargs.c:82: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from tree.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF matrix.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/matrix.h:44, from matrix.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_socket.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_socket.c:75: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_socket.c: In function ‘s_GetLocalPort’: ncbi_socket.c:440:50: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 440 | if (getsockname(fd, (struct sockaddr*) &sin, &sinlen) == 0 | ^~~~~~~ | | | TSOCK_socklen_t * {aka int *} In file included from ncbi_socketp.h:54, from ncbi_connssl.h:37, from ncbi_socket.c:76: /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_IsConnected_’: ncbi_socket.c:2572:73: warning: pointer targets in passing argument 5 of ‘getsockopt’ differ in signedness [-Wpointer-sign] 2572 | if (getsockopt(sock->sock, SOL_SOCKET, SO_ERROR, (void*) error, &len) | ^~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:257:46: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 257 | socklen_t *__restrict __optlen) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ ncbi_socket.c: In function ‘s_CreateOnTop’: ncbi_socket.c:4435:35: warning: pointer targets in passing argument 3 of ‘getpeername’ differ in signedness [-Wpointer-sign] 4435 | if (getpeername(fd, &peer.sa, &peerlen) != 0) { | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:131:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 131 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c:4471:43: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 4471 | if (getsockname(fd, &peer.sa, &peerlen) != 0) | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_CreateListening’: ncbi_socket.c:4865:48: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 4865 | error = getsockname(x_lsock, &addr.sa, &addrlen) != 0 | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ ncbi_socket.c: In function ‘s_Accept’: ncbi_socket.c:5105:49: warning: pointer targets in passing argument 3 of ‘accept’ differ in signedness [-Wpointer-sign] 5105 | if ((x_sock = accept(lsock->sock, &addr.sa, &addrlen)) == SOCK_INVALID) { | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:307:42: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 307 | socklen_t *__restrict __addr_len); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ncbi_socket.c: In function ‘s_RecvMsg’: ncbi_socket.c:5409:52: warning: pointer targets in passing argument 6 of ‘recvfrom’ differ in signedness [-Wpointer-sign] 5409 | (struct sockaddr*) &sin, &sinlen); | ^~~~~~~ | | | TSOCK_socklen_t * {aka int *} In file included from /usr/include/x86_64-linux-gnu/sys/socket.h:343: /usr/include/x86_64-linux-gnu/bits/socket2.h:62:56: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 62 | __SOCKADDR_ARG __addr, socklen_t *__restrict __addr_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ ncbi_socket.c: In function ‘TRIGGER_Create’: ncbi_socket.c:5661:18: warning: unused variable ‘x_id’ [-Wunused-variable] 5661 | unsigned int x_id = ++s_ID_Counter; | ^~~~ ncbi_socket.c: In function ‘DSOCK_Bind’: ncbi_socket.c:7390:51: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness [-Wpointer-sign] 7390 | error = getsockname(sock->sock, &addr.sa, &addrlen) != 0 | ^~~~~~~~ | | | TSOCK_socklen_t * {aka int *} /usr/include/x86_64-linux-gnu/sys/socket.h:117:47: note: expected ‘socklen_t * restrict’ {aka ‘unsigned int * restrict’} but argument is of type ‘TSOCK_socklen_t *’ {aka ‘int *’} 117 | socklen_t *__restrict __len) __THROW; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_buffer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_buffer.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_types.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_core.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_core.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_core_c.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_core_c.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_util.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_util.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_priv.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_priv.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_ansi_ext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ansi_ext.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_connection.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_connection.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_connector.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_connutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_connutil.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_file_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_file_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_heapmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_assert.h:35, from ncbi_priv.h:61, from ncbi_heapmgr.c:115: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_heapmgr.c: In function ‘s_HEAP_Take’: ncbi_heapmgr.c:617:12: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 617 | return &b->head; | ^~~~~~~~ ncbi_heapmgr.c: In function ‘s_HEAP_Walk’: ncbi_heapmgr.c:1169:12: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1169 | return &b->head; | ^~~~~~~~ ncbi_heapmgr.c: In function ‘HEAP_Walk’: ncbi_heapmgr.c:1184:20: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1184 | return &heap->base->head; | ^~~~~~~~~~~~~~~~~ ncbi_heapmgr.c:1187:15: warning: taking address of packed member of ‘struct ’ may result in an unaligned pointer value [-Waddress-of-packed-member] 1187 | ? &b->head : 0; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_http_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_http_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_memory_connector.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_lbsmd_stub.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_host_info.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_server_info.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_server_info.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strcpy’, inlined from ‘SERV_CreateNcbidInfoEx’ at ncbi_server_info.c:716:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strcpy’, inlined from ‘SERV_CreateHttpInfoEx’ at ncbi_server_info.c:902:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: warning: ‘__strcpy_chk’ writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_service.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_service.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_version.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_version.h:37, from ncbi_version.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_service_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_service_connector.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_ftp_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ftp_connector.c:49: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_dispd.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_dispd.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_lb.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_local.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_local.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_socket_connector.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_socket_connector.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urlquery.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from urlquery.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF binary.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/binary.h:60, from binary.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_sendmail.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_sendmail.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_base64.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn_connection.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_lbos.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_lbos.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_lbos.c: In function ‘s_LBOS_ReadLbosresolver’: ncbi_lbos.c:756:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 756 | if (s_LBOS_Lbosresolver == NULL) | ^~ ncbi_lbos.c:759:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 759 | s_LBOS_Lbosresolver = strdup(str + 7); | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF parson.c parson.c: In function ‘remove_comments’: parson.c:281:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 281 | for (i = 0; i < (ptr - string) + end_token_len; i++) | ^~~ parson.c:283:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 283 | string = ptr + end_token_len - 1; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_ipv6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_ipv6.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF raw_scoremat.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF drwnflpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnflpt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF drwnfspc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnfspc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF drwnmfls.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from drwnmfls.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rm -f libncbi.a ar cru libncbi.a ncbimain.o ncbibs.o wwwutils.o ncbierr.o ncbienv.o ncbifile.o ncbiprop.o ncbimath.o ncbimem.o ncbimisc.o ncbimsg.o ncbistr.o ncbisgml.o ncbitime.o ncbilang.o asnbufo.o asndebin.o asnenbin.o asngen.o asnio.o asnlex.o asnlext.o asnout.o asnprint.o asntypes.o asngenob.o gifgen.o togif.o ncbithrs.o regex.o tsprintf.o ncbiargs.o tree.o matrix.o ncbi_socket.o ncbi_buffer.o ncbi_types.o ncbi_core.o ncbi_core_c.o ncbi_util.o ncbi_priv.o ncbi_ansi_ext.o ncbi_connection.o ncbi_connector.o ncbi_connutil.o ncbi_file_connector.o ncbi_heapmgr.o ncbi_http_connector.o ncbi_memory_connector.o ncbi_lbsmd_stub.o ncbi_host_info.o ncbi_server_info.o ncbi_service.o ncbi_version.o ncbi_service_connector.o ncbi_ftp_connector.o ncbi_dispd.o ncbi_lb.o ncbi_local.o ncbi_socket_connector.o urlquery.o binary.o ncbi_sendmail.o ncbi_base64.o asn_connection.o ncbi_lbos.o parson.o ncbi_ipv6.o raw_scoremat.o drwnflpt.o drwnfspc.o drwnmfls.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbi.a ../lib ranlib ../lib/libncbi.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -DHAVE_LIBGNUTLS ncbi_gnutls.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ncbi_config.h:38, from ncbi_ansi_ext.h:37, from ncbi_gnutls.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbi_gnutls.c: In function ‘s_GnuTlsCreate’: ncbi_gnutls.c:293:5: warning: ‘gnutls_connection_end_t’ is deprecated [-Wdeprecated-declarations] 293 | gnutls_connection_end_t end = (side == eSOCK_Client | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ncbi_gnutls.c:35: ncbi_gnutls.c: In function ‘s_GnuTlsInit’: ncbi_priv.h:217:33: warning: ‘version’ may be used uninitialized [-Wmaybe-uninitialized] 217 | _mess.message = NcbiMessagePlusError(&_mess.dynamic, \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 | (_message), \ | ~~~~~~~~~~~~~~~~~~~~ 219 | (_error), \ | ~~~~~~~~~~~~~~~~~~~~ 220 | (_descr)); \ | ~~~~~~~~~ ncbi_gnutls.c:582:17: note: ‘version’ was declared here 582 | const char* version; | ^~~~~~~ rm -f libconnssl.a ar cru libconnssl.a ncbi_gnutls.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libconnssl.a ../lib ranlib ../lib/libconnssl.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objacces.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnacces.h:9, from objacces.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objacces.c: In function ‘LinkSetAsnWrite’: objacces.c:140:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 140 | if (atp == NULL) | ^~ objacces.c:143:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 143 | if (lsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objacces.c: In function ‘LinkSetAsnRead’: objacces.c:216:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 216 | if (atp == NULL) | ^~ objacces.c:219:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 219 | lsp = LinkSetNew(); | ^~~ objacces.c:220:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 220 | if (lsp == NULL) | ^~ objacces.c:223:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 223 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objacces.c:226:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 226 | if (atp == NULL) | ^~ objacces.c:228:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 228 | if (AsnReadVal(aip, atp, &av) <= 0) /* get the num */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objalign.h:103, from objalign.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objalign.c: In function ‘CommonSeqAlignLabelFunc’: objalign.c:135:34: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 135 | CharPtr curr, typelabel, tmp; | ^~~ objalign.c: In function ‘SeqAlignAsnRead’: objalign.c:597:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 597 | if (atp == NULL) | ^~ objalign.c:600:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 600 | sap = SeqAlignNew(); | ^~~ objalign.c:601:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 601 | if (sap == NULL) | ^~ objalign.c:604:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 604 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘DenseDiagAsnWrite’: objalign.c:1020:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1020 | if (atp == NULL) | ^~ objalign.c:1023:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1023 | if (ddp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c: In function ‘DenseDiagAsnRead’: objalign.c:1112:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1112 | if (atp == NULL) | ^~ objalign.c:1115:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1115 | ddp = DenseDiagNew(); | ^~~ objalign.c:1116:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1116 | if (ddp == NULL) | ^~ objalign.c:1119:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1119 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘DenseSegAsnWrite’: objalign.c:1268:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1268 | if (atp == NULL) | ^~ objalign.c:1271:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1271 | if (dsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c: In function ‘DenseSegAsnRead’: objalign.c:1374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1374 | if (atp == NULL) | ^~ objalign.c:1377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1377 | dsp = DenseSegNew(); | ^~~ objalign.c:1378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1378 | if (dsp == NULL) | ^~ objalign.c:1381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1381 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘StdSegAsnWrite’: objalign.c:1559:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1559 | if (atp == NULL) | ^~ objalign.c:1562:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1562 | if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c:1581:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1581 | if (! SeqLocSetAsnWrite(ssp->loc, aip, STD_SEG_loc, STD_SEG_loc_E)) | ^~ objalign.c:1584:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1584 | if (ssp->scores != NULL) | ^~ objalign.c: In function ‘StdSegAsnRead’: objalign.c:1626:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1626 | if (atp == NULL) | ^~ objalign.c:1629:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1629 | ssp = StdSegNew(); | ^~~ objalign.c:1630:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1630 | if (ssp == NULL) | ^~ objalign.c:1633:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1633 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘SeqAlignSetAsnWrite’: objalign.c:1704:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1704 | if (atp == NULL) | ^~ objalign.c:1708:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1708 | oldsap = sap; | ^~~~~~ objalign.c: In function ‘PackSegAsnWrite’: objalign.c:1892:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1892 | if (atp == NULL) | ^~ objalign.c:1895:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1895 | if (psp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objalign.c:1926:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1926 | if (! AsnCloseStruct(aip, PACKED_SEG_starts, (Pointer)psp->starts)) | ^~ objalign.c:1929:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1929 | av.ptrvalue = psp->present; | ^~ objalign.c: In function ‘PackSegAsnRead’: objalign.c:1999:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1999 | if (atp == NULL) | ^~ objalign.c:2002:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2002 | psp = PackSegNew(); | ^~~ objalign.c:2003:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2003 | if (psp == NULL) | ^~ objalign.c:2006:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2006 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ objalign.c: In function ‘SplicedSegAsnRead’: objalign.c:2179:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2179 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseSegAsnRead’: objalign.c:2422:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2422 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedExonAsnRead’: objalign.c:2614:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2614 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedSegModifierFree’: objalign.c:2875:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2875 | Pointer pnt; | ^~~ objalign.c: In function ‘ProductPosFree’: objalign.c:3050:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3050 | Pointer pnt; | ^~~ objalign.c: In function ‘SplicedExonChunkFree’: objalign.c:3225:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3225 | Pointer pnt; | ^~~ objalign.c: In function ‘SpliceSiteAsnRead’: objalign.c:3469:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3469 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘ProtPosAsnRead’: objalign.c:3626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3626 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseAlignAsnRead’: objalign.c:3798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3798 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SparseSegExtAsnRead’: objalign.c:4020:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4020 | AsnReadFunc func; | ^~~~ objalign.c: In function ‘SplicedSegModifierAsnRead’: objalign.c:2955:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2955 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:2903:10: note: ‘choice’ was declared here 2903 | Uint1 choice; | ^~~~~~ objalign.c: In function ‘SplicedExonChunkAsnRead’: objalign.c:3326:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3326 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:3253:10: note: ‘choice’ was declared here 3253 | Uint1 choice; | ^~~~~~ objalign.c: In function ‘ProductPosAsnRead’: objalign.c:3130:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3130 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalign.c:3081:10: note: ‘choice’ was declared here 3081 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objall.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objall.h:64, from objall.c:63: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objbibli.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnbibli.h:9, from objbibli.c:113: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objbibli.c: In function ‘AffilAsnRead’: objbibli.c:208:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 208 | if (atp == NULL) | ^~ objbibli.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 211 | afp = AffilNew(); | ^~~ objbibli.c: In function ‘AffilAsnWrite’: objbibli.c:296:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 296 | if (atp == NULL) | ^~ objbibli.c:299:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 299 | if (afp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘AuthListFree’: objbibli.c:458:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 458 | if (alp->affil != NULL) | ^~ objbibli.c:460:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 460 | return (AuthListPtr)MemFree(alp); | ^~~~~~ objbibli.c: In function ‘AuthListAsnRead’: objbibli.c:489:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 489 | if (atp == NULL) | ^~ objbibli.c:492:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 492 | alp = AuthListNew(); | ^~~ objbibli.c: In function ‘AuthListAsnWrite’: objbibli.c:583:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 583 | if (atp == NULL) | ^~ objbibli.c:586:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 586 | if (alp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:590:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 590 | if (! AsnOpenStruct(aip, atp, (Pointer)alp)) /* open AuthList SEQUENCE */ | ^~ objbibli.c:593:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 593 | av.ptrvalue = alp->names; | ^~ objbibli.c: In function ‘AuthorFree’: objbibli.c:677:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 677 | if (ap->affil != NULL) | ^~ objbibli.c:679:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 679 | return (AuthorPtr)MemFree(ap); | ^~~~~~ objbibli.c: In function ‘AuthorAsnRead’: objbibli.c:707:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 707 | if (atp == NULL) | ^~ objbibli.c:710:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 710 | ap = AuthorNew(); | ^~ objbibli.c: In function ‘AuthorAsnWrite’: objbibli.c:779:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 779 | if (atp == NULL) | ^~ objbibli.c:782:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 782 | if (ap == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitArtAsnRead’: objbibli.c:925:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 925 | if (atp == NULL) | ^~ objbibli.c:928:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 928 | cap = CitArtNew(); | ^~~ objbibli.c: In function ‘CitArtAsnWrite’: objbibli.c:1027:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1027 | if (atp == NULL) | ^~ objbibli.c:1030:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1030 | if (cap == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1034:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1034 | if (! AsnOpenStruct(aip, atp, (Pointer)cap)) /* open the SEQUENCE */ | ^~ objbibli.c:1037:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1037 | if (cap->title != NULL) | ^~ objbibli.c: In function ‘ImprintAsnRead’: objbibli.c:1152:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1152 | if (atp == NULL) | ^~ objbibli.c:1155:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1155 | ip = ImprintNew(); | ^~ objbibli.c: In function ‘ImprintAsnWrite’: objbibli.c:1251:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1251 | if (atp == NULL) | ^~ objbibli.c:1254:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1254 | if (ip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitRetractFree’: objbibli.c:1360:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1360 | if (crp == NULL) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objbibli.c:1363:9: note: in expansion of macro ‘MemFree’ 1363 | MemFree(crp->exp); | ^~~~~~~ objbibli.c: In function ‘CitRetractAsnRead’: objbibli.c:1391:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1391 | if (atp == NULL) | ^~ objbibli.c:1394:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1394 | crp = CitRetractNew(); | ^~~ objbibli.c: In function ‘CitRetractAsnWrite’: objbibli.c:1445:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1445 | if (atp == NULL) | ^~ objbibli.c:1448:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1448 | if (crp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitJourAsnRead’: objbibli.c:1524:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1524 | if (atp == NULL) | ^~ objbibli.c:1527:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1527 | cjp = CitJourNew(); | ^~~ objbibli.c: In function ‘CitJourAsnWrite’: objbibli.c:1576:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1576 | if (atp == NULL) | ^~ objbibli.c:1579:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1579 | if (cjp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1585:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1585 | if (! ImprintAsnWrite(cjp->imp, aip, CIT_JOUR_imp)) | ^~ objbibli.c:1587:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1587 | if (! AsnCloseStruct(aip, atp, (Pointer)cjp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitBookAsnRead’: objbibli.c:1676:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1676 | if (atp == NULL) | ^~ objbibli.c:1679:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1679 | cbp = CitBookNew(); | ^~~ objbibli.c: In function ‘CitBookAsnWrite’: objbibli.c:1744:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1744 | if (atp == NULL) | ^~ objbibli.c:1747:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1747 | if (cbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1760:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1760 | if (! ImprintAsnWrite(cbp->imp, aip, CIT_BOOK_imp)) | ^~ objbibli.c:1762:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1762 | if (! AsnCloseStruct(aip, atp, (Pointer)cbp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitProcAsnWrite’: objbibli.c:1879:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1879 | if (atp == NULL) | ^~ objbibli.c:1882:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1882 | if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:1901:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1901 | if (! AsnCloseStruct(aip, CIT_PROC_meet, (Pointer)cpp->otherdata)) | ^~ objbibli.c:1903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1903 | if (! AsnCloseStruct(aip, atp, (Pointer)cpp)) /* end SEQUENCE */ | ^~ objbibli.c: In function ‘CitLetAsnWrite’: objbibli.c:1995:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1995 | if (atp == NULL) | ^~ objbibli.c:1998:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1998 | if (clp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitPatAsnRead’: objbibli.c:2091:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2091 | if (atp == NULL) | ^~ objbibli.c:2094:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2094 | cpp = CitPatNew(); | ^~~ objbibli.c: In function ‘CitPatAsnWrite’: objbibli.c:2213:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2213 | if (atp == NULL) | ^~ objbibli.c:2216:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2216 | if (cpp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘IdPatAsnRead’: objbibli.c:2346:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2346 | if (atp == NULL) | ^~ objbibli.c:2349:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2349 | idp = IdPatNew(); | ^~~ objbibli.c: In function ‘IdPatAsnWrite’: objbibli.c:2412:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2412 | if (atp == NULL) | ^~ objbibli.c:2415:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2415 | if (idp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitGenAsnRead’: objbibli.c:2546:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2546 | if (atp == NULL) | ^~ objbibli.c:2549:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2549 | cgp = CitGenNew(); | ^~~ objbibli.c: In function ‘CitGenAsnWrite’: objbibli.c:2627:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2627 | if (atp == NULL) | ^~ objbibli.c:2630:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2630 | if (cgp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘TitleAsnWrite’: objbibli.c:2825:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2825 | if (atp == NULL) | ^~ objbibli.c:2828:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2828 | if (tp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘CitSubFree’: objbibli.c:2909:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2909 | if (csp == NULL) | ^~ objbibli.c:2912:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2912 | AuthListFree(csp->authors); | ^~~~~~~~~~~~ objbibli.c: In function ‘CitSubAsnRead’: objbibli.c:2943:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2943 | if (atp == NULL) | ^~ objbibli.c:2946:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2946 | csp = CitSubNew(); | ^~~ objbibli.c:2958:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2958 | if (atp == NULL) | ^~ objbibli.c:2961:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2961 | if (atp == CIT_SUB_imp) | ^~ objbibli.c: In function ‘CitSubAsnWrite’: objbibli.c:3029:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3029 | if (atp == NULL) | ^~ objbibli.c:3032:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3032 | if (csp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c:3038:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3038 | if (! AuthListAsnWrite(csp->authors, aip, CIT_SUB_authors)) | ^~ objbibli.c:3041:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3041 | if (csp->imp != NULL) | ^~ objbibli.c: In function ‘PatPrioritySetAsnRead’: objbibli.c:3694:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3694 | if (ppp == NULL) | ^~ objbibli.c:3697:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3697 | if (head == NULL) | ^~ objbibli.c:3715:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3715 | if (atp == NULL) | ^~ objbibli.c:3717:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3717 | ppp->date = DateAsnRead(aip, atp); | ^~~ objbibli.c: In function ‘PatPrioritySetAsnWrite’: objbibli.c:3755:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3755 | if (! AsnOpenStruct(aip, set, (Pointer)ppp)) /* open the SEQUENCE OF */ | ^~ objbibli.c:3758:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3758 | for (tmp = ppp; tmp != NULL; tmp = tmp->next) | ^~~ objbibli.c: In function ‘ArticleIdAsnRead’: objbibli.c:3849:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3849 | if (atp == NULL) | ^~ objbibli.c:3852:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3852 | aidp = ArticleIdNew(); | ^~~~ objbibli.c: In function ‘ArticleIdAsnWrite’: objbibli.c:3925:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3925 | if (atp == NULL) | ^~ objbibli.c:3928:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3928 | if (aidp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objbibli.c: In function ‘PubStatusDateAsnRead’: objbibli.c:4039:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4039 | if (atp == NULL) | ^~ objbibli.c:4042:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4042 | psdp = PubStatusDateNew(); | ^~~~ objbibli.c: In function ‘PubStatusDateAsnWrite’: objbibli.c:4091:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4091 | if (atp == NULL) | ^~ objbibli.c:4094:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4094 | if (psdp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objfeat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objfeat.h:48, from objfeat.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objfeat.c: In function ‘ModelEvidenceSupportAsnRead’: objfeat.c:1500:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1500 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ExperimentSupportAsnRead’: objfeat.c:1748:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1748 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ProgramIdAsnRead’: objfeat.c:1933:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1933 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘EvidenceBasisAsnRead’: objfeat.c:2103:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2103 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘InferenceSupportAsnRead’: objfeat.c:2267:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2267 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ModelEvidenceItemAsnRead’: objfeat.c:2483:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2483 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SeqFeatSupportAsnRead’: objfeat.c:2688:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2688 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAQualAsnRead’: objfeat.c:4244:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4244 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAQualSetAsnRead’: objfeat.c:4396:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4396 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘RNAGenAsnRead’: objfeat.c:4524:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4524 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘GeneNomenclatureAsnRead’: objfeat.c:4707:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4707 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘OrgNameMatch’: objfeat.c:5957:28: warning: self-comparison always evaluates to false [-Wtautological-compare] 5957 | || onp2->mgcode != onp2->mgcode | ^~ objfeat.c: In function ‘TaxElementAsnWrite’: objfeat.c:7399:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 7399 | if (! AsnOpenStruct(aip, atp, (Pointer)tep)) | ^~ objfeat.c:7402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 7402 | av.intvalue = (Int4)(tep->fixed_level); | ^~ objfeat.c: In function ‘PCRPrimerAsnRead’: objfeat.c:8276:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8276 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRPrimerSetAsnRead’: objfeat.c:8421:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8421 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRReactionAsnRead’: objfeat.c:8542:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8542 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PCRReactionSetAsnRead’: objfeat.c:8685:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8685 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneRefAsnRead’: objfeat.c:8812:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8812 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneSeqSetAsnRead’: objfeat.c:9005:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9005 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘CloneSeqAsnRead’: objfeat.c:9135:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9135 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SomaticOriginAsnRead’: objfeat.c:9487:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9487 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘SomaticOriginConditionAsnRead’: objfeat.c:9566:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9566 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘VariationRefAsnRead’: objfeat.c:9645:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9645 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_loss_of_heterozygosityAsnRead’: objfeat.c:10687:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10687 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_frameshiftAsnRead’: objfeat.c:10765:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10765 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘VarRefDataFree’: objfeat.c:10865:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 10865 | Pointer pnt; | ^~~ objfeat.c: In function ‘VarRefDataSetAsnRead’: objfeat.c:10918:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10918 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Consequence_elementFree’: objfeat.c:11112:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 11112 | Pointer pnt; | ^~~ objfeat.c: In function ‘VariationInstAsnRead’: objfeat.c:11241:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11241 | AsnReadFunc func; | ^~~~ objfeat.c: At top level: objfeat.c:11393:1: warning: "/*" within comment [-Wcomment] 11393 | /************************************************** | objfeat.c: In function ‘VariantPropertiesAsnRead’: objfeat.c:11422:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11422 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PhenotypeAsnRead’: objfeat.c:11746:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11746 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘PopulationDataAsnRead’: objfeat.c:11945:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11945 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘ExtLocAsnRead’: objfeat.c:12161:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12161 | AsnReadFunc func; | ^~~~ objfeat.c: In function ‘Seq_seqFree’: objfeat.c:12327:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12327 | Pointer pnt; | ^~~ objfeat.c: In function ‘DeltaItemAsnRead’: objfeat.c:12360:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12360 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objgen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asngen.h:9, from objgen.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objgen.c: In function ‘DateFree’: objgen.c:147:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 147 | if (dp == NULL) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objgen.c:150:9: note: in expansion of macro ‘MemFree’ 150 | MemFree(dp->str); | ^~~~~~~ objgen.c: In function ‘DateClean’: objgen.c:161:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 161 | if (dp == NULL) | ^~ objgen.c:164:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 164 | memset(dp, 0, sizeof(NCBI_Date)); | ^~~~~~ objgen.c: In function ‘DateAsnWrite’: objgen.c:399:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 399 | if (atp == NULL) | ^~ objgen.c:402:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 402 | if (dp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘DateAsnRead’: objgen.c:494:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 494 | if (atp == NULL) | ^~ objgen.c:497:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 497 | dp = DateNew(); | ^~ objgen.c:498:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 498 | if (dp == NULL) | ^~ objgen.c:501:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 501 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */ | ^~ objgen.c: In function ‘DbtagFree’: objgen.c:752:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | if (dbt == NULL) | ^~ objgen.c:755:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 755 | dbt->tag = ObjectIdFree(dbt->tag); | ^~~ objgen.c: In function ‘DbtagAsnRead’: objgen.c:784:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 784 | if (atp == NULL) | ^~ objgen.c:787:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 787 | dbt = DbtagNew(); | ^~~ objgen.c:788:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 788 | if (dbt == NULL) | ^~ objgen.c:791:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 791 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */ | ^~ objgen.c:799:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 799 | if (dbt->tag == NULL) | ^~ objgen.c:802:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 802 | atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret; /* END_STRUCT */ | ^~~ objgen.c: In function ‘DbtagAsnWrite’: objgen.c:833:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 833 | if (atp == NULL) | ^~ objgen.c:836:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 836 | if (dbt == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘ObjectIdFree’: objgen.c:949:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 949 | if (oid == NULL) | ^~ ../include/ncbimem.h:232:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 232 | #define MemFree Nlm_MemFree | ^~~~~~~~~~~ objgen.c:952:9: note: in expansion of macro ‘MemFree’ 952 | MemFree(oid->str); | ^~~~~~~ objgen.c: In function ‘ObjectIdAsnRead’: objgen.c:980:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 980 | if (atp == NULL) | ^~ objgen.c:983:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 983 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE value (nothing) */ | ^~ objgen.c:989:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 989 | if (oid == NULL) | ^~ objgen.c:991:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 991 | if (atp == OBJECT_ID_id) | ^~ objgen.c: In function ‘ObjectIdAsnWrite’: objgen.c:1024:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1024 | if (atp == NULL) | ^~ objgen.c:1027:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1027 | if (oid == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘NameStdFree’: objgen.c:1174:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1174 | if (nsp == NULL) | ^~ objgen.c:1177:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1177 | for (i = 0; i < 7; i++) | ^~~ objgen.c: In function ‘NameStdAsnRead’: objgen.c:1208:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1208 | if (atp == NULL) | ^~ objgen.c:1211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1211 | nsp = NameStdNew(); | ^~~ objgen.c:1212:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1212 | if (nsp == NULL) | ^~ objgen.c:1215:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1215 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the START_STRUCT */ | ^~ objgen.c: In function ‘NameStdAsnWrite’: objgen.c:1271:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1271 | if (atp == NULL) | ^~ objgen.c:1274:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1274 | if (nsp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘PersonIdFree’: objgen.c:1368:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1368 | if (pid == NULL) | ^~ objgen.c:1371:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1371 | if (pid->choice == 1) /* Dbtag */ | ^~ objgen.c: In function ‘PersonIdAsnWrite’: objgen.c:1464:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1464 | if (atp == NULL) | ^~ objgen.c:1467:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1467 | if (pid == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objgen.c: In function ‘IntFuzzAsnRead’: objgen.c:1682:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1682 | if (atp == NULL) | ^~ objgen.c:1685:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1685 | ifp = IntFuzzNew(); | ^~~ objgen.c:1686:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1686 | if (ifp == NULL) | ^~ objgen.c:1689:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1689 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the CHOICE (nothing) */ | ^~ objgen.c: In function ‘UserFieldAsnRead’: objgen.c:1944:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1944 | if (atp == NULL) | ^~ objgen.c:1947:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1947 | ufp = UserFieldNew(); | ^~~ objgen.c: In function ‘UserObjectAsnRead’: objgen.c:2434:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2434 | if (atp == NULL) | ^~ objgen.c:2437:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2437 | uop = UserObjectNew(); | ^~~ objgen.c:2438:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2438 | if (uop == NULL) | ^~ objgen.c:2441:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2441 | if (AsnReadVal(aip, atp, &av) <= 0) goto erret; /* read the start struct */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objloc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from objloc.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objloc.c: In function ‘SeqIdAsnWrite’: objloc.c:313:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 313 | if (atp == NULL) | ^~ objloc.c:316:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 316 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqIdAsnRead’: objloc.c:443:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 443 | if (atp == NULL) | ^~ objloc.c:446:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 446 | anp = ValNodeNew(NULL); | ^~~ objloc.c: In function ‘SeqIdDup’: objloc.c:587:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 587 | if (oldid == NULL) | ^~ objloc.c:590:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 590 | newid = ValNodeNew(NULL); | ^~~~~ objloc.c: In function ‘SeqIdSetAsnRead’: objloc.c:752:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | if (AsnReadVal(aip, atp, &av) <= 0) /* end struct */ | ^~ objloc.c:754:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 754 | if (first == NULL) | ^~ objloc.c: In function ‘SeqIdSetAsnWrite’: objloc.c:786:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 786 | if (atp2 == NULL) | ^~ objloc.c:789:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 789 | if (anp == NULL) { AsnNullValueMsg(aip, settype); goto erret; } | ^~ objloc.c: In function ‘TextSeqIdAsnWrite’: objloc.c:864:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 864 | if (atp == NULL) | ^~ objloc.c:867:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 867 | if (tsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘TextSeqIdAsnRead’: objloc.c:934:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 934 | if (atp == NULL) | ^~ objloc.c:937:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 937 | tsip = TextSeqIdNew(); | ^~~~ objloc.c:938:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 938 | if (tsip == NULL) | ^~ objloc.c:941:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 941 | if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PatentSeqIdAsnWrite’: objloc.c:1018:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1018 | if (atp == NULL) | ^~ objloc.c:1021:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1021 | if (psip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PatentSeqIdAsnRead’: objloc.c:1068:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1068 | if (atp == NULL) | ^~ objloc.c:1071:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1071 | psip = PatentSeqIdNew(); | ^~~~ objloc.c:1072:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1072 | if (psip == NULL) | ^~ objloc.c:1075:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1075 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘GiimAsnWrite’: objloc.c:1151:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1151 | if (atp == NULL) | ^~ objloc.c:1154:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1154 | if (gip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘GiimAsnRead’: objloc.c:1216:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1216 | if (gip == NULL) | ^~ objloc.c:1219:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1219 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PDBSeqIdAsnWrite’: objloc.c:1305:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1305 | if (atp == NULL) | ^~ objloc.c:1308:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1308 | if (pdbsip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PDBSeqIdAsnRead’: objloc.c:1374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1374 | if (atp == NULL) | ^~ objloc.c:1377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1377 | pdbsip = PDBSeqIdNew(); | ^~~~~~ objloc.c:1378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1378 | if (pdbsip == NULL) | ^~ objloc.c:1381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1381 | if ((AsnReadVal(aip, oldtype, &av)) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘SeqLocAsnWrite’: objloc.c:1528:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1528 | if (atp == NULL) | ^~ objloc.c:1531:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1531 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocAsnRead’: objloc.c:1624:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1624 | if (atp == NULL) | ^~ objloc.c:1627:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1627 | anp = ValNodeNew(NULL); | ^~~ objloc.c:1628:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1628 | if (anp == NULL) | ^~ objloc.c:1631:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1631 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the CHOICE value (nothing) */ | ^~ objloc.c: In function ‘SeqLocMixAsnWrite’: objloc.c:1738:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1738 | if (atp == NULL) | ^~ objloc.c:1741:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1741 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocEquivAsnWrite’: objloc.c:1805:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1805 | if (atp == NULL) | ^~ objloc.c:1808:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1808 | if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqLocSetAsnWrite’: objloc.c:1873:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1873 | if (atp2 == NULL) | ^~ objloc.c:1876:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1876 | if (anp == NULL) { AsnNullValueMsg(aip, set); goto erret; } | ^~ objloc.c: In function ‘SeqLocSetAsnRead’: objloc.c:1940:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1940 | if (AsnReadVal(aip, atp, &av) <= 0) /* read END_STRUCT */ | ^~ objloc.c:1942:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1942 | if (first == NULL) | ^~ objloc.c: In function ‘SeqIntAsnWrite’: objloc.c:2022:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022 | if (atp == NULL) | ^~ objloc.c:2025:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025 | if (sip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqIntAsnRead’: objloc.c:2095:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2095 | if (atp == NULL) | ^~ objloc.c:2098:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2098 | sip = SeqIntNew(); | ^~~ objloc.c:2099:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if (sip == NULL) | ^~ objloc.c:2102:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2102 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PackSeqIntAsnWrite’: objloc.c:2179:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2179 | if (atp == NULL) | ^~ objloc.c:2181:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2181 | oldsip = sip; | ^~~~~~ objloc.c:2185:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2185 | if (! AsnOpenStruct(aip, atp, (Pointer)oldsip)) | ^~ objloc.c:2187:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2187 | for ( ;sip != NULL; sip = sip->next) | ^~~ objloc.c: In function ‘SeqPntAsnWrite’: objloc.c:2309:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2309 | if (atp == NULL) | ^~ objloc.c:2312:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2312 | if (spp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqPntAsnRead’: objloc.c:2374:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2374 | if (atp == NULL) | ^~ objloc.c:2377:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2377 | spp = SeqPntNew(); | ^~~ objloc.c:2378:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2378 | if (spp == NULL) | ^~ objloc.c:2381:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2381 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘PackSeqPntAsnWrite’: objloc.c:2479:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2479 | if (atp == NULL) | ^~ objloc.c:2482:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2482 | if (pspp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘PackSeqPntAsnRead’: objloc.c:2553:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2553 | if (atp == NULL) | ^~ objloc.c:2556:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2556 | pspp = PackSeqPntNew(); | ^~~~ objloc.c:2557:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2557 | if (pspp == NULL) | ^~ objloc.c:2560:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2560 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ objloc.c: In function ‘SeqBondAsnWrite’: objloc.c:2724:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2724 | if (atp == NULL) | ^~ objloc.c:2727:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2727 | if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objloc.c: In function ‘SeqBondAsnRead’: objloc.c:2776:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2776 | if (atp == NULL) | ^~ objloc.c:2779:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2779 | sbp = SeqBondNew(); | ^~~ objloc.c:2780:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2780 | if (sbp == NULL) | ^~ objloc.c:2783:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2783 | if (AsnReadVal(aip, oldtype, &av) <= 0) /* read the START_STRUCT */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmedli.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmedli.h:80, from objmedli.c:104: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmedli.c: In function ‘MedlineMeshAsnRead’: objmedli.c:248:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 248 | if (atp == NULL) | ^~ objmedli.c:251:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 251 | mmp = MedlineMeshNew(); | ^~~ objmedli.c: In function ‘DocRefFree’: objmedli.c:1190:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1190 | if (drp == NULL) | ^~ objmedli.c:1193:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1193 | return (DocRefPtr)MemFree(drp); | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objpub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objpub.h:70, from objpub.c:125: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objpub.c: In function ‘PubSetAsnRead’: objpub.c:831:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 831 | if (AsnReadVal(aip, settype, &av) <= 0) /* read START_STRUCT */ | ^~ objpub.c:834:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 834 | if (settype == PUB_SET_pub) | ^~ objpub.c:901:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 901 | if (AsnReadVal(aip, settype, &av) <= 0) /* read END_STRUCT for SET OF */ | ^~ objpub.c:903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 903 | if (anp == NULL) | ^~ objpub.c: In function ‘PubLabelUnique’: objpub.c:1360:24: warning: unused variable ‘pmid’ [-Wunused-variable] 1360 | Int4 muid = 0, pmid = 0; | ^~~~ objpub.c:1360:14: warning: unused variable ‘muid’ [-Wunused-variable] 1360 | Int4 muid = 0, pmid = 0; | ^~~~ objpub.c: In function ‘PubSetAsnRead’: objpub.c:870:17: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 870 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objpub.c:805:11: note: ‘choice’ was declared here 805 | Uint1 choice; | ^~~~~~ objpub.c:876:16: warning: ‘func’ may be used uninitialized [-Wmaybe-uninitialized] 876 | pnt = (* func)(aip, atp); | ~^~~~~~~~~~~~~~~~~ objpub.c:806:17: note: ‘func’ was declared here 806 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objres.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from objres.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objres.c: In function ‘SeqGraphFree’: objres.c:208:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 208 | else /* byte */ | ^~~~ objres.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 211 | ObjMgrDelete(OBJ_SEQGRAPH, (Pointer)sgp); | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objscoremat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objscoremat.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objscoremat.c: In function ‘PssmAsnRead’: objscoremat.c:93:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 93 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmIntermediateDataAsnRead’: objscoremat.c:339:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 339 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmFinalDataAsnRead’: objscoremat.c:548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 548 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmParametersAsnRead’: objscoremat.c:766:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 766 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘PssmWithParametersAsnRead’: objscoremat.c:946:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 946 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘BlockPropertyAsnRead’: objscoremat.c:1113:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1113 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘CoreBlockAsnRead’: objscoremat.c:1289:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1289 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘LoopConstraintAsnRead’: objscoremat.c:1480:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1480 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘CoreDefAsnRead’: objscoremat.c:1646:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1646 | AsnReadFunc func; | ^~~~ objscoremat.c: In function ‘FormatRpsDbParametersAsnRead’: objscoremat.c:1817:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1817 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from objseq.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objseq.c: In function ‘LinkageEvidenceAsnRead’: objseq.c:1609:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1609 | AsnReadFunc func; | ^~~~ objseq.c: In function ‘SeqGapAsnRead’: objseq.c:1764:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1764 | AsnReadFunc func; | ^~~~ objseq.c: In function ‘SeqDescrAsnWriteExtra’: objseq.c:2035:48: warning: variable ‘had_anp’ set but not used [-Wunused-but-set-variable] 2035 | Boolean retval = FALSE, had_extra = FALSE, had_anp = FALSE; | ^~~~~~~ objseq.c: In function ‘AnnotIdAsnWrite’: objseq.c:4841:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 4841 | else | ^~~~ objseq.c:4843:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 4843 | break; | ^~~~~ objseq.c:4849:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 4849 | else | ^~~~ objseq.c:4851:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 4851 | break; | ^~~~~ objseq.c: In function ‘AnnotDescAsnWrite’: objseq.c:5226:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 5226 | else | ^~~~ objseq.c:5228:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 5228 | break; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objblock.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objblock.h:70, from objblock.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objblock.c: In function ‘EMBLBlockFree’: objblock.c:900:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 900 | if (ebp == NULL) | ^~ objblock.c:903:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 903 | DateFree(ebp->creation_date); | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objcode.c objcode.c:48:51: warning: "/*" within comment [-Wcomment] 48 | * environment variables to allow reading from data/*.val, replaced tabs in source code with spaces | In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objcode.h:64, from objcode.c:105: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objsset.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from objsset.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objsset.c: In function ‘BioseqSetFree’: objsset.c:363:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 363 | if (bsp == NULL) | ^~ objsset.c:366:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 366 | if (bsp->idx.parentptr == NULL || bsp->idx.parenttype == OBJ_SEQSUB) { | ^~ objsset.c: In function ‘SeqEntryFree’: objsset.c:878:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 878 | else if (sep->choice == 2) | ^~ objsset.c:881:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 881 | return (SeqEntryPtr)MemFree(sep); | ^~~~~~ objsset.c: In function ‘SeqEntryFreeComponents’: objsset.c:898:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 898 | else if (sep->choice == 2) | ^~ objsset.c:901:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 901 | return sep; | ^~~~~~ objsset.c: In function ‘SeqEntryAsnGet’: objsset.c:1075:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1075 | if (retcode == 1) /* just after a Bioseq */ | ^~ objsset.c:1077:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1077 | av.ptrvalue = (Pointer) osp; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objsub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnsubmt.h:9, from objsub.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objsub.c: In function ‘SubmitAsnLoad’: objsub.c:341:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 341 | if (loaded) | ^~ objsub.c:344:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 344 | if (! SeqSetAsnLoad ()) | ^~ objsub.c:347:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 347 | if (AsnLoad()) | ^~ objsub.c:350:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 350 | ObjMgrTypeLoad(OBJ_SEQSUB, "Seq-submit", seqsubtypename, "Sequence Data Submission", | ^~~~~~~~~~~~~~ objsub.c: In function ‘SeqSubmitAsnWrite’: objsub.c:455:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 455 | if (atp == NULL) | ^~ objsub.c:458:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 458 | if (ssp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:462:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 462 | if (! AsnOpenStruct(aip, atp, (Pointer)ssp)) | ^~ objsub.c:465:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 465 | if (! SubmitBlockAsnWrite(ssp->sub, aip, SEQ_SUBMIT_sub)) goto erret; | ^~ objsub.c: In function ‘SeqSubmitAsnRead’: objsub.c:539:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 539 | if (atp == NULL) | ^~ objsub.c:542:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 542 | ssp = SeqSubmitNew(); | ^~~ objsub.c:543:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 543 | if (ssp == NULL) | ^~ objsub.c:546:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 546 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objsub.c: In function ‘SubmitBlockAsnWrite’: objsub.c:682:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 682 | if (atp == NULL) | ^~ objsub.c:685:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 685 | if (sbp == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:689:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 689 | if (! AsnOpenStruct(aip, atp, (Pointer)sbp)) | ^~ objsub.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 692 | if (! ContactInfoAsnWrite(sbp->contact, aip, SUBMIT_BLOCK_contact)) | ^~ objsub.c: In function ‘SubmitBlockAsnRead’: objsub.c:770:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 770 | if (atp == NULL) | ^~ objsub.c:773:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 773 | oldatp = atp; | ^~~~~~ objsub.c:775:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 775 | if (sbp == NULL) | ^~ objsub.c:778:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 778 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ objsub.c: In function ‘ContactInfoAsnWrite’: objsub.c:942:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 942 | if (atp == NULL) | ^~ objsub.c:945:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 945 | if (cip == NULL) { AsnNullValueMsg(aip, atp); goto erret; } | ^~ objsub.c:949:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 949 | if (! AsnOpenStruct(aip, atp, (Pointer)cip)) | ^~ objsub.c:952:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 952 | if (cip->name != NULL) | ^~ objsub.c: In function ‘ContactInfoAsnRead’: objsub.c:1068:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1068 | if (atp == NULL) | ^~ objsub.c:1070:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1070 | oldatp = atp; | ^~~~~~ objsub.c:1073:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1073 | if (cip == NULL) | ^~ objsub.c:1076:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1076 | if (AsnReadVal(aip, atp, &av) <= 0) /* read the start struct */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objprt.h:67, from objprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘PrintFormTextFree’, inlined from ‘PrintFormTextFree’ at objprt.c:1068:37, inlined from ‘PrintFormTextAsnRead’ at objprt.c:1119:6: objprt.c:1072:21: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1072 | MemFree(ptr -> textfunc); | ~~~~^~~~~~~~~~~ objprt.c: In function ‘PrintFormTextAsnRead’: objprt.c:1086:26: note: ‘ptr’ was declared here 1086 | PrintFormTextPtr ptr; | ^~~ In function ‘PrintFormEnumFree’, inlined from ‘PrintFormEnumFree’ at objprt.c:950:37, inlined from ‘PrintFormEnumAsnRead’ at objprt.c:1010:6: objprt.c:954:9: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 954 | ValNodeFreeData(ptr -> values); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objprt.c: In function ‘PrintFormEnumAsnRead’: objprt.c:969:26: note: ‘ptr’ was declared here 969 | PrintFormEnumPtr ptr; | ^~~ In function ‘PrintFormBooleanFree’, inlined from ‘PrintFormBooleanFree’ at objprt.c:834:40, inlined from ‘PrintFormBooleanAsnRead’ at objprt.c:892:6: objprt.c:839:21: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 839 | MemFree(ptr -> falsepfb); | ~~~~^~~~~~~~~~~ objprt.c: In function ‘PrintFormBooleanAsnRead’: objprt.c:853:29: note: ‘ptr’ was declared here 853 | PrintFormBooleanPtr ptr; | ^~~ In function ‘UserFormatFree’, inlined from ‘UserFormatFree’ at objprt.c:1173:34, inlined from ‘UserFormatAsnRead’ at objprt.c:1231:6: objprt.c:1178:21: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1178 | MemFree(ptr -> defaultfunc); | ~~~~^~~~~~~~~~~~~~ objprt.c: In function ‘UserFormatAsnRead’: objprt.c:1192:23: note: ‘ptr’ was declared here 1192 | UserFormatPtr ptr; | ^~~ objprt.c: In function ‘PrintFormAsnRead’: objprt.c:600:15: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 600 | vnp = PrintFormFree(vnp); | ^~~~~~~~~~~~~~~~~~ objprt.c:533:20: note: ‘vnp’ was declared here 533 | ValNodePtr vnp; | ^~~ objprt.c: In function ‘PrintFormatAsnRead’: objprt.c:379:24: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 379 | PrintFormatPtr ptr; | ^~~ objprt.c: In function ‘PrintTemplateAsnRead’: objprt.c:250:13: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 250 | ptr=PrintTemplateFree(ptr); | ^~~~~~~~~~~~~~~~~~~~~~ objprt.c:206:26: note: ‘ptr’ was declared here 206 | PrintTemplatePtr ptr; | ^~~ In function ‘PrintFormBlockFree’, inlined from ‘PrintFormBlockFree’ at objprt.c:688:38, inlined from ‘PrintFormBlockAsnRead’ at objprt.c:767:6: objprt.c:693:9: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 693 | PrintFormatFree( ptr -> components); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objprt.c: In function ‘PrintFormBlockAsnRead’: objprt.c:707:27: note: ‘ptr’ was declared here 707 | PrintFormBlockPtr ptr; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objfdef.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objfeat.h:48, from ../include/objfdef.h:48, from objfdef.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objalignloc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objalignloc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objalignloc.c: In function ‘AlignLocSetAsnRead’: objalignloc.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objalignloc.c: In function ‘Loc_locFree’: objalignloc.c:196:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 196 | Pointer pnt; | ^~~ objalignloc.c: In function ‘AlignLocAsnRead’: objalignloc.c:233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 233 | AsnReadFunc func; | ^~~~ objalignloc.c:232:12: warning: unused variable ‘isError’ [-Wunused-variable] 232 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘Loc_locAsnRead’: objalignloc.c:313:12: warning: unused variable ‘isError’ [-Wunused-variable] 313 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignIdFree’: objalignloc.c:527:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 527 | Pointer pnt; | ^~~ objalignloc.c: In function ‘AlignIdAsnRead’: objalignloc.c:559:12: warning: unused variable ‘isError’ [-Wunused-variable] 559 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignBoxAsnRead’: objalignloc.c:750:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 750 | AsnReadFunc func; | ^~~~ objalignloc.c:749:12: warning: unused variable ‘isError’ [-Wunused-variable] 749 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignRowsAsnRead’: objalignloc.c:932:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 932 | AsnReadFunc func; | ^~~~ objalignloc.c:931:12: warning: unused variable ‘isError’ [-Wunused-variable] 931 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignColumnsAsnRead’: objalignloc.c:1096:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1096 | AsnReadFunc func; | ^~~~ objalignloc.c:1095:12: warning: unused variable ‘isError’ [-Wunused-variable] 1095 | Boolean isError = FALSE; | ^~~~~~~ objalignloc.c: In function ‘AlignIdAsnRead’: objalignloc.c:615:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 615 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalignloc.c:558:10: note: ‘choice’ was declared here 558 | Uint1 choice; | ^~~~~~ In function ‘Loc_locAsnRead’, inlined from ‘AlignLocAsnRead’ at objalignloc.c:276:24: objalignloc.c:370:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 370 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objalignloc.c: In function ‘AlignLocAsnRead’: objalignloc.c:312:10: note: ‘choice’ was declared here 312 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objtable.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtable.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtable.c: In function ‘SeqTableColumnInfoAsnRead’: objtable.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objtable.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableColumnAsnRead’: objtable.c:269:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 269 | AsnReadFunc func; | ^~~~ objtable.c:268:12: warning: unused variable ‘isError’ [-Wunused-variable] 268 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableAsnRead’: objtable.c:474:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 474 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘CommonStringTableAsnRead’: objtable.c:657:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 657 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘CommonBytesTableAsnRead’: objtable.c:819:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 819 | AsnReadFunc func; | ^~~~ objtable.c: In function ‘SeqTableSingleDataFree’: objtable.c:1225:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1225 | Pointer pnt; | ^~~ objtable.c: In function ‘SeqTableSingleDataAsnRead’: objtable.c:1269:12: warning: unused variable ‘isError’ [-Wunused-variable] 1269 | Boolean isError = FALSE; | ^~~~~~~ objtable.c: In function ‘SeqTableMultiDataAsnRead’: objtable.c:1111:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1111 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1001:10: note: ‘choice’ was declared here 1001 | Uint1 choice; | ^~~~~~ objtable.c: In function ‘SeqTableSingleDataAsnRead’: objtable.c:1354:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1354 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1268:10: note: ‘choice’ was declared here 1268 | Uint1 choice; | ^~~~~~ objtable.c: In function ‘SeqTableSparseIndexAsnRead’: objtable.c:1559:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1559 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtable.c:1505:10: note: ‘choice’ was declared here 1505 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objpubme.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objpubme.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objpubme.c: In function ‘PubmedEntryAsnRead’: objpubme.c:89:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 89 | AsnReadFunc func; | ^~~~ objpubme.c: In function ‘PubmedUrlAsnRead’: objpubme.c:288:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 288 | AsnReadFunc func; | ^~~~ objpubme.c:287:12: warning: unused variable ‘isError’ [-Wunused-variable] 287 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmdrs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmdrs.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmdrs.c: In function ‘MedlarsEntryAsnRead’: objmdrs.c:85:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 85 | AsnReadFunc func; | ^~~~ objmdrs.c: In function ‘MedlarsRecordAsnRead’: objmdrs.c:259:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 259 | AsnReadFunc func; | ^~~~ objmdrs.c:258:12: warning: unused variable ‘isError’ [-Wunused-variable] 258 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objproj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objproj.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objproj.c: In function ‘ProjectAsnRead’: objproj.c:116:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 116 | AsnReadFunc func; | ^~~~ objproj.c:115:12: warning: unused variable ‘isError’ [-Wunused-variable] 115 | Boolean isError = FALSE; | ^~~~~~~ objproj.c: In function ‘ProjectDescrAsnRead’: objproj.c:720:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 720 | AsnReadFunc func; | ^~~~ objproj.c: In function ‘ProjdescFree’: objproj.c:857:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 857 | Pointer pnt; | ^~~ objproj.c: In function ‘ProjdescAsnRead’: objproj.c:898:12: warning: unused variable ‘isError’ [-Wunused-variable] 898 | Boolean isError = FALSE; | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/mmdbapi.h:92, from ../include/mapproj.h:45, from objproj.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objproj.c: In function ‘ProjdescAsnRead’: objproj.c:958:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 958 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objproj.c:897:10: note: ‘choice’ was declared here 897 | Uint1 choice; | ^~~~~~ objproj.c: In function ‘ProjectItemAsnRead’: objproj.c:536:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 536 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objproj.c:331:10: note: ‘choice’ was declared here 331 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objgbseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objgbseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objgbseq.c: In function ‘GBSetAsnRead’: objgbseq.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objgbseq.c:66:12: warning: unused variable ‘av’ [-Wunused-variable] 66 | DataVal av; | ^~ objgbseq.c: In function ‘GBSeqAsnRead’: objgbseq.c:235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 235 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBReferenceAsnRead’: objgbseq.c:742:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 742 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBCommentAsnRead’: objgbseq.c:983:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 983 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBStrucCommentAsnRead’: objgbseq.c:1150:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1150 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBFeatureAsnRead’: objgbseq.c:1321:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1321 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBFeatureSetAsnRead’: objgbseq.c:1548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1548 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBAltSeqDataAsnRead’: objgbseq.c:1715:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1715 | AsnReadFunc func; | ^~~~ objgbseq.c: In function ‘GBXrefAsnRead’: objgbseq.c:1882:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1882 | AsnReadFunc func; | ^~~~ objgbseq.c:1881:12: warning: unused variable ‘isError’ [-Wunused-variable] 1881 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBStrucCommentItemAsnRead’: objgbseq.c:2053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2053 | AsnReadFunc func; | ^~~~ objgbseq.c:2052:12: warning: unused variable ‘isError’ [-Wunused-variable] 2052 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBIntervalAsnRead’: objgbseq.c:2233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2233 | AsnReadFunc func; | ^~~~ objgbseq.c:2232:12: warning: unused variable ‘isError’ [-Wunused-variable] 2232 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBQualifierAsnRead’: objgbseq.c:2447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2447 | AsnReadFunc func; | ^~~~ objgbseq.c:2446:12: warning: unused variable ‘isError’ [-Wunused-variable] 2446 | Boolean isError = FALSE; | ^~~~~~~ objgbseq.c: In function ‘GBAltSeqItemAsnRead’: objgbseq.c:2622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2622 | AsnReadFunc func; | ^~~~ objgbseq.c:2621:12: warning: unused variable ‘isError’ [-Wunused-variable] 2621 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objtseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtseq.c: In function ‘TSeqAsnRead’: objtseq.c:89:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 89 | AsnReadFunc func; | ^~~~ objtseq.c: In function ‘TSeqSetAsnRead’: objtseq.c:325:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 325 | AsnReadFunc func; | ^~~~ objtseq.c: In function ‘BioseqToTSeq’: objtseq.c:452:15: warning: variable ‘seqcode’ set but not used [-Wunused-but-set-variable] 452 | Uint1 seqcode; | ^~~~~~~ objtseq.c: In function ‘BioseqToMiniTSeq’: objtseq.c:564:15: warning: variable ‘seqcode’ set but not used [-Wunused-but-set-variable] 564 | Uint1 seqcode; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objinsdseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objinsdseq.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objinsdseq.c: In function ‘INSDSetAsnRead’: objinsdseq.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ objinsdseq.c:66:12: warning: unused variable ‘av’ [-Wunused-variable] 66 | DataVal av; | ^~ objinsdseq.c: In function ‘INSDSeqAsnRead’: objinsdseq.c:235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 235 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDReferenceAsnRead’: objinsdseq.c:742:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 742 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDCommentAsnRead’: objinsdseq.c:983:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 983 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDStrucCommentAsnRead’: objinsdseq.c:1150:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1150 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDFeatureAsnRead’: objinsdseq.c:1321:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1321 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDFeatureSetAsnRead’: objinsdseq.c:1548:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1548 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDAltSeqDataAsnRead’: objinsdseq.c:1715:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1715 | AsnReadFunc func; | ^~~~ objinsdseq.c: In function ‘INSDXrefAsnRead’: objinsdseq.c:1882:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1882 | AsnReadFunc func; | ^~~~ objinsdseq.c:1881:12: warning: unused variable ‘isError’ [-Wunused-variable] 1881 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDStrucCommentItemAsnRead’: objinsdseq.c:2053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2053 | AsnReadFunc func; | ^~~~ objinsdseq.c:2052:12: warning: unused variable ‘isError’ [-Wunused-variable] 2052 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDIntervalAsnRead’: objinsdseq.c:2233:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2233 | AsnReadFunc func; | ^~~~ objinsdseq.c:2232:12: warning: unused variable ‘isError’ [-Wunused-variable] 2232 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDQualifierAsnRead’: objinsdseq.c:2447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2447 | AsnReadFunc func; | ^~~~ objinsdseq.c:2446:12: warning: unused variable ‘isError’ [-Wunused-variable] 2446 | Boolean isError = FALSE; | ^~~~~~~ objinsdseq.c: In function ‘INSDAltSeqItemAsnRead’: objinsdseq.c:2622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2622 | AsnReadFunc func; | ^~~~ objinsdseq.c:2621:12: warning: unused variable ‘isError’ [-Wunused-variable] 2621 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmacro.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmacro.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmacro.c: In function ‘AECRActionAsnRead’: objmacro.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objmacro.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseActionAsnRead’: objmacro.c:272:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 272 | AsnReadFunc func; | ^~~~ objmacro.c:271:12: warning: unused variable ‘isError’ [-Wunused-variable] 271 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MacroActionListAsnRead’: objmacro.c:478:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 478 | AsnReadFunc func; | ^~~~ objmacro.c:475:12: warning: unused variable ‘av’ [-Wunused-variable] 475 | DataVal av; | ^~ objmacro.c: In function ‘SuspectRuleSetAsnRead’: objmacro.c:595:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 595 | AsnReadFunc func; | ^~~~ objmacro.c:592:12: warning: unused variable ‘av’ [-Wunused-variable] 592 | DataVal av; | ^~ objmacro.c: In function ‘WordSubstitutionAsnRead’: objmacro.c:731:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 731 | AsnReadFunc func; | ^~~~ objmacro.c: In function ‘WordSubstitutionSetAsnRead’: objmacro.c:899:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 899 | AsnReadFunc func; | ^~~~ objmacro.c:896:12: warning: unused variable ‘av’ [-Wunused-variable] 896 | DataVal av; | ^~ objmacro.c: In function ‘StringConstraintAsnRead’: objmacro.c:1045:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1045 | AsnReadFunc func; | ^~~~ objmacro.c:1044:12: warning: unused variable ‘isError’ [-Wunused-variable] 1044 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StringConstraintSetAsnRead’: objmacro.c:1307:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1307 | AsnReadFunc func; | ^~~~ objmacro.c:1304:12: warning: unused variable ‘av’ [-Wunused-variable] 1304 | DataVal av; | ^~ objmacro.c: In function ‘LocationPosConstraintFree’: objmacro.c:1403:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1403 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationPosConstraintAsnRead’: objmacro.c:1432:12: warning: unused variable ‘isError’ [-Wunused-variable] 1432 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationConstraintAsnRead’: objmacro.c:1633:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1633 | AsnReadFunc func; | ^~~~ objmacro.c:1632:12: warning: unused variable ‘isError’ [-Wunused-variable] 1632 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalValAsnRead’: objmacro.c:1849:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1849 | AsnReadFunc func; | ^~~~ objmacro.c:1848:12: warning: unused variable ‘isError’ [-Wunused-variable] 1848 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalValChoiceFree’: objmacro.c:1979:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1979 | Pointer pnt; | ^~~ objmacro.c: In function ‘FeatQualLegalValChoiceAsnRead’: objmacro.c:2011:12: warning: unused variable ‘isError’ [-Wunused-variable] 2011 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatQualLegalSetAsnRead’: objmacro.c:2165:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2165 | AsnReadFunc func; | ^~~~ objmacro.c:2162:12: warning: unused variable ‘av’ [-Wunused-variable] 2162 | DataVal av; | ^~ objmacro.c: In function ‘FeatQualChoiceFree’: objmacro.c:2261:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2261 | Pointer pnt; | ^~~ objmacro.c: In function ‘FeatQualChoiceAsnRead’: objmacro.c:2293:12: warning: unused variable ‘isError’ [-Wunused-variable] 2293 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldAsnRead’: objmacro.c:2474:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2474 | AsnReadFunc func; | ^~~~ objmacro.c:2473:12: warning: unused variable ‘isError’ [-Wunused-variable] 2473 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldLegalAsnRead’: objmacro.c:2641:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2641 | AsnReadFunc func; | ^~~~ objmacro.c:2640:12: warning: unused variable ‘isError’ [-Wunused-variable] 2640 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FeatureFieldPairAsnRead’: objmacro.c:2807:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2807 | AsnReadFunc func; | ^~~~ objmacro.c:2806:12: warning: unused variable ‘isError’ [-Wunused-variable] 2806 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaFeatTypeFree’: objmacro.c:2950:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2950 | Pointer pnt; | ^~~ objmacro.c: In function ‘RnaFeatTypeAsnRead’: objmacro.c:2982:12: warning: unused variable ‘isError’ [-Wunused-variable] 2982 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaQualAsnRead’: objmacro.c:3232:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3232 | AsnReadFunc func; | ^~~~ objmacro.c:3231:12: warning: unused variable ‘isError’ [-Wunused-variable] 3231 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RnaQualPairAsnRead’: objmacro.c:3400:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3400 | AsnReadFunc func; | ^~~~ objmacro.c:3399:12: warning: unused variable ‘isError’ [-Wunused-variable] 3399 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualPairAsnRead’: objmacro.c:3576:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3576 | AsnReadFunc func; | ^~~~ objmacro.c:3575:12: warning: unused variable ‘isError’ [-Wunused-variable] 3575 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualChoiceFree’: objmacro.c:3704:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3704 | Pointer pnt; | ^~~ objmacro.c: In function ‘SourceQualChoiceAsnRead’: objmacro.c:3733:12: warning: unused variable ‘isError’ [-Wunused-variable] 3733 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualTextValAsnRead’: objmacro.c:3950:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3950 | AsnReadFunc func; | ^~~~ objmacro.c:3949:12: warning: unused variable ‘isError’ [-Wunused-variable] 3949 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualValChoiceFree’: objmacro.c:4080:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4080 | Pointer pnt; | ^~~ objmacro.c: In function ‘SourceQualValChoiceAsnRead’: objmacro.c:4112:12: warning: unused variable ‘isError’ [-Wunused-variable] 4112 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceQualValSetAsnRead’: objmacro.c:4310:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4310 | AsnReadFunc func; | ^~~~ objmacro.c:4307:12: warning: unused variable ‘av’ [-Wunused-variable] 4307 | DataVal av; | ^~ objmacro.c: In function ‘CDSGeneProtFieldPairAsnRead’: objmacro.c:4442:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4442 | AsnReadFunc func; | ^~~~ objmacro.c:4441:12: warning: unused variable ‘isError’ [-Wunused-variable] 4441 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldFree’: objmacro.c:4570:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4570 | Pointer pnt; | ^~~ objmacro.c: In function ‘MolinfoFieldAsnRead’: objmacro.c:4599:12: warning: unused variable ‘isError’ [-Wunused-variable] 4599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoMoleculePairAsnRead’: objmacro.c:4826:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4826 | AsnReadFunc func; | ^~~~ objmacro.c:4825:12: warning: unused variable ‘isError’ [-Wunused-variable] 4825 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoTechniquePairAsnRead’: objmacro.c:4990:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4990 | AsnReadFunc func; | ^~~~ objmacro.c:4989:12: warning: unused variable ‘isError’ [-Wunused-variable] 4989 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoCompletednessPairAsnRead’: objmacro.c:5154:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5154 | AsnReadFunc func; | ^~~~ objmacro.c:5153:12: warning: unused variable ‘isError’ [-Wunused-variable] 5153 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoMolClassPairAsnRead’: objmacro.c:5318:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5318 | AsnReadFunc func; | ^~~~ objmacro.c:5317:12: warning: unused variable ‘isError’ [-Wunused-variable] 5317 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoTopologyPairAsnRead’: objmacro.c:5482:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5482 | AsnReadFunc func; | ^~~~ objmacro.c:5481:12: warning: unused variable ‘isError’ [-Wunused-variable] 5481 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoStrandPairAsnRead’: objmacro.c:5646:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5646 | AsnReadFunc func; | ^~~~ objmacro.c:5645:12: warning: unused variable ‘isError’ [-Wunused-variable] 5645 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldPairFree’: objmacro.c:5774:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 5774 | Pointer pnt; | ^~~ objmacro.c: In function ‘MolinfoFieldPairAsnRead’: objmacro.c:5821:12: warning: unused variable ‘isError’ [-Wunused-variable] 5821 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldListAsnRead’: objmacro.c:6015:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6015 | AsnReadFunc func; | ^~~~ objmacro.c:6012:12: warning: unused variable ‘av’ [-Wunused-variable] 6012 | DataVal av; | ^~ objmacro.c: In function ‘MolinfoFieldConstraintAsnRead’: objmacro.c:6149:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6149 | AsnReadFunc func; | ^~~~ objmacro.c:6148:12: warning: unused variable ‘isError’ [-Wunused-variable] 6148 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StructuredCommentFieldFree’: objmacro.c:6280:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 6280 | Pointer pnt; | ^~~ objmacro.c: In function ‘StructuredCommentFieldAsnRead’: objmacro.c:6312:12: warning: unused variable ‘isError’ [-Wunused-variable] 6312 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘StructuredCommentFieldPairAsnRead’: objmacro.c:6508:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6508 | AsnReadFunc func; | ^~~~ objmacro.c:6507:12: warning: unused variable ‘isError’ [-Wunused-variable] 6507 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘DBLinkFieldPairAsnRead’: objmacro.c:6678:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6678 | AsnReadFunc func; | ^~~~ objmacro.c:6677:12: warning: unused variable ‘isError’ [-Wunused-variable] 6677 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldConstraintAsnRead’: objmacro.c:6843:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6843 | AsnReadFunc func; | ^~~~ objmacro.c:6842:12: warning: unused variable ‘isError’ [-Wunused-variable] 6842 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeFree’: objmacro.c:6974:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 6974 | Pointer pnt; | ^~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeAsnRead’: objmacro.c:7003:12: warning: unused variable ‘isError’ [-Wunused-variable] 7003 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintAsnRead’: objmacro.c:7220:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7220 | AsnReadFunc func; | ^~~~ objmacro.c:7219:12: warning: unused variable ‘isError’ [-Wunused-variable] 7219 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PublicationConstraintAsnRead’: objmacro.c:7389:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7389 | AsnReadFunc func; | ^~~~ objmacro.c:7388:12: warning: unused variable ‘isError’ [-Wunused-variable] 7388 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SourceConstraintAsnRead’: objmacro.c:7571:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7571 | AsnReadFunc func; | ^~~~ objmacro.c:7570:12: warning: unused variable ‘isError’ [-Wunused-variable] 7570 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtPseudoConstraintAsnRead’: objmacro.c:7763:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 7763 | AsnReadFunc func; | ^~~~ objmacro.c:7762:12: warning: unused variable ‘isError’ [-Wunused-variable] 7762 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtConstraintFieldFree’: objmacro.c:7891:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 7891 | Pointer pnt; | ^~~ objmacro.c: In function ‘CDSGeneProtConstraintFieldAsnRead’: objmacro.c:7920:12: warning: unused variable ‘isError’ [-Wunused-variable] 7920 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CDSGeneProtQualConstraintAsnRead’: objmacro.c:8095:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8095 | AsnReadFunc func; | ^~~~ objmacro.c:8094:12: warning: unused variable ‘isError’ [-Wunused-variable] 8094 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldConstraintAsnRead’: objmacro.c:8279:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 8279 | AsnReadFunc func; | ^~~~ objmacro.c:8278:12: warning: unused variable ‘isError’ [-Wunused-variable] 8278 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldTypeFree’: objmacro.c:8413:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8413 | Pointer pnt; | ^~~ objmacro.c: In function ‘FieldTypeAsnRead’: objmacro.c:8457:12: warning: unused variable ‘isError’ [-Wunused-variable] 8457 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintFree’: objmacro.c:8666:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8666 | Pointer pnt; | ^~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintAsnRead’: objmacro.c:8695:12: warning: unused variable ‘isError’ [-Wunused-variable] 8695 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘QuantityConstraintFree’: objmacro.c:8875:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 8875 | Pointer pnt; | ^~~ objmacro.c: In function ‘QuantityConstraintAsnRead’: objmacro.c:8904:12: warning: unused variable ‘isError’ [-Wunused-variable] 8904 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceConstraintAsnRead’: objmacro.c:9104:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9104 | AsnReadFunc func; | ^~~~ objmacro.c:9103:12: warning: unused variable ‘isError’ [-Wunused-variable] 9103 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TranslationConstraintAsnRead’: objmacro.c:9332:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9332 | AsnReadFunc func; | ^~~~ objmacro.c:9331:12: warning: unused variable ‘isError’ [-Wunused-variable] 9331 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConstraintChoiceFree’: objmacro.c:9487:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 9487 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConstraintChoiceAsnRead’: objmacro.c:9549:12: warning: unused variable ‘isError’ [-Wunused-variable] 9549 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConstraintChoiceSetAsnRead’: objmacro.c:9783:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 9783 | AsnReadFunc func; | ^~~~ objmacro.c:9780:12: warning: unused variable ‘av’ [-Wunused-variable] 9780 | DataVal av; | ^~ objmacro.c: In function ‘TextMarkerFree’: objmacro.c:9879:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 9879 | Pointer pnt; | ^~~ objmacro.c: In function ‘TextMarkerAsnRead’: objmacro.c:9911:12: warning: unused variable ‘isError’ [-Wunused-variable] 9911 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextPortionAsnRead’: objmacro.c:10109:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10109 | AsnReadFunc func; | ^~~~ objmacro.c:10108:12: warning: unused variable ‘isError’ [-Wunused-variable] 10108 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldEditAsnRead’: objmacro.c:10328:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10328 | AsnReadFunc func; | ^~~~ objmacro.c:10327:12: warning: unused variable ‘isError’ [-Wunused-variable] 10327 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FieldPairTypeFree’: objmacro.c:10478:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 10478 | Pointer pnt; | ^~~ objmacro.c: In function ‘FieldPairTypeAsnRead’: objmacro.c:10528:12: warning: unused variable ‘isError’ [-Wunused-variable] 10528 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyActionAsnRead’: objmacro.c:10747:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10747 | AsnReadFunc func; | ^~~~ objmacro.c:10746:12: warning: unused variable ‘isError’ [-Wunused-variable] 10746 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditActionAsnRead’: objmacro.c:10927:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 10927 | AsnReadFunc func; | ^~~~ objmacro.c:10926:12: warning: unused variable ‘isError’ [-Wunused-variable] 10926 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextTransformFree’: objmacro.c:11061:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 11061 | Pointer pnt; | ^~~ objmacro.c: In function ‘TextTransformAsnRead’: objmacro.c:11096:12: warning: unused variable ‘isError’ [-Wunused-variable] 11096 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TextTransformSetAsnRead’: objmacro.c:11269:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11269 | AsnReadFunc func; | ^~~~ objmacro.c:11266:12: warning: unused variable ‘av’ [-Wunused-variable] 11266 | DataVal av; | ^~ objmacro.c: In function ‘ConvertActionAsnRead’: objmacro.c:11405:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11405 | AsnReadFunc func; | ^~~~ objmacro.c:11404:12: warning: unused variable ‘isError’ [-Wunused-variable] 11404 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CopyActionAsnRead’: objmacro.c:11600:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11600 | AsnReadFunc func; | ^~~~ objmacro.c:11599:12: warning: unused variable ‘isError’ [-Wunused-variable] 11599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SwapActionAsnRead’: objmacro.c:11768:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11768 | AsnReadFunc func; | ^~~~ objmacro.c:11767:12: warning: unused variable ‘isError’ [-Wunused-variable] 11767 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AECRParseActionAsnRead’: objmacro.c:11932:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 11932 | AsnReadFunc func; | ^~~~ objmacro.c:11931:12: warning: unused variable ‘isError’ [-Wunused-variable] 11931 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveActionAsnRead’: objmacro.c:12151:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12151 | AsnReadFunc func; | ^~~~ objmacro.c:12150:12: warning: unused variable ‘isError’ [-Wunused-variable] 12150 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveOutsideActionAsnRead’: objmacro.c:12312:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12312 | AsnReadFunc func; | ^~~~ objmacro.c:12311:12: warning: unused variable ‘isError’ [-Wunused-variable] 12311 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ActionChoiceFree’: objmacro.c:12455:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12455 | Pointer pnt; | ^~~ objmacro.c: In function ‘ActionChoiceAsnRead’: objmacro.c:12508:12: warning: unused variable ‘isError’ [-Wunused-variable] 12508 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcOrgChoiceFree’: objmacro.c:12697:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 12697 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcOrgChoiceAsnRead’: objmacro.c:12726:12: warning: unused variable ‘isError’ [-Wunused-variable] 12726 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcOrgAsnRead’: objmacro.c:12911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 12911 | AsnReadFunc func; | ^~~~ objmacro.c:12910:12: warning: unused variable ‘isError’ [-Wunused-variable] 12910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcGeneralIdFree’: objmacro.c:13042:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13042 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcGeneralIdAsnRead’: objmacro.c:13074:12: warning: unused variable ‘isError’ [-Wunused-variable] 13074 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseSrcFree’: objmacro.c:13232:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13232 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseSrcAsnRead’: objmacro.c:13270:12: warning: unused variable ‘isError’ [-Wunused-variable] 13270 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseDstOrgAsnRead’: objmacro.c:13526:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 13526 | AsnReadFunc func; | ^~~~ objmacro.c:13525:12: warning: unused variable ‘isError’ [-Wunused-variable] 13525 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ParseDestFree’: objmacro.c:13657:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 13657 | Pointer pnt; | ^~~ objmacro.c: In function ‘ParseDestAsnRead’: objmacro.c:13695:12: warning: unused variable ‘isError’ [-Wunused-variable] 13695 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationIntervalAsnRead’: objmacro.c:13905:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 13905 | AsnReadFunc func; | ^~~~ objmacro.c:13904:12: warning: unused variable ‘isError’ [-Wunused-variable] 13904 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationChoiceFree’: objmacro.c:14033:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 14033 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationChoiceAsnRead’: objmacro.c:14065:12: warning: unused variable ‘isError’ [-Wunused-variable] 14065 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SequenceListAsnRead’: objmacro.c:14241:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14241 | AsnReadFunc func; | ^~~~ objmacro.c:14238:12: warning: unused variable ‘av’ [-Wunused-variable] 14238 | DataVal av; | ^~ objmacro.c: In function ‘SequenceListChoiceFree’: objmacro.c:14337:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 14337 | Pointer pnt; | ^~~ objmacro.c: In function ‘SequenceListChoiceAsnRead’: objmacro.c:14369:12: warning: unused variable ‘isError’ [-Wunused-variable] 14369 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyFeatureActionAsnRead’: objmacro.c:14560:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14560 | AsnReadFunc func; | ^~~~ objmacro.c:14559:12: warning: unused variable ‘isError’ [-Wunused-variable] 14559 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveFeatureActionAsnRead’: objmacro.c:14827:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14827 | AsnReadFunc func; | ^~~~ objmacro.c:14826:12: warning: unused variable ‘isError’ [-Wunused-variable] 14826 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFromCDSOptionsAsnRead’: objmacro.c:14994:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 14994 | AsnReadFunc func; | ^~~~ objmacro.c:14993:12: warning: unused variable ‘isError’ [-Wunused-variable] 14993 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureSrcOptionsFree’: objmacro.c:15131:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 15131 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConvertFeatureSrcOptionsAsnRead’: objmacro.c:15163:12: warning: unused variable ‘isError’ [-Wunused-variable] 15163 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RegionTypeAsnRead’: objmacro.c:15332:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15332 | AsnReadFunc func; | ^~~~ objmacro.c:15331:12: warning: unused variable ‘isError’ [-Wunused-variable] 15331 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureDstOptionsFree’: objmacro.c:15451:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 15451 | Pointer pnt; | ^~~ objmacro.c: In function ‘ConvertFeatureDstOptionsAsnRead’: objmacro.c:15486:12: warning: unused variable ‘isError’ [-Wunused-variable] 15486 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ConvertFeatureActionAsnRead’: objmacro.c:15702:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15702 | AsnReadFunc func; | ^~~~ objmacro.c:15701:12: warning: unused variable ‘isError’ [-Wunused-variable] 15701 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditLocationStrandAsnRead’: objmacro.c:15911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 15911 | AsnReadFunc func; | ^~~~ objmacro.c:15910:12: warning: unused variable ‘isError’ [-Wunused-variable] 15910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘Partial5SetActionAsnRead’: objmacro.c:16075:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16075 | AsnReadFunc func; | ^~~~ objmacro.c:16074:12: warning: unused variable ‘isError’ [-Wunused-variable] 16074 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘Partial3SetActionAsnRead’: objmacro.c:16239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16239 | AsnReadFunc func; | ^~~~ objmacro.c:16238:12: warning: unused variable ‘isError’ [-Wunused-variable] 16238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘PartialBothSetActionAsnRead’: objmacro.c:16403:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16403 | AsnReadFunc func; | ^~~~ objmacro.c:16402:12: warning: unused variable ‘isError’ [-Wunused-variable] 16402 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ExtendToFeatureAsnRead’: objmacro.c:16568:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 16568 | AsnReadFunc func; | ^~~~ objmacro.c:16567:12: warning: unused variable ‘isError’ [-Wunused-variable] 16567 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘LocationEditTypeFree’: objmacro.c:16708:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 16708 | Pointer pnt; | ^~~ objmacro.c: In function ‘LocationEditTypeAsnRead’: objmacro.c:16755:12: warning: unused variable ‘isError’ [-Wunused-variable] 16755 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘EditFeatureLocationActionAsnRead’: objmacro.c:17032:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17032 | AsnReadFunc func; | ^~~~ objmacro.c:17031:12: warning: unused variable ‘isError’ [-Wunused-variable] 17031 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoBlockAsnRead’: objmacro.c:17232:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17232 | AsnReadFunc func; | ^~~~ objmacro.c:17231:12: warning: unused variable ‘isError’ [-Wunused-variable] 17231 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveDescriptorActionAsnRead’: objmacro.c:17415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17415 | AsnReadFunc func; | ^~~~ objmacro.c:17414:12: warning: unused variable ‘isError’ [-Wunused-variable] 17414 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AutodefActionAsnRead’: objmacro.c:17584:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17584 | AsnReadFunc func; | ^~~~ objmacro.c: In function ‘FixPubCapsActionAsnRead’: objmacro.c:17758:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17758 | AsnReadFunc func; | ^~~~ objmacro.c:17757:12: warning: unused variable ‘isError’ [-Wunused-variable] 17757 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SortFieldsActionAsnRead’: objmacro.c:17963:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 17963 | AsnReadFunc func; | ^~~~ objmacro.c:17962:12: warning: unused variable ‘isError’ [-Wunused-variable] 17962 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixAuthorCapsAsnRead’: objmacro.c:18142:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18142 | AsnReadFunc func; | ^~~~ objmacro.c:18141:12: warning: unused variable ‘isError’ [-Wunused-variable] 18141 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixCapsActionFree’: objmacro.c:18261:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 18261 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixCapsActionAsnRead’: objmacro.c:18296:12: warning: unused variable ‘isError’ [-Wunused-variable] 18296 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixFormatActionFree’: objmacro.c:18470:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 18470 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixFormatActionAsnRead’: objmacro.c:18499:12: warning: unused variable ‘isError’ [-Wunused-variable] 18499 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveDuplicateFeatureActionAsnRead’: objmacro.c:18705:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18705 | AsnReadFunc func; | ^~~~ objmacro.c:18704:12: warning: unused variable ‘isError’ [-Wunused-variable] 18704 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘GeneXrefTypeAsnRead’: objmacro.c:18899:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 18899 | AsnReadFunc func; | ^~~~ objmacro.c:18898:12: warning: unused variable ‘isError’ [-Wunused-variable] 18898 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘XrefTypeFree’: objmacro.c:19036:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 19036 | Pointer pnt; | ^~~ objmacro.c: In function ‘XrefTypeAsnRead’: objmacro.c:19068:12: warning: unused variable ‘isError’ [-Wunused-variable] 19068 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveXrefsActionAsnRead’: objmacro.c:19239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19239 | AsnReadFunc func; | ^~~~ objmacro.c:19238:12: warning: unused variable ‘isError’ [-Wunused-variable] 19238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MakeGeneXrefActionAsnRead’: objmacro.c:19410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19410 | AsnReadFunc func; | ^~~~ objmacro.c:19409:12: warning: unused variable ‘isError’ [-Wunused-variable] 19409 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AuthorFixActionAsnRead’: objmacro.c:19578:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19578 | AsnReadFunc func; | ^~~~ objmacro.c:19577:12: warning: unused variable ‘isError’ [-Wunused-variable] 19577 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘UpdateSequencesActionAsnRead’: objmacro.c:19747:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 19747 | AsnReadFunc func; | ^~~~ objmacro.c:19746:12: warning: unused variable ‘isError’ [-Wunused-variable] 19746 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CreateTSAIdsSrcFree’: objmacro.c:19877:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 19877 | Pointer pnt; | ^~~ objmacro.c: In function ‘CreateTSAIdsSrcAsnRead’: objmacro.c:19909:12: warning: unused variable ‘isError’ [-Wunused-variable] 19909 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘CreateTSAIdsActionAsnRead’: objmacro.c:20092:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20092 | AsnReadFunc func; | ^~~~ objmacro.c:20091:12: warning: unused variable ‘isError’ [-Wunused-variable] 20091 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AutofixActionAsnRead’: objmacro.c:20274:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20274 | AsnReadFunc func; | ^~~~ objmacro.c:20273:12: warning: unused variable ‘isError’ [-Wunused-variable] 20273 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘FixSetsActionFree’: objmacro.c:20395:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 20395 | Pointer pnt; | ^~~ objmacro.c: In function ‘FixSetsActionAsnRead’: objmacro.c:20424:12: warning: unused variable ‘isError’ [-Wunused-variable] 20424 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TableMatchTypeFree’: objmacro.c:20582:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 20582 | Pointer pnt; | ^~~ objmacro.c: In function ‘TableMatchTypeAsnRead’: objmacro.c:20614:12: warning: unused variable ‘isError’ [-Wunused-variable] 20614 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘TableMatchAsnRead’: objmacro.c:20873:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 20873 | AsnReadFunc func; | ^~~~ objmacro.c:20872:12: warning: unused variable ‘isError’ [-Wunused-variable] 20872 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyTableExtraDataFree’: objmacro.c:21004:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 21004 | Pointer pnt; | ^~~ objmacro.c: In function ‘ApplyTableExtraDataAsnRead’: objmacro.c:21033:12: warning: unused variable ‘isError’ [-Wunused-variable] 21033 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ApplyTableActionAsnRead’: objmacro.c:21210:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21210 | AsnReadFunc func; | ^~~~ objmacro.c:21209:12: warning: unused variable ‘isError’ [-Wunused-variable] 21209 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AddFileActionAsnRead’: objmacro.c:21411:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21411 | AsnReadFunc func; | ^~~~ objmacro.c:21410:12: warning: unused variable ‘isError’ [-Wunused-variable] 21410 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AddDescriptorListActionAsnRead’: objmacro.c:21582:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21582 | AsnReadFunc func; | ^~~~ objmacro.c:21581:12: warning: unused variable ‘isError’ [-Wunused-variable] 21581 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RemoveSequencesActionAsnRead’: objmacro.c:21753:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21753 | AsnReadFunc func; | ^~~~ objmacro.c:21752:12: warning: unused variable ‘isError’ [-Wunused-variable] 21752 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘UpdateReplacedEcNumbersActionAsnRead’: objmacro.c:21911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 21911 | AsnReadFunc func; | ^~~~ objmacro.c:21910:12: warning: unused variable ‘isError’ [-Wunused-variable] 21910 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘RetranslateCdsActionAsnRead’: objmacro.c:22084:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 22084 | AsnReadFunc func; | ^~~~ objmacro.c:22083:12: warning: unused variable ‘isError’ [-Wunused-variable] 22083 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘AdjustFeaturesForGapsActionAsnRead’: objmacro.c:22239:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 22239 | AsnReadFunc func; | ^~~~ objmacro.c:22238:12: warning: unused variable ‘isError’ [-Wunused-variable] 22238 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MacroActionChoiceFree’: objmacro.c:22412:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 22412 | Pointer pnt; | ^~~ objmacro.c: In function ‘MacroActionChoiceAsnRead’: objmacro.c:22522:12: warning: unused variable ‘isError’ [-Wunused-variable] 22522 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SearchFuncFree’: objmacro.c:23116:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 23116 | Pointer pnt; | ^~~ objmacro.c: In function ‘SearchFuncAsnRead’: objmacro.c:23154:12: warning: unused variable ‘isError’ [-Wunused-variable] 23154 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SimpleReplaceAsnRead’: objmacro.c:23425:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23425 | AsnReadFunc func; | ^~~~ objmacro.c:23424:12: warning: unused variable ‘isError’ [-Wunused-variable] 23424 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ReplaceFuncFree’: objmacro.c:23564:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 23564 | Pointer pnt; | ^~~ objmacro.c: In function ‘ReplaceFuncAsnRead’: objmacro.c:23599:12: warning: unused variable ‘isError’ [-Wunused-variable] 23599 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘ReplaceRuleAsnRead’: objmacro.c:23781:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23781 | AsnReadFunc func; | ^~~~ objmacro.c:23780:12: warning: unused variable ‘isError’ [-Wunused-variable] 23780 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘SuspectRuleAsnRead’: objmacro.c:23955:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 23955 | AsnReadFunc func; | ^~~~ objmacro.c:23954:12: warning: unused variable ‘isError’ [-Wunused-variable] 23954 | Boolean isError = FALSE; | ^~~~~~~ objmacro.c: In function ‘MolinfoFieldPairAsnRead’: objmacro.c:5883:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5883 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:5820:10: note: ‘choice’ was declared here 5820 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TextTransformAsnRead’: objmacro.c:11149:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 11149 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:11095:10: note: ‘choice’ was declared here 11095 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcGeneralIdAsnRead’: objmacro.c:13133:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13133 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13073:10: note: ‘choice’ was declared here 13073 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixSetsActionAsnRead’: objmacro.c:20483:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 20483 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:20423:10: note: ‘choice’ was declared here 20423 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘StructuredCommentFieldAsnRead’: objmacro.c:6371:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 6371 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:6311:10: note: ‘choice’ was declared here 6311 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ConstraintChoiceAsnRead’: objmacro.c:9631:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 9631 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:9548:10: note: ‘choice’ was declared here 9548 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixFormatActionAsnRead’: objmacro.c:18565:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 18565 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:18498:10: note: ‘choice’ was declared here 18498 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FixCapsActionAsnRead’: objmacro.c:18363:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 18363 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:18295:10: note: ‘choice’ was declared here 18295 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SourceQualChoiceAsnRead’: objmacro.c:3806:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3806 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:3732:10: note: ‘choice’ was declared here 3732 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SourceQualValChoiceAsnRead’: objmacro.c:4182:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4182 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:4111:10: note: ‘choice’ was declared here 4111 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘MolinfoFieldAsnRead’: objmacro.c:4679:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4679 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:4598:10: note: ‘choice’ was declared here 4598 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FieldTypeAsnRead’: objmacro.c:8543:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8543 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8456:10: note: ‘choice’ was declared here 8456 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘MacroActionChoiceAsnRead’: objmacro.c:22829:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 22829 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:22521:10: note: ‘choice’ was declared here 22521 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationPosConstraintAsnRead’: objmacro.c:1491:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1491 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:1431:10: note: ‘choice’ was declared here 1431 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FeatQualChoiceAsnRead’: objmacro.c:2342:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2342 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:2292:10: note: ‘choice’ was declared here 2292 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘RnaFeatTypeAsnRead’: objmacro.c:3076:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3076 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:2981:10: note: ‘choice’ was declared here 2981 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘PubFieldSpecialConstraintTypeAsnRead’: objmacro.c:7076:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 7076 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:7002:10: note: ‘choice’ was declared here 7002 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SequenceConstraintMolTypeConstraintAsnRead’: objmacro.c:8768:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8768 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8694:10: note: ‘choice’ was declared here 8694 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘QuantityConstraintAsnRead’: objmacro.c:8963:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 8963 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:8903:10: note: ‘choice’ was declared here 8903 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TextMarkerAsnRead’: objmacro.c:9970:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 9970 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:9910:10: note: ‘choice’ was declared here 9910 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘FieldPairTypeAsnRead’: objmacro.c:10594:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 10594 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:10527:10: note: ‘choice’ was declared here 10527 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ActionChoiceAsnRead’: objmacro.c:12578:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 12578 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:12507:10: note: ‘choice’ was declared here 12507 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcOrgChoiceAsnRead’: objmacro.c:12778:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 12778 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:12725:10: note: ‘choice’ was declared here 12725 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseSrcAsnRead’: objmacro.c:13365:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13365 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13269:10: note: ‘choice’ was declared here 13269 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ParseDestAsnRead’: objmacro.c:13762:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 13762 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:13694:10: note: ‘choice’ was declared here 13694 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationChoiceAsnRead’: objmacro.c:14121:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 14121 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:14064:10: note: ‘choice’ was declared here 14064 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SequenceListChoiceAsnRead’: objmacro.c:14418:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 14418 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:14368:10: note: ‘choice’ was declared here 14368 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ConvertFeatureDstOptionsAsnRead’: objmacro.c:15556:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 15556 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:15485:10: note: ‘choice’ was declared here 15485 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘LocationEditTypeAsnRead’: objmacro.c:16859:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 16859 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:16754:10: note: ‘choice’ was declared here 16754 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘CreateTSAIdsSrcAsnRead’: objmacro.c:19958:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 19958 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:19908:10: note: ‘choice’ was declared here 19908 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘TableMatchTypeAsnRead’: objmacro.c:20712:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 20712 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:20613:10: note: ‘choice’ was declared here 20613 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘SearchFuncAsnRead’: objmacro.c:23259:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 23259 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:23153:10: note: ‘choice’ was declared here 23153 | Uint1 choice; | ^~~~~~ objmacro.c: In function ‘ReplaceFuncAsnRead’: objmacro.c:23648:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 23648 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmacro.c:23598:10: note: ‘choice’ was declared here 23598 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objent2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objent2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objent2.c: In function ‘Entrez2IdListAsnRead’: objent2.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objent2.c:86:12: warning: unused variable ‘isError’ [-Wunused-variable] 86 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanExpAsnRead’: objent2.c:277:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 277 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2BooleanElementFree’: objent2.c:416:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 416 | Pointer pnt; | ^~~ objent2.c: In function ‘Entrez2BooleanElementAsnRead’: objent2.c:457:12: warning: unused variable ‘isError’ [-Wunused-variable] 457 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LimitsAsnRead’: objent2.c:666:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 666 | AsnReadFunc func; | ^~~~ objent2.c:665:12: warning: unused variable ‘isError’ [-Wunused-variable] 665 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanTermAsnRead’: objent2.c:844:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 844 | AsnReadFunc func; | ^~~~ objent2.c:843:12: warning: unused variable ‘isError’ [-Wunused-variable] 843 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2RequestAsnRead’: objent2.c:1041:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1041 | AsnReadFunc func; | ^~~~ objent2.c:1040:12: warning: unused variable ‘isError’ [-Wunused-variable] 1040 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘E2RequestFree’: objent2.c:1203:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1203 | Pointer pnt; | ^~~ objent2.c: In function ‘E2RequestAsnRead’: objent2.c:1256:12: warning: unused variable ‘isError’ [-Wunused-variable] 1256 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2EvalBooleanAsnRead’: objent2.c:1493:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1493 | AsnReadFunc func; | ^~~~ objent2.c:1492:12: warning: unused variable ‘isError’ [-Wunused-variable] 1492 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermQueryAsnRead’: objent2.c:1670:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1670 | AsnReadFunc func; | ^~~~ objent2.c:1669:12: warning: unused variable ‘isError’ [-Wunused-variable] 1669 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermPosAsnRead’: objent2.c:1849:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1849 | AsnReadFunc func; | ^~~~ objent2.c:1848:12: warning: unused variable ‘isError’ [-Wunused-variable] 1848 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2HierQueryAsnRead’: objent2.c:2036:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2036 | AsnReadFunc func; | ^~~~ objent2.c:2035:12: warning: unused variable ‘isError’ [-Wunused-variable] 2035 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2GetLinksAsnRead’: objent2.c:2224:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2224 | AsnReadFunc func; | ^~~~ objent2.c:2223:12: warning: unused variable ‘isError’ [-Wunused-variable] 2223 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2IdAsnRead’: objent2.c:2419:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2419 | AsnReadFunc func; | ^~~~ objent2.c:2418:12: warning: unused variable ‘isError’ [-Wunused-variable] 2418 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DtFilterAsnRead’: objent2.c:2584:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2584 | AsnReadFunc func; | ^~~~ objent2.c:2583:12: warning: unused variable ‘isError’ [-Wunused-variable] 2583 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2ReplyAsnRead’: objent2.c:2762:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2762 | AsnReadFunc func; | ^~~~ objent2.c:2761:12: warning: unused variable ‘isError’ [-Wunused-variable] 2761 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘E2ReplyFree’: objent2.c:2935:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2935 | Pointer pnt; | ^~~ objent2.c: In function ‘E2ReplyAsnRead’: objent2.c:2991:12: warning: unused variable ‘isError’ [-Wunused-variable] 2991 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2InfoAsnRead’: objent2.c:3237:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3237 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2BooleanReplyAsnRead’: objent2.c:3409:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3409 | AsnReadFunc func; | ^~~~ objent2.c:3408:12: warning: unused variable ‘isError’ [-Wunused-variable] 3408 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumListAsnRead’: objent2.c:3587:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3587 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2TermListAsnRead’: objent2.c:3749:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3749 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2HierNodeAsnRead’: objent2.c:3922:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3922 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2LinkSetAsnRead’: objent2.c:4122:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4122 | AsnReadFunc func; | ^~~~ objent2.c:4121:12: warning: unused variable ‘isError’ [-Wunused-variable] 4121 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkCountListAsnRead’: objent2.c:4299:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4299 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2DbInfoAsnRead’: objent2.c:4466:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4466 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2FieldInfoAsnRead’: objent2.c:4706:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4706 | AsnReadFunc func; | ^~~~ objent2.c:4705:12: warning: unused variable ‘isError’ [-Wunused-variable] 4705 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkInfoAsnRead’: objent2.c:4950:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4950 | AsnReadFunc func; | ^~~~ objent2.c:4949:12: warning: unused variable ‘isError’ [-Wunused-variable] 4949 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumFieldInfoAsnRead’: objent2.c:5149:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5149 | AsnReadFunc func; | ^~~~ objent2.c:5148:12: warning: unused variable ‘isError’ [-Wunused-variable] 5148 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2DocsumAsnRead’: objent2.c:5325:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5325 | AsnReadFunc func; | ^~~~ objent2.c: In function ‘Entrez2DocsumDataAsnRead’: objent2.c:5488:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5488 | AsnReadFunc func; | ^~~~ objent2.c:5487:12: warning: unused variable ‘isError’ [-Wunused-variable] 5487 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2TermAsnRead’: objent2.c:5655:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5655 | AsnReadFunc func; | ^~~~ objent2.c:5654:12: warning: unused variable ‘isError’ [-Wunused-variable] 5654 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2LinkCountAsnRead’: objent2.c:5838:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5838 | AsnReadFunc func; | ^~~~ objent2.c:5837:12: warning: unused variable ‘isError’ [-Wunused-variable] 5837 | Boolean isError = FALSE; | ^~~~~~~ objent2.c: In function ‘Entrez2BooleanElementAsnRead’: objent2.c:524:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 524 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:456:10: note: ‘choice’ was declared here 456 | Uint1 choice; | ^~~~~~ objent2.c: In function ‘E2RequestAsnRead’: objent2.c:1333:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1333 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:1255:10: note: ‘choice’ was declared here 1255 | Uint1 choice; | ^~~~~~ objent2.c: In function ‘E2ReplyAsnRead’: objent2.c:3075:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3075 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objent2.c:2990:10: note: ‘choice’ was declared here 2990 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ent2api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ent2api.h:45, from ent2api.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pmfapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pmfapi.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pmfapi.c:2813:24: warning: ‘SortByInt4’ defined but not used [-Wunused-function] 2813 | static int LIBCALLBACK SortByInt4 (VoidPtr vp1, VoidPtr vp2) | ^~~~~~~~~~ pmfapi.c: In function ‘ConfirmAccStrInSep’: pmfapi.c:1314:3: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1314 | SeqIdFree (tmp); | ^~~~~~~~~~~~~~~ pmfapi.c:1294:22: note: ‘tmp’ was declared here 1294 | SeqIdPtr sip, tmp; | ^~~ pmfapi.c: In function ‘PubMedSynchronousQuery’: pmfapi.c:1224:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1224 | printf ("PubMedWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1187:19: note: ‘starttime’ was declared here 1187 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQueryEx’: pmfapi.c:1479:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1479 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1434:16: note: ‘starttime’ was declared here 1434 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQueryTI’: pmfapi.c:1663:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1663 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1622:16: note: ‘starttime’ was declared here 1622 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘PubSeqSynchronousQuerySRA’: pmfapi.c:1744:58: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1744 | printf ("PubSeqWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1703:16: note: ‘starttime’ was declared here 1703 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiRevHistSynchronousQuery’: pmfapi.c:1817:61: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1817 | printf ("GiRevHistWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1783:15: note: ‘starttime’ was declared here 1783 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiAccVerSynchronousQuery’: pmfapi.c:1869:60: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1869 | printf ("GiAccVerWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1835:15: note: ‘starttime’ was declared here 1835 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘AccnRevHistSynchronousQuery’: pmfapi.c:1920:63: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1920 | printf ("AccnRevHistWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1885:15: note: ‘starttime’ was declared here 1885 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘GiSeqIdSetSynchronousQuery’: pmfapi.c:1971:62: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 1971 | printf ("GiSeqIdSetWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1936:15: note: ‘starttime’ was declared here 1936 | clock_t starttime; | ^~~~~~~~~ pmfapi.c: In function ‘AccnListSynchronousQuery’: pmfapi.c:2021:60: warning: ‘starttime’ may be used uninitialized [-Wmaybe-uninitialized] 2021 | printf ("AccnListWaitForReply %ld\n", (long) (stoptime - starttime)); | ~~~~~~~~~~^~~~~~~~~~~~ pmfapi.c:1987:15: note: ‘starttime’ was declared here 1987 | clock_t starttime; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objtax3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtax3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtax3.c: In function ‘Taxon3RequestAsnRead’: objtax3.c:86:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 86 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3RequestFree’: objtax3.c:200:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 200 | Pointer pnt; | ^~~ objtax3.c: In function ‘SequenceOfIntAsnRead’: objtax3.c:418:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 418 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘Taxon3ReplyAsnRead’: objtax3.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3ReplyFree’: objtax3.c:661:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 661 | Pointer pnt; | ^~~ objtax3.c: In function ‘T3ErrorAsnRead’: objtax3.c:872:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 872 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3DataAsnRead’: objtax3.c:1072:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1072 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘Value_valueFree’: objtax3.c:1253:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1253 | Pointer pnt; | ^~~ objtax3.c: In function ‘T3StatusFlagsAsnRead’: objtax3.c:1283:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1283 | AsnReadFunc func; | ^~~~ objtax3.c: In function ‘T3RefreshFlagsAsnRead’: objtax3.c:1608:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1608 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objtax3.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objtax3.c: In function ‘T3ReplyAsnRead’: objtax3.c:741:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 741 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c:695:10: note: ‘choice’ was declared here 695 | Uint1 choice; | ^~~~~~ In function ‘Value_valueAsnRead’, inlined from ‘T3StatusFlagsAsnRead’ at objtax3.c:1326:28: objtax3.c:1421:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1421 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c: In function ‘T3StatusFlagsAsnRead’: objtax3.c:1362:10: note: ‘choice’ was declared here 1362 | Uint1 choice; | ^~~~~~ objtax3.c: In function ‘T3RequestAsnRead’: objtax3.c:297:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 297 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax3.c:237:10: note: ‘choice’ was declared here 237 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tax3api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from tax3api.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tax3api.c: In function ‘Tax3SynchronousQuery’: tax3api.c:189:27: warning: variable ‘t3’ set but not used [-Wunused-but-set-variable] 189 | time_t t1, t2, t3; | ^~ tax3api.c: In function ‘CheckSuggestedFixes’: tax3api.c:1030:20: warning: variable ‘tep’ set but not used [-Wunused-but-set-variable] 1030 | T3ErrorPtr tep; | ^~~ tax3api.c: In function ‘TryNewSuggestedFixes’: tax3api.c:1142:20: warning: variable ‘tep’ set but not used [-Wunused-but-set-variable] 1142 | T3ErrorPtr tep; | ^~~ tax3api.c: In function ‘RemoveSpeciesSpecific’: tax3api.c:1398:13: warning: unused variable ‘cp’ [-Wunused-variable] 1398 | CharPtr cp; | ^~ tax3api.c: At top level: tax3api.c:3399:13: warning: ‘AddBioSourcesToChecklist’ defined but not used [-Wunused-function] 3399 | static void AddBioSourcesToChecklist (ValNodePtr biop_list, ValNodePtr check_list) | ^~~~~~~~~~~~~~~~~~~~~~~~ tax3api.c:2699:16: warning: ‘MatchesGenBankSynonym’ defined but not used [-Wunused-function] 2699 | static Boolean MatchesGenBankSynonym (CharPtr txt, OrgRefPtr response_org) | ^~~~~~~~~~~~~~~~~~~~~ tax3api.c:2682:16: warning: ‘MatchesSynonym’ defined but not used [-Wunused-function] 2682 | static Boolean MatchesSynonym (CharPtr txt, OrgRefPtr response_org) | ^~~~~~~~~~~~~~ tax3api.c:2273:16: warning: ‘EndsWithSp’ defined but not used [-Wunused-function] 2273 | static Boolean EndsWithSp (CharPtr str) | ^~~~~~~~~~ tax3api.c:990:19: warning: ‘MakeTaxFixRequestList’ defined but not used [-Wunused-function] 990 | static ValNodePtr MakeTaxFixRequestList (ValNodePtr biop_list) | ^~~~~~~~~~~~~~~~~~~~~ tax3api.c:362:16: warning: ‘HasMisspellingFlag’ defined but not used [-Wunused-function] 362 | static Boolean HasMisspellingFlag (T3DataPtr t) | ^~~~~~~~~~~~~~~~~~ tax3api.c:298:13: warning: ‘SaveTaxon3Request’ defined but not used [-Wunused-function] 298 | static void SaveTaxon3Request (Taxon3RequestPtr t3rp, CharPtr path) | ^~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objegkludge.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objegkludge.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objentgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objentgene.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objentgene.c: In function ‘EntrezgeneAsnRead’: objentgene.c:103:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 103 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘EntrezgeneSetAsnRead’: objentgene.c:412:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 412 | AsnReadFunc func; | ^~~~ objentgene.c:409:12: warning: unused variable ‘av’ [-Wunused-variable] 409 | DataVal av; | ^~ objentgene.c: In function ‘GeneTrackAsnRead’: objentgene.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘GeneCommentaryAsnRead’: objentgene.c:768:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 768 | AsnReadFunc func; | ^~~~ objentgene.c: In function ‘Method_methodFree’: objentgene.c:1073:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1073 | Pointer pnt; | ^~~ objentgene.c: In function ‘MapsAsnRead’: objentgene.c:1104:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1104 | AsnReadFunc func; | ^~~~ objentgene.c:1103:12: warning: unused variable ‘isError’ [-Wunused-variable] 1103 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘Method_methodAsnRead’: objentgene.c:1184:12: warning: unused variable ‘isError’ [-Wunused-variable] 1184 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘GeneSourceAsnRead’: objentgene.c:1426:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1426 | AsnReadFunc func; | ^~~~ objentgene.c:1425:12: warning: unused variable ‘isError’ [-Wunused-variable] 1425 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘XtraTermsAsnRead’: objentgene.c:1641:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1641 | AsnReadFunc func; | ^~~~ objentgene.c:1640:12: warning: unused variable ‘isError’ [-Wunused-variable] 1640 | Boolean isError = FALSE; | ^~~~~~~ objentgene.c: In function ‘OtherSourceAsnRead’: objentgene.c:1812:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1812 | AsnReadFunc func; | ^~~~ objentgene.c:1811:12: warning: unused variable ‘isError’ [-Wunused-variable] 1811 | Boolean isError = FALSE; | ^~~~~~~ In function ‘Method_methodAsnRead’, inlined from ‘MapsAsnRead’ at objentgene.c:1147:30: objentgene.c:1236:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1236 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objentgene.c: In function ‘MapsAsnRead’: objentgene.c:1183:10: note: ‘choice’ was declared here 1183 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmla2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmla2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmla2.c: In function ‘Mla2RequestFree’: objmla2.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objmla2.c: In function ‘Mla22RequestAsnRead’: objmla2.c:96:12: warning: unused variable ‘isError’ [-Wunused-variable] 96 | Boolean isError = FALSE; | ^~~~~~~ objmla2.c: In function ‘TitleMsg2AsnRead’: objmla2.c:447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 447 | AsnReadFunc func; | ^~~~ objmla2.c:446:12: warning: unused variable ‘isError’ [-Wunused-variable] 446 | Boolean isError = FALSE; | ^~~~~~~ objmla2.c: In function ‘TitleMsgList2AsnRead’: objmla2.c:613:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 613 | AsnReadFunc func; | ^~~~ objmla2.c: In function ‘Mla22RequestAsnRead’: objmla2.c:249:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 249 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla2.c:95:10: note: ‘choice’ was declared here 95 | Uint1 choice; | ^~~~~~ objmla2.c: In function ‘Mla2BackAsnRead’: objmla2.c:904:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 904 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla2.c:787:10: note: ‘choice’ was declared here 787 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mla2api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/mla2api.h:45, from mla2api.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF qblastapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from qblastapi.c:123: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ qblastapi.c: In function ‘SecondQBlastCallback’: qblastapi.c:262:15: warning: variable ‘waiting’ set but not used [-Wunused-but-set-variable] 262 | Boolean waiting = FALSE; | ^~~~~~~ qblastapi.c: In function ‘BLASTGetSeqAnnotByRIDEx’: qblastapi.c:826:18: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 826 | EIO_Status status; | ^~~~~~ qblastapi.c: In function ‘BLASTGetQueryBioseqByRIDEx’: qblastapi.c:871:18: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 871 | EIO_Status status; | ^~~~~~ qblastapi.c: In function ‘QBlastCheckQueue’: qblastapi.c:688:36: warning: ‘&FORMAT_OBJECT=Alignment&FOR...’ directive writing 43 bytes into a region of size between 5 and 68 [-Wformat-overflow=] 688 | sprintf (str, "CMD=Get&RID=%s&FORMAT_OBJECT=Alignment&FORMAT_TYPE=ASN.1\n", curr->rid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘QBlastCheckQueue’ at qblastapi.c:688:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 56 and 119 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vecscnapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from vecscnapi.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmim.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmim.c: In function ‘MimSetAsnRead’: objmim.c:86:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 86 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimDateAsnRead’: objmim.c:248:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 248 | AsnReadFunc func; | ^~~~ objmim.c:247:12: warning: unused variable ‘isError’ [-Wunused-variable] 247 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimEntryAsnRead’: objmim.c:448:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 448 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimCitAsnRead’: objmim.c:909:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 909 | AsnReadFunc func; | ^~~~ objmim.c:908:12: warning: unused variable ‘isError’ [-Wunused-variable] 908 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimTextAsnRead’: objmim.c:1096:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1096 | AsnReadFunc func; | ^~~~ objmim.c:1095:12: warning: unused variable ‘isError’ [-Wunused-variable] 1095 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimEditItemAsnRead’: objmim.c:1276:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1276 | AsnReadFunc func; | ^~~~ objmim.c:1275:12: warning: unused variable ‘isError’ [-Wunused-variable] 1275 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimAllelicVariantAsnRead’: objmim.c:1448:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1448 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimIndexTermAsnRead’: objmim.c:1640:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1640 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimReferenceAsnRead’: objmim.c:1819:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1819 | AsnReadFunc func; | ^~~~ objmim.c: In function ‘MimLinkAsnRead’: objmim.c:2195:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2195 | AsnReadFunc func; | ^~~~ objmim.c:2194:12: warning: unused variable ‘isError’ [-Wunused-variable] 2194 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimAuthorAsnRead’: objmim.c:2369:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2369 | AsnReadFunc func; | ^~~~ objmim.c:2368:12: warning: unused variable ‘isError’ [-Wunused-variable] 2368 | Boolean isError = FALSE; | ^~~~~~~ objmim.c: In function ‘MimPageAsnRead’: objmim.c:2535:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2535 | AsnReadFunc func; | ^~~~ objmim.c:2534:12: warning: unused variable ‘isError’ [-Wunused-variable] 2534 | Boolean isError = FALSE; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objvalid.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objvalid.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objvalid.c: In function ‘FieldRuleAsnRead’: objvalid.c:88:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 88 | AsnReadFunc func; | ^~~~ objvalid.c:87:12: warning: unused variable ‘isError’ [-Wunused-variable] 87 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘FieldSetAsnRead’: objvalid.c:259:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 259 | AsnReadFunc func; | ^~~~ objvalid.c:256:12: warning: unused variable ‘av’ [-Wunused-variable] 256 | DataVal av; | ^~ objvalid.c: In function ‘DependentFieldRuleAsnRead’: objvalid.c:396:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 396 | AsnReadFunc func; | ^~~~ objvalid.c:395:12: warning: unused variable ‘isError’ [-Wunused-variable] 395 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘DependentFieldSetAsnRead’: objvalid.c:582:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 582 | AsnReadFunc func; | ^~~~ objvalid.c:579:12: warning: unused variable ‘av’ [-Wunused-variable] 579 | DataVal av; | ^~ objvalid.c: In function ‘CommentRuleAsnRead’: objvalid.c:721:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 721 | AsnReadFunc func; | ^~~~ objvalid.c:720:12: warning: unused variable ‘isError’ [-Wunused-variable] 720 | Boolean isError = FALSE; | ^~~~~~~ objvalid.c: In function ‘CommentSetAsnRead’: objvalid.c:926:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 926 | AsnReadFunc func; | ^~~~ objvalid.c:923:12: warning: unused variable ‘av’ [-Wunused-variable] 923 | DataVal av; | ^~ objvalid.c: In function ‘PhraseListAsnRead’: objvalid.c:1043:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1043 | AsnReadFunc func; | ^~~~ objvalid.c:1040:12: warning: unused variable ‘av’ [-Wunused-variable] 1040 | DataVal av; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mimapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mimapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cddapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqport.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from seqport.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqport.c: In function ‘productLoc_to_locationLoc’: seqport.c:4260:13: warning: variable ‘is_cdregion’ set but not used [-Wunused-but-set-variable] 4260 | Boolean is_cdregion = FALSE; | ^~~~~~~~~~~ seqport.c: In function ‘NaLocFromNaInterval’: seqport.c:4590:8: warning: variable ‘p_end_pos’ set but not used [-Wunused-but-set-variable] 4590 | Int4 p_end_pos; /*the end of the product sequence in the current loc*/ | ^~~~~~~~~ seqport.c: In function ‘dnaLoc_to_aaLoc’: seqport.c:4706:18: warning: variable ‘cds_right’ set but not used [-Wunused-but-set-variable] 4706 | Int4 cds_left, cds_right; | ^~~~~~~~~ seqport.c:4706:8: warning: variable ‘cds_left’ set but not used [-Wunused-but-set-variable] 4706 | Int4 cds_left, cds_right; | ^~~~~~~~ seqport.c: In function ‘DeltaRevComp’: seqport.c:5388:21: warning: variable ‘dspnext’ set but not used [-Wunused-but-set-variable] 5388 | DeltaSeqPtr dsp, dspnext; | ^~~~~~~ seqport.c: In function ‘SeqSearchEnterNucWord’: seqport.c:6943:18: warning: variable ‘patLen’ set but not used [-Wunused-but-set-variable] 6943 | Int2 next, patLen, state; | ^~~~~~ seqport.c: In function ‘ProtSearchEnterProtWord’: seqport.c:7817:18: warning: variable ‘patLen’ set but not used [-Wunused-but-set-variable] 7817 | Int2 next, patLen, state; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from seqport.c:62: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sequtil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from sequtil.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequtil.c: In function ‘GetPointsForLeftAndRightOffsets’: sequtil.c:7994:11: warning: variable ‘first_strand’ set but not used [-Wunused-but-set-variable] 7994 | Uint1 first_strand, last_strand; | ^~~~~~~~~~~~ sequtil.c: In function ‘SeqPointWriteEx’: sequtil.c:8532:15: warning: variable ‘fuzzlen’ set but not used [-Wunused-but-set-variable] 8532 | Int4 fuzzlen, id_len; | ^~~~~~~ sequtil.c: In function ‘TaxNameFromCommon’: sequtil.c:8687:42: warning: missing braces around initializer [-Wmissing-braces] 8687 | static Nlm_TaxCommon taxcommon[40] = { | ^ 8688 | "Chinese hamsters", "Cricetulus sp." | { 8689 | ,"Syrian golden hamsters", "Mesocricetus auratus" | }{ 8690 | ,"Syrian hamsters", "Mesocricetus sp." | }{ 8691 | ,"barley", "Hordeum sp." | }{ 8692 | ,"carrots", "Daucus sp." | }{ 8693 | ,"cats", "Felis sp." | }{ 8694 | ,"cattles", "Bos sp." | }{ 8695 | ,"chickens", "Gallus sp." | }{ 8696 | ,"chimpanzees", "Pan sp." | }{ 8697 | ,"chimpanzes", "Pan sp." | }{ 8698 | ,"corn", "Zea sp." | }{ 8699 | ,"cucumber", "Cucumis sativus" | }{ 8700 | ,"dogs", "Canis sp." | }{ 8701 | ,"goats", "Capra sp." | }{ 8702 | ,"gorillas", "Gorilla sp." | }{ 8703 | ,"guinea pigs", "Cavia sp." | }{ 8704 | ,"hamsters", "Cricetidae gen. sp." | }{ 8705 | ,"horses", "Equus sp." | }{ 8706 | ,"humans", "Homo sapiens" | }{ 8707 | ,"maize", "Zea sp." | }{ 8708 | ,"mice", "Mus sp." | }{ 8709 | ,"mouse", "Mus sp." | }{ 8710 | ,"peas", "Pisum sp." | }{ 8711 | ,"potatoes", "Solanum sp." | }{ 8712 | ,"potato", "Solanum sp." | }{ 8713 | ,"quails", "Phasianidae gen. sp." | }{ 8714 | ,"rabbits", "Oryctolagus sp." | }{ 8715 | ,"rats", "Rattus sp." | }{ 8716 | ,"rices", "Oryza sp." | }{ 8717 | ,"sheeps", "Ovis sp." | }{ 8718 | ,"sorghums", "Sorghum sp." | }{ 8719 | ,"soybeans", "Glycine sp." | }{ 8720 | ,"spinach", "Spinacia sp." | }{ 8721 | ,"swine", "Sus sp." | }{ 8722 | ,"tobacco", "Nicotiania sp." | }{ 8723 | ,"tomatoes", "Lycopersicon sp." | }{ 8724 | ,"tomato", "Lycopersicon sp." | }{ 8725 | ,"turkeys", "Meleagris sp." | }{ 8726 | ,"wheat", "Triticum sp." | }{ 8727 | ,"zebrafish", "Brachydanio sp." | }{ 8728 | }; | } sequtil.c: In function ‘GetBestScoreAndEvalueFromScorePtr’: sequtil.c:9510:48: warning: variable ‘sum_set’ set but not used [-Wunused-but-set-variable] 9510 | Boolean score_set=FALSE, evalue_set=FALSE, sum_set=FALSE, bit_set=FALSE; | ^~~~~~~ sequtil.c: In function ‘SeqIdFromAccessionEx’: sequtil.c:10110:38: warning: variable ‘sip2’ set but not used [-Wunused-but-set-variable] 10110 | SeqIdPtr sip2; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prtutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objprt.h:67, from ../include/prtutil.h:69, from prtutil.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prtutil.c: In function ‘StdFormatPrint’: prtutil.c:1422:17: warning: unused variable ‘ptr’ [-Wunused-variable] 1422 | CharPtr ptr = NULL; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF simple.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/simple.h:63, from simple.c:68: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from simple.c:69: ../include/all.h:7293: warning: "RNA_QUAL" redefined 7293 | #define RNA_QUAL &at[2254] | ../include/all.h:5823: note: this is the location of the previous definition 5823 | #define RNA_QUAL &at[1025] | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tofasta.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/tofasta.h:47, from tofasta.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tofasta.c: In function ‘DoSpecialDefline’: tofasta.c:1461:22: warning: variable ‘gene’ set but not used [-Wunused-but-set-variable] 1461 | SeqFeatPtr gene = NULL; | ^~~~ tofasta.c: In function ‘FastaIdEx’: tofasta.c:3100:15: warning: variable ‘sip’ set but not used [-Wunused-but-set-variable] 3100 | SeqIdPtr sip; | ^~~ tofasta.c: In function ‘CreateDefLineExEx’: tofasta.c:4991:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4991 | if (vnp != NULL) | ^~ tofasta.c:4993:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4993 | if (title != NULL) { | ^~ tofasta.c: In function ‘x_SetSuffix’: tofasta.c:8313:24: warning: variable ‘buf2’ set but not used [-Wunused-but-set-variable] 8313 | Char buf1 [512], buf2 [256]; | ^~~~ tofasta.c: In function ‘FastaToSeqEntryInternalExEx’: tofasta.c:2838:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2838 | fgets(buffer+1, BuffSize, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c:2863:13: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2863 | fgets(buffer+i+1, FTSE_BUFF_CHUNK, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c: At top level: tofasta.c:8058:17: warning: ‘x_StringInList’ defined but not used [-Wunused-function] 8058 | static Boolean x_StringInList ( | ^~~~~~~~~~~~~~ tofasta.c:3661:19: warning: ‘GatherGenesForCDS’ defined but not used [-Wunused-function] 3661 | static ValNodePtr GatherGenesForCDS(SeqLocPtr slp) | ^~~~~~~~~~~~~~~~~ tofasta.c:3627:19: warning: ‘GatherSeqFeatProt’ defined but not used [-Wunused-function] 3627 | static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~ tofasta.c:3541:19: warning: ‘GetCDSProtUnindexed’ defined but not used [-Wunused-function] 3541 | static SeqFeatPtr GetCDSProtUnindexed ( | ^~~~~~~~~~~~~~~~~~~ tofasta.c:3378:19: warning: ‘IndexedGatherDescrOnBioseq’ defined but not used [-Wunused-function] 3378 | static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ tofasta.c:3283:16: warning: ‘get_descr’ defined but not used [-Wunused-function] 3283 | static Boolean get_descr (GatherContextPtr gcp) | ^~~~~~~~~ tofasta.c:3254:16: warning: ‘get_descr_on_top’ defined but not used [-Wunused-function] 3254 | static Boolean get_descr_on_top (GatherContextPtr gcp) | ^~~~~~~~~~~~~~~~ tofasta.c: In function ‘FastaReadSequenceInternalEx’: tofasta.c:2578:43: warning: ‘mask_to’ may be used uninitialized [-Wmaybe-uninitialized] 2578 | mask_sint->to = mask_to; | ~~~~~~~~~~~~~~^~~~~~~~~ tofasta.c:2512:20: note: ‘mask_to’ was declared here 2512 | Int4 mask_to; | ^~~~~~~ tofasta.c: In function ‘FastaToSeqEntryInternalExEx’: tofasta.c:2866:29: warning: ‘firstchar’ may be used uninitialized [-Wmaybe-uninitialized] 2866 | for(i =0; (ch = *firstchar) != NULLB; firstchar++, i++) { | ^~~~~~~~~~ tofasta.c:2774:25: note: ‘firstchar’ was declared here 2774 | const Char PNTR firstchar; | ^~~~~~~~~ tofasta.c:2954:13: warning: ‘fd’ may be used uninitialized [-Wmaybe-uninitialized] 2954 | ungetc(ch, fd); | ^~~~~~~~~~~~~~ tofasta.c:2773:21: note: ‘fd’ was declared here 2773 | FILE *fd; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tofile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from tofile.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tomedlin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmedli.h:80, from tomedlin.c:153: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF valid.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from valid.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valid.c: In function ‘GetUserFieldValueString’: valid.c:2212:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 2212 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld valid.c: In function ‘ValidateSeqIdCase’: valid.c:3574:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 3574 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘ValidateGenProdSet’: valid.c:6046:19: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 6046 | GeneRefPtr grp; | ^~~ valid.c: In function ‘CountAdjacentProc’: valid.c:6730:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 6730 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘CheckBioseqEndsForNAndGap’: valid.c:7040:44: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 7040 | if (str [0] == 'n' || str [0] == 'N' && begin_n != NULL) { | ^ valid.c:7061:56: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 7061 | if (str [len - 1] == 'n' || str [len - 1] == 'N' && end_n != NULL) { | ^ valid.c: In function ‘ValidateBioseqInst’: valid.c:7341:19: warning: variable ‘tech’ set but not used [-Wunused-but-set-variable] 7341 | Uint1 tech; | ^~~~ valid.c:7278:19: warning: variable ‘prot’ set but not used [-Wunused-but-set-variable] 7278 | SeqFeatPtr prot; | ^~~~ valid.c: In function ‘FixOrgModVoucher’: valid.c:13882:22: warning: unused variable ‘allowed_type’ [-Wunused-variable] 13882 | Uint1 type = 0, allowed_type = 0; | ^~~~~~~~~~~~ valid.c: In function ‘ValidateBioSource’: valid.c:15514:19: warning: variable ‘isMicrosporidia’ set but not used [-Wunused-but-set-variable] 15514 | Boolean isMicrosporidia = FALSE; | ^~~~~~~~~~~~~~~ valid.c:15512:19: warning: variable ‘isEukaryote’ set but not used [-Wunused-but-set-variable] 15512 | Boolean isEukaryote = FALSE; | ^~~~~~~~~~~ valid.c:15503:19: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 15503 | Int4 id; | ^~ valid.c: In function ‘ValidateDblink’: valid.c:16786:21: warning: variable ‘gcp’ set but not used [-Wunused-but-set-variable] 16786 | GatherContextPtr gcp; | ^~~ valid.c: In function ‘ValidateSeqDescrCommon’: valid.c:16883:19: warning: variable ‘pdp’ set but not used [-Wunused-but-set-variable] 16883 | PubdescPtr pdp; | ^~~ valid.c: In function ‘GetFeatsInGaps’: valid.c:18858:21: warning: variable ‘realBases’ set but not used [-Wunused-but-set-variable] 18858 | Int4 realBases; | ^~~~~~~~~ valid.c:18857:21: warning: variable ‘plusses’ set but not used [-Wunused-but-set-variable] 18857 | Int4 plusses; | ^~~~~~~ valid.c:18854:21: warning: variable ‘Ns’ set but not used [-Wunused-but-set-variable] 18854 | Int4 Ns; | ^~ valid.c:18851:21: warning: variable ‘dashes’ set but not used [-Wunused-but-set-variable] 18851 | Int4 dashes; | ^~~~~~ valid.c: In function ‘ValidateBioseqContextIndexed’: valid.c:20267:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 20267 | if (bvsp->is_mrna || cdscount == 1 && genecount < 2) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ valid.c:19476:65: warning: variable ‘cdsmgene’ set but not used [-Wunused-but-set-variable] 19476 | SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene; | ^~~~~~~~ valid.c:19476:33: warning: variable ‘cdspgene’ set but not used [-Wunused-but-set-variable] 19476 | SeqFeatPtr utr5pgene, cdspgene, utr3pgene, utr5mgene, cdsmgene, utr3mgene; | ^~~~~~~~ valid.c:19475:51: warning: variable ‘utr5minus’ set but not used [-Wunused-but-set-variable] 19475 | SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus; | ^~~~~~~~~ valid.c:19475:41: warning: variable ‘utr3plus’ set but not used [-Wunused-but-set-variable] 19475 | SeqFeatPtr utr5plus, cdsplus, utr3plus, utr5minus, cdsminus, utr3minus; | ^~~~~~~~ valid.c:19442:41: warning: variable ‘utr3gene’ set but not used [-Wunused-but-set-variable] 19442 | SeqFeatPtr cdsgene, utr5gene, utr3gene; | ^~~~~~~~ valid.c: In function ‘ReportBadWGSGap’: valid.c:21153:18: warning: unused variable ‘is_wgs’ [-Wunused-variable] 21153 | Boolean is_wgs = FALSE; | ^~~~~~ valid.c: In function ‘ValidateBarcodeIndexNumber’: valid.c:21432:21: warning: variable ‘bin_len’ set but not used [-Wunused-but-set-variable] 21432 | Int4 bin_len; | ^~~~~~~ valid.c: In function ‘ValidateRptUnit’: valid.c:23411:32: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 23411 | Boolean badchars, found, just_nuc_letters, multi_rpt_unit, in_range; | ^~~~~ valid.c: In function ‘CheckForCommonCDSProduct’: valid.c:25628:19: warning: variable ‘is_nw’ set but not used [-Wunused-but-set-variable] 25628 | Boolean is_nw = FALSE; | ^~~~~ valid.c:25625:19: warning: variable ‘is_nc’ set but not used [-Wunused-but-set-variable] 25625 | Boolean is_nc = FALSE; | ^~~~~ valid.c: In function ‘CheckForIllegalDbxref’: valid.c:26017:16: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 26017 | Int4 id; | ^~ valid.c: In function ‘ValidateAnticodon’: valid.c:26781:53: warning: variable ‘circular’ set but not used [-Wunused-but-set-variable] 26781 | ordered = TRUE, adjacent = FALSE, circular = FALSE, exception = FALSE; | ^~~~~~~~ valid.c:26780:19: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 26780 | Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE, | ^~~~~~ valid.c: In function ‘IsGeneXrefRedundant’: valid.c:28000:17: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 28000 | Int2 count; | ^~~~~ valid.c: In function ‘ValidateSeqFeat’: valid.c:28328:19: warning: unused variable ‘is_nc’ [-Wunused-variable] 28328 | Boolean is_nc = FALSE; | ^~~~~ valid.c:28308:19: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 28308 | Int2 count; | ^~~~~ valid.c:28286:19: warning: variable ‘pdp’ set but not used [-Wunused-but-set-variable] 28286 | PubdescPtr pdp; | ^~~ valid.c: In function ‘CdTransCheck’: valid.c:30490:19: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 30490 | GeneRefPtr grp; | ^~~ valid.c: In function ‘SpliceCheckEx’: valid.c:31313:19: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 31313 | SeqEntryPtr sep; | ^~~ valid.c: In function ‘CdsProductIdCheck’: valid.c:31689:15: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 31689 | GeneRefPtr grp; | ^~~ valid.c: In function ‘ValidateSeqLoc’: valid.c:31754:19: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 31754 | Boolean retval = TRUE, tmpval, mixed_strand = FALSE, unmarked_strand = FALSE, | ^~~~~~ valid.c:31753:24: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 31753 | SeqLocPtr tmp, prev; | ^~~~ valid.c: In function ‘SortSeqGraphProc’: valid.c:32156:26: warning: self-comparison always evaluates to false [-Wtautological-compare] 32156 | } else if (gip2->right < gip2->right) { | ^ valid.c: At top level: valid.c:30138:13: warning: ‘ValidateTranslExcept’ defined but not used [-Wunused-function] 30138 | static void ValidateTranslExcept ( | ^~~~~~~~~~~~~~~~~~~~ valid.c:27650:16: warning: ‘CouldExtendPartial’ defined but not used [-Wunused-function] 27650 | static Boolean CouldExtendPartial (SeqLocPtr slp, Boolean partial5) | ^~~~~~~~~~~~~~~~~~ valid.c:20878:28: warning: ‘MultiGeneOverlapFree’ defined but not used [-Wunused-function] 20878 | static MultiGeneOverlapPtr MultiGeneOverlapFree (MultiGeneOverlapPtr m) | ^~~~~~~~~~~~~~~~~~~~ valid.c:20828:19: warning: ‘ListFeaturesContainedInLocation’ defined but not used [-Wunused-function] 20828 | static ValNodePtr ListFeaturesContainedInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ valid.c:17541:16: warning: ‘IsEMBLAccn’ defined but not used [-Wunused-function] 17541 | static Boolean IsEMBLAccn (SeqEntryPtr sep, SeqLocPtr location) | ^~~~~~~~~~ valid.c:14642:16: warning: ‘CountryIsClosestToLatLon’ defined but not used [-Wunused-function] 14642 | static Boolean CountryIsClosestToLatLon ( | ^~~~~~~~~~~~~~~~~~~~~~~~ valid.c:14545:16: warning: ‘LatLonInRange’ defined but not used [-Wunused-function] 14545 | static Boolean LatLonInRange ( | ^~~~~~~~~~~~~ valid.c:13478:16: warning: ‘LatLonIsValid’ defined but not used [-Wunused-function] 13478 | static Boolean LatLonIsValid (CharPtr name) | ^~~~~~~~~~~~~ valid.c:10462:16: warning: ‘ConsistentWithC’ defined but not used [-Wunused-function] 10462 | static Boolean ConsistentWithC (Char ch) | ^~~~~~~~~~~~~~~ valid.c:6952:13: warning: ‘ReportLongSeqId’ defined but not used [-Wunused-function] 6952 | static void ReportLongSeqId (SeqIdPtr sip, ValidStructPtr vsp, Int4 max_len) | ^~~~~~~~~~~~~~~ valid.c:5932:13: warning: ‘CheckMutSetSources’ defined but not used [-Wunused-function] 5932 | static void CheckMutSetSources (BioSourcePtr biop, Pointer userdata) | ^~~~~~~~~~~~~~~~~~ valid.c:4360:13: warning: ‘FindLongIdsThatCollideWhenTruncated’ defined but not used [-Wunused-function] 4360 | static void FindLongIdsThatCollideWhenTruncated (SeqEntryPtr sep, ValidStructPtr vsp, Int4 trunc_len) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ valid.c:1511:16: warning: ‘IsNotUnclassifiedExcept’ defined but not used [-Wunused-function] 1511 | static Boolean IsNotUnclassifiedExcept (ValidStructPtr vsp) | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF valapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from valapi.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valapi.c: In function ‘DoesStringMatchExpression’: valapi.c:263:15: warning: variable ‘errstr’ set but not used [-Wunused-but-set-variable] 263 | const char *errstr; | ^~~~~~ valapi.c: In function ‘DoesFieldValueMatchExpression’: valapi.c:292:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 292 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF alignmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/alignmgr.h:261, from alignmgr.c:584: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignmgr.c: In function ‘AlnMgrIndexParentSA’: alignmgr.c:1607:19: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1607 | sap->saip = (Pointer)AMAlignIndexFree(amaip); | ^ alignmgr.c: In function ‘AlnMgrGetNthBlockRange’: alignmgr.c:4182:21: warning: variable ‘amaip’ set but not used [-Wunused-but-set-variable] 4182 | AMAlignIndexPtr amaip; | ^~~~~ alignmgr.c: In function ‘AlnMgrMakeFakeMultipleEx’: alignmgr.c:5157:21: warning: variable ‘nogap’ set but not used [-Wunused-but-set-variable] 5157 | Boolean nogap; | ^~~~~ alignmgr.c: In function ‘AlnMgrMapBioseqToBioseq’: alignmgr.c:10840:19: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 10840 | Uint1 gap; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignmgr.c:10572:16: warning: ‘am_merge_after_edit’ defined but not used [-Wunused-function] 10572 | static Boolean am_merge_after_edit (SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~ alignmgr.c:6650:16: warning: ‘AlnMgrJaggedIndex’ defined but not used [-Wunused-function] 6650 | static Boolean AlnMgrJaggedIndex(SeqAlignPtr sap, AMmsmsPtr ams_head, AMmsmsPtr *ams_mhead, Int4 numrows) | ^~~~~~~~~~~~~~~~~ alignmgr.c:6123:18: warning: ‘AlnMgrConstructOverlaps’ defined but not used [-Wunused-function] 6123 | static AMmsmsPtr AlnMgrConstructOverlaps(AMmsmsPtr ams_head) | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:5405:13: warning: ‘AlnMgrMergeNeighbors’ defined but not used [-Wunused-function] 5405 | static void AlnMgrMergeNeighbors(SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~ alignmgr.c: In function ‘AlnMgrUnpackSeqAlign’: alignmgr.c:1149:33: warning: ‘sap_segs_prev’ may be used uninitialized [-Wmaybe-uninitialized] 1149 | sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:1117:17: note: ‘sap_segs_prev’ was declared here 1117 | SeqAlignPtr sap_segs_prev; | ^~~~~~~~~~~~~ alignmgr.c: In function ‘AlnMgrGetNthSeqRangeInSA’: alignmgr.c:4113:20: warning: ‘tmp_beg’ may be used uninitialized [-Wmaybe-uninitialized] 4113 | *start = tmp_beg; | ~~~~~~~^~~~~~~~~ alignmgr.c:3974:21: note: ‘tmp_beg’ was declared here 3974 | Int4 tmp_beg; | ^~~~~~~ alignmgr.c:4115:19: warning: ‘tmp_end’ may be used uninitialized [-Wmaybe-uninitialized] 4115 | *stop = tmp_end; | ~~~~~~^~~~~~~~~ alignmgr.c:3975:21: note: ‘tmp_end’ was declared here 3975 | Int4 tmp_end; | ^~~~~~~ alignmgr.c: In function ‘am_is_consistent’: alignmgr.c:10114:13: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 10114 | AlnMgrGetNthUnalignedForNthRow(sap, n, i, &u_start, &u_stop); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr.c:10009:21: note: ‘n’ was declared here 10009 | Int4 n; | ^ alignmgr.c: In function ‘am_print_seqalign_indexes’: alignmgr.c:2436:27: warning: ‘amaip’ may be used uninitialized [-Wmaybe-uninitialized] 2436 | for (i=0; inumbsqs; i++) | ~~~~~^~~~~~~~~ alignmgr.c:2389:21: note: ‘amaip’ was declared here 2389 | AMAlignIndexPtr amaip; | ^~~~~ alignmgr.c:2409:31: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 2409 | printf("%d ", saip->aligncoords[i]); | ~~~~^~~~~~~~~~~~~ alignmgr.c:2393:21: note: ‘saip’ was declared here 2393 | SAIndexPtr saip; | ^~~~ alignmgr.c: In function ‘AlnMgrGetSubAlign’: alignmgr.c:9097:17: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 9097 | salp = am_cleanupsalp(salp); | ^~~~~~~~~~~~~~~~~~~~ alignmgr.c:8885:21: note: ‘salp’ was declared here 8885 | SeqAlignPtr salp; | ^~~~ In function ‘am_find_master’, inlined from ‘AlnMgrMakeMultByIntersectOnMaster’ at alignmgr.c:5588:17: alignmgr.c:5865:15: warning: ‘sip_head’ may be used uninitialized [-Wmaybe-uninitialized] 5865 | while (sip && !done) | ~~~~^~~~~~~~ alignmgr.c: In function ‘AlnMgrMakeMultByIntersectOnMaster’: alignmgr.c:5845:18: note: ‘sip_head’ was declared here 5845 | SeqIdPtr sip_head; | ^~~~~~~~ alignmgr.c:5589:7: warning: ‘sip_tmp’ may be used uninitialized [-Wmaybe-uninitialized] 5589 | if (sip_tmp == NULL) | ^ alignmgr.c:5553:17: note: ‘sip_tmp’ was declared here 5553 | SeqIdPtr sip_tmp; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF aliparse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/aliparse.h:12, from aliparse.c:9: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ aliparse.c: In function ‘s_IsInterleaved’: aliparse.c:929:51: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 929 | (s_configInfo.useMaybes == FALSE) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 930 | (seqLinePtr->maybe == FALSE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:823:20: warning: variable ‘isMaybe’ set but not used [-Wunused-but-set-variable] 823 | Boolean isMaybe; | ^~~~~~~ aliparse.c: In function ‘s_ProcessInterId’: aliparse.c:1000:15: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1000 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_ProcessInterSeq’: aliparse.c:1090:15: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1090 | ErrInfoPtr errPtr = NULL; | ^~~~~~ aliparse.c: In function ‘s_AnalyzeInterleaved’: aliparse.c:1193:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1193 | (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘s_ProcessContigId’: aliparse.c:1385:18: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1385 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_ProcessContigSeq’: aliparse.c:1476:18: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 1476 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘s_AnalyzeContiguous’: aliparse.c:1603:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1603 | (seqLinePtr->maybe == TRUE) && (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘s_CheckContext’: aliparse.c:2150:47: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2150 | (seqLinePtr->maybe == TRUE) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2151 | (s_configInfo.useMaybes == TRUE)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:2131:20: warning: variable ‘errPtr’ set but not used [-Wunused-but-set-variable] 2131 | ErrInfoPtr errPtr; | ^~~~~~ aliparse.c: In function ‘PrintOutMultAlign’: aliparse.c:3161:10: warning: statement with no effect [-Wunused-value] 3161 | for (d; dnext = newSeqPart; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ aliparse.c:633:18: note: ‘lastSeqPart’ was declared here 633 | SeqPartPtr lastSeqPart; | ^~~~~~~~~~~ aliparse.c:641:10: warning: ‘newIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 641 | if (idStr != NULL) | ^ aliparse.c:543:20: note: ‘newIdStr’ was declared here 543 | CharPtr newIdStr; | ^~~~~~~~ aliparse.c:669:39: warning: ‘currentIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 669 | currentId->id = currentIdStr; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ aliparse.c:631:18: note: ‘currentIdStr’ was declared here 631 | CharPtr currentIdStr; | ^~~~~~~~~~~~ In function ‘s_CheckContext’, inlined from ‘Ali_Read’ at aliparse.c:2565:7: aliparse.c:2294:25: warning: ‘newIdStr’ may be used uninitialized [-Wmaybe-uninitialized] 2294 | if ((lastRow != NULL) && | ~~~~~~~~~~~~~~~~~~^~ 2295 | ((idStr = s_GetRowIdString (lastRow)) != NULL) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:543:20: note: ‘newIdStr’ was declared here 543 | CharPtr newIdStr; | ^~~~~~~~ In function ‘s_DisplayRowList’, inlined from ‘Ali_Read’ at aliparse.c:2568:3: aliparse.c:760:17: warning: ‘cLineType’ may be used uninitialized [-Wmaybe-uninitialized] 760 | fprintf(stderr,"%04d: MAYBE SEQUENCE[%c] : %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 761 | seqLinePtr->rowNum, | ~~~~~~~~~~~~~~~~~~~ 762 | cLineType, | ~~~~~~~~~~ 763 | seqLinePtr->sequence); | ~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:723:20: note: ‘cLineType’ was declared here 723 | Char cLineType; | ^~~~~~~~~ In function ‘s_IsInterleaved’, inlined from ‘s_AnalyzeContents’ at aliparse.c:2004:7, inlined from ‘Ali_Read’ at aliparse.c:2572:3: aliparse.c:927:25: warning: ‘seqLinePtr’ may be used uninitialized [-Wmaybe-uninitialized] 927 | if (seqLinePtr->sequence != NULL) | ~~~~~~~~~~^~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:820:20: note: ‘seqLinePtr’ was declared here 820 | SeqLineInfoPtr seqLinePtr; | ^~~~~~~~~~ In function ‘s_AnalyzeInterleaved’, inlined from ‘s_AnalyzeContents’ at aliparse.c:2007:16, inlined from ‘Ali_Read’ at aliparse.c:2572:3: aliparse.c:1352:50: warning: ‘previousLength’ may be used uninitialized [-Wmaybe-uninitialized] 1352 | if ((s_configInfo.declaredInfo.seqLength != 0) && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 1353 | (s_configInfo.declaredInfo.seqLength != previousLength)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c: In function ‘Ali_Read’: aliparse.c:1154:20: note: ‘previousLength’ was declared here 1154 | Int4 previousLength; | ^~~~~~~~~~~~~~ aliparse.c: In function ‘ALI_ConvertToNCBIData’: aliparse.c:3276:4: warning: ‘sep_new’ may be used uninitialized [-Wmaybe-uninitialized] 3276 | SeqAlignAddInSeqEntry (sep_head, sanp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aliparse.c:2974:18: note: ‘sep_new’ was declared here 2974 | SeqEntryPtr sep_new; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF aliread.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from aliread.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/aliparse.h:15, from aliread.c:6: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF alignval.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from alignval.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignval.c: In function ‘ValidateSeqlengthInDenseSeg’: alignval.c:1267:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1267 | if(stptrtemp[j+i*aligndim]+lenptrtemp[i]>bslen) | ^ alignval.c: In function ‘PercentStringMatch’: alignval.c:1579:32: warning: variable ‘max_len’ set but not used [-Wunused-but-set-variable] 1579 | Int4 len1, len2, min_len, k, max_len; | ^~~~~~~ alignval.c: In function ‘CheckAlnSeqLens’: alignval.c:2004:12: warning: variable ‘aln_len’ set but not used [-Wunused-but-set-variable] 2004 | Int4 aln_len, start, stop; | ^~~~~~~ alignval.c: In function ‘ValidateSeqAlign’: alignval.c:2125:16: warning: variable ‘ans’ set but not used [-Wunused-but-set-variable] 2125 | MsgAnswer ans; | ^~~ alignval.c: In function ‘GetAlignmentColumnPercentIdentities’: alignval.c:2511:14: warning: variable ‘num_match’ set but not used [-Wunused-but-set-variable] 2511 | Int4 num_match; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from alignval.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignval.c:2002:13: warning: ‘CheckAlnSeqLens’ defined but not used [-Wunused-function] 2002 | static void CheckAlnSeqLens (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~ alignval.c:1560:16: warning: ‘IsSipContainedInStdseg’ defined but not used [-Wunused-function] 1560 | static Boolean IsSipContainedInStdseg(SeqIdPtr sip, StdSegPtr ssp) | ^~~~~~~~~~~~~~~~~~~~~~ alignval.c:602:13: warning: ‘delete_bioseqs’ defined but not used [-Wunused-function] 602 | static void delete_bioseqs (ValNodePtr ids, Uint2 entityID) | ^~~~~~~~~~~~~~ alignval.c: In function ‘ValMessage’: alignval.c:465:92: warning: ‘, the alignment claims to co...’ directive writing 195 bytes into a region of size between 155 and 493 [-Wformat-overflow=] 465 | sprintf(string2, "In sequence %s, segment %ld (near sequence position %ld) context %s, the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment", buf, (long) Intvalue, (long) pos, buf3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ValMessage’ at alignval.c:465:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 255 and 593 bytes into a destination of size 552 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ alignval.c: In function ‘ValMessage’: alignval.c:448:92: warning: ‘, the alignment claims to co...’ directive writing 195 bytes into a region of size between 155 and 493 [-Wformat-overflow=] 448 | sprintf(string2, "In sequence %s, segment %ld (near sequence position %ld) context %s, the alignment claims to contain residue coordinates that are past the end of the sequence. Either the sequence is too short, or there are extra characters or formatting errors in the alignment", buf, (long) Intvalue, (long) pos, buf3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘ValMessage’ at alignval.c:448:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 255 and 593 bytes into a destination of size 552 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sqnutil1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil1.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil1.c: In function ‘GeneExtendFunc’: sqnutil1.c:2012:18: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 2012 | GeneRefPtr grp; | ^~~ sqnutil1.c: In function ‘ParseAnticodon’: sqnutil1.c:3494:14: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 3494 | Uint1 strand; | ^~~~~~ sqnutil1.c: In function ‘ParseCodeBreak’: sqnutil1.c:3617:17: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 3617 | Uint1 strand; | ^~~~~~ sqnutil1.c: In function ‘CleanUpPubdescAuthors’: sqnutil1.c:9093:20: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 9093 | ValNodePtr PNTR prev; | ^~~~ sqnutil1.c: In function ‘FixWrongFuzzOnPlusStrand’: sqnutil1.c:11948:15: warning: unused variable ‘spp’ [-Wunused-variable] 11948 | SeqPntPtr spp; | ^~~ sqnutil1.c: In function ‘FixWrongFuzzOnMinusStrand’: sqnutil1.c:12007:15: warning: unused variable ‘spp’ [-Wunused-variable] 12007 | SeqPntPtr spp; | ^~~ sqnutil1.c: In function ‘ConsolidateBioSourceNotes’: sqnutil1.c:13250:21: warning: variable ‘note_mod’ set but not used [-Wunused-but-set-variable] 13250 | OrgModPtr mod, note_mod; | ^~~~~~~~ sqnutil1.c:13249:21: warning: variable ‘note_ssp’ set but not used [-Wunused-but-set-variable] 13249 | SubSourcePtr ssp, note_ssp; | ^~~~~~~~ sqnutil1.c: In function ‘RemoveUnnecessaryGeneXrefs’: sqnutil1.c:15059:24: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 15059 | Int2 count; | ^~~~~ sqnutil1.c: In function ‘LinkTwoFeatures’: sqnutil1.c:17930:25: warning: variable ‘prev_xref’ set but not used [-Wunused-but-set-variable] 17930 | SeqFeatXrefPtr xref, prev_xref, next_xref; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil1.c:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil1.c:10386:16: warning: ‘CleanUpSgml’ defined but not used [-Wunused-function] 10386 | static CharPtr CleanUpSgml ( | ^~~~~~~~~~~ sqnutil1.c:10272:13: warning: ‘SortGoTermsSfp’ defined but not used [-Wunused-function] 10272 | static void SortGoTermsSfp ( | ^~~~~~~~~~~~~~ sqnutil1.c:7405:16: warning: ‘IsStringSingleToken’ defined but not used [-Wunused-function] 7405 | static Boolean IsStringSingleToken (CharPtr str) | ^~~~~~~~~~~~~~~~~~~ sqnutil1.c:4942:13: warning: ‘CleanupConsSplice’ defined but not used [-Wunused-function] 4942 | static void CleanupConsSplice (GBQualPtr gbq) | ^~~~~~~~~~~~~~~~~ sqnutil1.c:2007:16: warning: ‘GeneExtendFunc’ defined but not used [-Wunused-function] 2007 | static Boolean GeneExtendFunc (GatherContextPtr gcp) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sqnutil2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil2.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil2.c: In function ‘FindResidueByName’: sqnutil2.c:5223:11: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 5223 | Uint1 last; | ^~~~ sqnutil2.c: In function ‘ReadFeatureTableEx’: sqnutil2.c:7254:18: warning: variable ‘isnote’ set but not used [-Wunused-but-set-variable] 7254 | Boolean isnote; | ^~~~~~ sqnutil2.c:7246:18: warning: variable ‘endsinspace’ set but not used [-Wunused-but-set-variable] 7246 | Boolean endsinspace; | ^~~~~~~~~~~ sqnutil2.c: In function ‘SeqEntryCopyReplace’: sqnutil2.c:9270:15: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 9270 | Uint1 type = 0; | ^~~~ sqnutil2.c: In function ‘StreamingReadBioseq’: sqnutil2.c:10095:10: warning: variable ‘level’ set but not used [-Wunused-but-set-variable] 10095 | Int2 level; | ^~~~~ sqnutil2.c: In function ‘StreamAsnForDescriptors’: sqnutil2.c:10328:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 10328 | while (rval = StreamingReadSeqEntry (aip, sp, &sr)) { | ^~~~ sqnutil2.c: In function ‘WriteAsnWithReplacedDescriptors’: sqnutil2.c:10749:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 10749 | while (rval = StreamingReadWriteSeqEntry(desc_stream_list, aip_in, aip_out, sp)) { | ^~~~ sqnutil2.c: In function ‘ReadFeatureTableFile’: sqnutil2.c:11700:18: warning: variable ‘begin’ set but not used [-Wunused-but-set-variable] 11700 | Int4 begin; | ^~~~~ sqnutil2.c: In function ‘ReadFastaOnly’: sqnutil2.c:11894:18: warning: variable ‘seqid’ set but not used [-Wunused-but-set-variable] 11894 | Char seqid [2048]; | ^~~~~ sqnutil2.c: In function ‘ReadDeltaFastaWithEmptyDefline’: sqnutil2.c:12446:29: warning: variable ‘seqid’ set but not used [-Wunused-but-set-variable] 12446 | Char line [4096], seqid [2048]; | ^~~~~ sqnutil2.c: In function ‘SortSeqGraphProc’: sqnutil2.c:13002:26: warning: self-comparison always evaluates to false [-Wtautological-compare] 13002 | } else if (gip2->right < gip2->right) { | ^ sqnutil2.c: In function ‘PrintQualityScoresToBuffer’: sqnutil2.c:13052:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 13052 | Uint2 entityID; | ^~~~~~~~ sqnutil2.c: In function ‘GetScoresbySeqId’: sqnutil2.c:13461:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 13461 | Uint2 entityID; | ^~~~~~~~ sqnutil2.c: In function ‘RemoveGapsFromDeltaLocation’: sqnutil2.c:15480:15: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 15480 | Uint1 strand; | ^~~~~~ sqnutil2.c: In function ‘IsStringInSpanInList’: sqnutil2.c:16693:11: warning: variable ‘str_val’ set but not used [-Wunused-but-set-variable] 16693 | Int4 str_val; | ^~~~~~~ sqnutil2.c:16691:27: warning: variable ‘suffix_len’ set but not used [-Wunused-but-set-variable] 16691 | Int4 prefix_len = 0, suffix_len; | ^~~~~~~~~~ sqnutil2.c: In function ‘CreateStructuredCommentsFromFile’: sqnutil2.c:18415:35: warning: variable ‘vnp_h’ set but not used [-Wunused-but-set-variable] 18415 | ValNodePtr table, header, line, vnp_h, vnp_l, tmp; | ^~~~~ sqnutil2.c: In function ‘AlignmentIntervalToString’: sqnutil2.c:18779:14: warning: variable ‘target_strand’ set but not used [-Wunused-but-set-variable] 18779 | Uint1 target_strand; | ^~~~~~~~~~~~~ sqnutil2.c:18778:14: warning: variable ‘seq_len’ set but not used [-Wunused-but-set-variable] 18778 | Int4 seq_len; | ^~~~~~~ sqnutil2.c: In function ‘AdjustForConsensusSpliceCallback’: sqnutil2.c:20313:33: warning: variable ‘partial5_last’ set but not used [-Wunused-but-set-variable] 20313 | Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE; | ^~~~~~~~~~~~~ sqnutil2.c: In function ‘RemoveGIProc’: sqnutil2.c:20926:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 20926 | SeqIdPtr nextid, sip; | ^~~~~~ sqnutil2.c: In function ‘RemoveBadCodonRecognizedCallback’: sqnutil2.c:22812:13: warning: variable ‘rcodon’ set but not used [-Wunused-but-set-variable] 22812 | Uint1 rcodon [4]; | ^~~~~~ sqnutil2.c: In function ‘CompareStructuredComment’: sqnutil2.c:25151:23: warning: variable ‘ovp2’ set but not used [-Wunused-but-set-variable] 25151 | ObjValNodePtr ovp1, ovp2; | ^~~~ sqnutil2.c:25151:17: warning: variable ‘ovp1’ set but not used [-Wunused-but-set-variable] 25151 | ObjValNodePtr ovp1, ovp2; | ^~~~ sqnutil2.c: In function ‘UniqueAndCountValNodeCS’: sqnutil2.c:25546:17: warning: variable ‘curr’ set but not used [-Wunused-but-set-variable] 25546 | ValNodePtr curr; | ^~~~ sqnutil2.c: In function ‘PerformArticleQuery’: sqnutil2.c:25810:20: warning: variable ‘debug_mode’ set but not used [-Wunused-but-set-variable] 25810 | Boolean debug_mode = FALSE; | ^~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil2.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil2.c:18065:19: warning: ‘AuthAffilListFree’ defined but not used [-Wunused-function] 18065 | static ValNodePtr AuthAffilListFree (ValNodePtr list) | ^~~~~~~~~~~~~~~~~ sqnutil2.c:18044:21: warning: ‘AuthAffilNew’ defined but not used [-Wunused-function] 18044 | static AuthAffilPtr AuthAffilNew (CharPtr affil) | ^~~~~~~~~~~~ sqnutil2.c:16282:19: warning: ‘MakeTranscriptomeIDTokensFromLine’ defined but not used [-Wunused-function] 16282 | static ValNodePtr MakeTranscriptomeIDTokensFromLine (CharPtr line) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil2.c:16188:13: warning: ‘RevCompFeatsOnBioseq’ defined but not used [-Wunused-function] 16188 | static void RevCompFeatsOnBioseq (BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~ sqnutil2.c:8333:16: warning: ‘DoesSeqEntryAccessionMatchList’ defined but not used [-Wunused-function] 8333 | static Boolean DoesSeqEntryAccessionMatchList (SeqEntryPtr sep, ValNodePtr accn_list) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil2.c:4684:16: warning: ‘IsNonSeqChar’ defined but not used [-Wunused-function] 4684 | static Boolean IsNonSeqChar (Char ch, Boolean is_prot) | ^~~~~~~~~~~~ sqnutil2.c: In function ‘DoAddToSecAccn’: sqnutil2.c:2429:28: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 2429 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ sqnutil2.c:2429:27: note: directive argument in the range [-2147483648, 2147483647] 2429 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DoAddToSecAccn’ at sqnutil2.c:2429:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘DoAddToSeqHist’: sqnutil2.c:2593:28: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 2593 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ sqnutil2.c:2593:27: note: directive argument in the range [-2147483648, 2147483647] 2593 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In function ‘sprintf’, inlined from ‘DoAddToSeqHist’ at sqnutil2.c:2593:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘ReplaceLocalID’: sqnutil2.c:23605:22: warning: ‘%d’ directive writing between 1 and 6 bytes into a region of size between 5 and 68 [-Wformat-overflow=] 23605 | sprintf (tmp, "%s__%d", str, (int) count); | ^~ sqnutil2.c:23605:17: note: directive argument in the range [-32768, 32767] 23605 | sprintf (tmp, "%s__%d", str, (int) count); | ^~~~~~~~ In function ‘sprintf’, inlined from ‘ReplaceLocalID’ at sqnutil2.c:23605:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 72 bytes into a destination of size 70 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil2.c: In function ‘AdjustSeqEntryForConsensusSpliceBioseqCallback’: sqnutil2.c:20313:48: warning: ‘partial3_last’ may be used uninitialized [-Wmaybe-uninitialized] 20313 | Boolean partial5, partial3, partial5_last, partial3_last, first = TRUE; | ^~~~~~~~~~~~~ sqnutil2.c: In function ‘PrintQualityScoresToBuffer’: sqnutil2.c:13110:47: warning: ‘, Max: ’ directive writing 7 bytes into a region of size between 2 and 63 [-Wformat-overflow=] 13110 | sprintf (buf, ">%s %s (Length: %ld, Min: %ld, Max: %ld)\n", id, title, | ^~~~~~~ sqnutil2.c:13110:17: note: directive argument in the range [-2147483647, 2147483647] 13110 | sprintf (buf, ">%s %s (Length: %ld, Min: %ld, Max: %ld)\n", id, title, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintQualityScoresToBuffer’ at sqnutil2.c:13110:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 32 or more bytes (assuming 103) into a destination of size 84 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sqnutil3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil3.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil3.c: In function ‘BspLinkCDSmRNAbyOverlap’: sqnutil3.c:528:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 528 | Int2 count; | ^~~~~ sqnutil3.c: In function ‘CautiousSeqEntryCleanup’: sqnutil3.c:2178:16: warning: variable ‘taxserver’ set but not used [-Wunused-but-set-variable] 2178 | Boolean taxserver; | ^~~~~~~~~ sqnutil3.c: In function ‘AddGapSeqLit’: sqnutil3.c:3127:19: warning: unused variable ‘gap_chars’ [-Wunused-variable] 3127 | CharPtr gap_chars = "NNNNNNNNNN" | ^~~~~~~~~ sqnutil3.c: In function ‘ConvertSegSetsToDeltaSequencesInt’: sqnutil3.c:3382:26: warning: variable ‘prev_sep’ set but not used [-Wunused-but-set-variable] 3382 | SeqEntryPtr sub_sep, prev_sep, next_sep; | ^~~~~~~~ sqnutil3.c: In function ‘MakeSequinDataFromAlignmentEx’: sqnutil3.c:4797:32: warning: variable ‘num_sets’ set but not used [-Wunused-but-set-variable] 4797 | Int4 index, curr_seg, num_sets; | ^~~~~~~~ sqnutil3.c:4791:26: warning: variable ‘salp_last’ set but not used [-Wunused-but-set-variable] 4791 | SeqAlignPtr salp_list, salp_last; | ^~~~~~~~~ sqnutil3.c:4791:15: warning: variable ‘salp_list’ set but not used [-Wunused-but-set-variable] 4791 | SeqAlignPtr salp_list, salp_last; | ^~~~~~~~~ sqnutil3.c: In function ‘ConvertContainedCDSToMiscFeat’: sqnutil3.c:12824:14: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 12824 | Uint1 strand; | ^~~~~~ sqnutil3.c: In function ‘OrgNameMatchExceptOldName’: sqnutil3.c:13713:28: warning: self-comparison always evaluates to false [-Wtautological-compare] 13713 | || onp2->mgcode != onp2->mgcode | ^~ sqnutil3.c: In function ‘FindMismatchedCitSubAffiliations’: sqnutil3.c:19281:14: warning: variable ‘has_seq_submit’ set but not used [-Wunused-but-set-variable] 19281 | Boolean has_seq_submit = TRUE; | ^~~~~~~~~~~~~~ sqnutil3.c: In function ‘GetCDSformRNA’: sqnutil3.c:20267:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 20267 | Int2 count; | ^~~~~ sqnutil3.c: In function ‘FindTextInFlatfileOncaller’: sqnutil3.c:22140:19: warning: variable ‘okay’ set but not used [-Wunused-but-set-variable] 22140 | Boolean okay; | ^~~~ sqnutil3.c: In function ‘CheckForTitleAuthorConflicts’: sqnutil3.c:23168:14: warning: variable ‘author_conflict’ set but not used [-Wunused-but-set-variable] 23168 | Boolean author_conflict = FALSE; | ^~~~~~~~~~~~~~~ sqnutil3.c: In function ‘SortVnpByBspProjectId’: sqnutil3.c:26956:31: warning: the comparison will always evaluate as ‘true’ for the address of ‘vnp2’ will never be NULL [-Waddress] 26956 | if (vnp1 != NULL &&& vnp2 != NULL) { | ^~ sqnutil3.c:26948:15: note: ‘vnp2’ declared here 26948 | ValNodePtr vnp2; | ^~~~ sqnutil3.c: In function ‘GetDiscrepancyItemTextEx’: sqnutil3.c:31033:21: warning: variable ‘special_flag’ set but not used [-Wunused-but-set-variable] 31033 | Boolean special_flag = FALSE; | ^~~~~~~~~~~~ sqnutil3.c: In function ‘CollectionDateIsInTheFuture’: sqnutil3.c:34586:20: warning: variable ‘time’ set but not used [-Wunused-but-set-variable] 34586 | CharPtr str, time; | ^~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sqnutil3.c:62: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35189:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35189 | system (cmmd); | ^~~~~~~~~~~~~ sqnutil3.c: At top level: sqnutil3.c:36777:13: warning: ‘TestLatLonFormatting’ defined but not used [-Wunused-function] 36777 | static void TestLatLonFormatting (FILE *fp) | ^~~~~~~~~~~~~~~~~~~~ sqnutil3.c:34406:22: warning: ‘BetterDateFree’ defined but not used [-Wunused-function] 34406 | static BetterDatePtr BetterDateFree (BetterDatePtr dp) | ^~~~~~~~~~~~~~ sqnutil3.c:33998:16: warning: ‘GetColon’ defined but not used [-Wunused-function] 33998 | static CharPtr GetColon (CharPtr str) | ^~~~~~~~ sqnutil3.c:17224:24: warning: ‘IntervalPairFree’ defined but not used [-Wunused-function] 17224 | static IntervalPairPtr IntervalPairFree (IntervalPairPtr i) | ^~~~~~~~~~~~~~~~ sqnutil3.c:10883:16: warning: ‘IsMitochondrionBioseq’ defined but not used [-Wunused-function] 10883 | static Boolean IsMitochondrionBioseq(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35188:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 252 [-Wformat-overflow=] 35188 | sprintf (cmmd, "%s -i %s -o %s", tracefetchcmd, path_in, path_out); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FillInMissingTraces’ at sqnutil3.c:35188:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 9 or more bytes (assuming 8199) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil3.c: In function ‘FillInMissingTraces’: sqnutil3.c:35188:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 252 [-Wformat-overflow=] 35188 | sprintf (cmmd, "%s -i %s -o %s", tracefetchcmd, path_in, path_out); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘FillInMissingTraces’ at sqnutil3.c:35188:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 9 or more bytes (assuming 8199) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sqnutil3.c: In function ‘tRNASameStrandBioseqCallback’: sqnutil3.c:16757:19: warning: ‘strand’ may be used uninitialized [-Wmaybe-uninitialized] 16757 | if ((strand == Seq_strand_minus && this_strand != Seq_strand_minus) sqnutil3.c:16728:22: note: ‘strand’ was declared here 16728 | Uint1 strand, this_strand; | ^~~~~~ sqnutil3.c: In function ‘CheckForDivConflicts’: sqnutil3.c:8137:21: warning: ‘sdp’ may be used uninitialized [-Wmaybe-uninitialized] 8137 | ValNodeAddPointer(&(grp_sdp_sfp[i]), OBJ_SEQDESC, sdp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil3.c:8087:17: note: ‘sdp’ was declared here 8087 | SeqDescrPtr sdp; | ^~~ sqnutil3.c:8138:15: warning: ‘sfp’ may be used uninitialized [-Wmaybe-uninitialized] 8138 | else ValNodeAddPointer(&(grp_sdp_sfp[i]), OBJ_SEQFEAT, sfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil3.c:8088:17: note: ‘sfp’ was declared here 8088 | SeqFeatPtr sfp; | ^~~ sqnutil3.c: In function ‘FindMismatchedComments’: sqnutil3.c:26612:47: warning: ‘sdp’ may be used uninitialized [-Wmaybe-uninitialized] 26612 | sprintf (fmt, sub_fmt, (CharPtr) sdp->data.ptrvalue); | ~~~~~~~~~^~~~~~~~~ sqnutil3.c:26580:15: note: ‘sdp’ was declared here 26580 | SeqDescrPtr sdp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sqnutil4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/sqnutils.h:48, from sqnutil4.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sqnutil4.c: In function ‘ListClauses’: sqnutil4.c:8566:43: warning: variable ‘twobefore’ set but not used [-Wunused-but-set-variable] 8566 | FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter; | ^~~~~~~~~ sqnutil4.c: In function ‘SmashOneTallClause’: sqnutil4.c:9900:20: warning: variable ‘subclause_featlist’ set but not used [-Wunused-but-set-variable] 9900 | ValNodePtr subclause_featlist; | ^~~~~~~~~~~~~~~~~~ sqnutil4.c: In function ‘GetFeatureClauseForSeg’: sqnutil4.c:10787:21: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 10787 | Int4 start, stop; | ^~~~~ sqnutil4.c: In function ‘RemoveAutodefObjectsForDesc’: sqnutil4.c:13618:18: warning: unused variable ‘bssp’ [-Wunused-variable] 13618 | BioseqSetPtr bssp; | ^~~~ sqnutil4.c:13617:15: warning: unused variable ‘bsp’ [-Wunused-variable] 13617 | BioseqPtr bsp; | ^~~ sqnutil4.c: In function ‘ConvertProtToImpFunc’: sqnutil4.c:15072:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 15072 | Uint2 entityID; | ^~~~~~~~ sqnutil4.c: In function ‘ExtraCDSCreationActions’: sqnutil4.c:15989:28: warning: variable ‘nsep’ set but not used [-Wunused-but-set-variable] 15989 | SeqEntryPtr psep, nsep; | ^~~~ sqnutil4.c: In function ‘TESTDisplayQualCombo’: sqnutil4.c:17099:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 17099 | Int4 val; | ^~~ sqnutil4.c: In function ‘ConvertCDSToMatPeptideForOverlappingCDS’: sqnutil4.c:18589:15: warning: variable ‘crp’ set but not used [-Wunused-but-set-variable] 18589 | CdRegionPtr crp; | ^~~ sqnutil4.c: In function ‘AddNewUniqueAnnotations’: sqnutil4.c:18780:39: warning: variable ‘sap_tmp_next’ set but not used [-Wunused-but-set-variable] 18780 | SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap; | ^~~~~~~~~~~~ sqnutil4.c: In function ‘AssignBioseqToLineageGroup’: sqnutil4.c:19443:27: warning: variable ‘vnp_last’ set but not used [-Wunused-but-set-variable] 19443 | ValNodePtr list, vnp, vnp_last = NULL; | ^~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from sqnutil4.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sqnutil4.c:64: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sqnutil4.c:17248:13: warning: ‘TESTDisplayList’ defined but not used [-Wunused-function] 17248 | static void TESTDisplayList (ValNodePtr new_list) | ^~~~~~~~~~~~~~~ sqnutil4.c:17219:19: warning: ‘ExpandOneComboListUsingAllPresentQuals’ defined but not used [-Wunused-function] 17219 | static ValNodePtr ExpandOneComboListUsingAllPresentQuals (QualComboPtr q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil4.c:16930:16: warning: ‘RemoveFieldFromUniqBioSrcGrpList’ defined but not used [-Wunused-function] 16930 | static Boolean RemoveFieldFromUniqBioSrcGrpList (ValNodePtr list, FieldTypePtr field) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sqnutil4.c:10029:19: warning: ‘RemoveAllButLastCDS’ defined but not used [-Wunused-function] 10029 | static ValNodePtr RemoveAllButLastCDS ( | ^~~~~~~~~~~~~~~~~~~ sqnutil4.c:9998:13: warning: ‘SmashTallClauses’ defined but not used [-Wunused-function] 9998 | static void SmashTallClauses ( | ^~~~~~~~~~~~~~~~ sqnutil4.c:9834:13: warning: ‘RemoveFeats’ defined but not used [-Wunused-function] 9834 | static void RemoveFeats ( | ^~~~~~~~~~~ sqnutil4.c:5211:13: warning: ‘CountFeatures’ defined but not used [-Wunused-function] 5211 | static Int4 CountFeatures ( | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF subutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from ../include/subutil.h:50, from subutil.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ subutil.c: In function ‘AddSeqLitToBioseq’: subutil.c:769:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 769 | ValNodePtr vnp; | ^~~ subutil.c: In function ‘AddReferenceToSegmentedEntry’: subutil.c:1163:22: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 1163 | SeqEntryPtr tmp, prev; | ^~~~ subutil.c: In function ‘GetDNAConv’: subutil.c:1624:16: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1624 | dnaconv[*ptr] = *ptr; | ^~~~ subutil.c: In function ‘GetProteinConv’: subutil.c:1646:17: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1646 | protconv[*ptr] = *ptr; | ^~~~ subutil.c: In function ‘AddBasesToByteStore’: subutil.c:1669:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1669 | residue = dnaconv[ch]; | ^ subutil.c: In function ‘AddAAsToByteStore’: subutil.c:1700:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1700 | residue = aaconv[ch]; | ^ subutil.c: In function ‘CitArtBuild’: subutil.c:2683:21: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 2683 | ValNodePtr vnp, tmp; | ^~~ subutil.c: In function ‘MakeRNAFeature’: subutil.c:3639:29: warning: comparison between pointer and zero character constant [-Wpointer-compare] 3639 | if (AA_for_tRNA != '\0') | ^~ subutil.c:3639:17: note: did you mean to dereference the pointer? 3639 | if (AA_for_tRNA != '\0') | ^ subutil.c: At top level: subutil.c:3546:20: warning: ‘TranslateCdRegionNew’ defined but not used [-Wunused-function] 3546 | static SeqEntryPtr TranslateCdRegionNew ( | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF edutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/edutil.h:188, from edutil.c:365: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ edutil.c: In function ‘SeqLocsToDeltaSeqs’: edutil.c:795:14: warning: variable ‘sip’ set but not used [-Wunused-but-set-variable] 795 | SeqIdPtr sip; | ^~~ edutil.c: In function ‘SeqLocCopyPart’: edutil.c:2243:13: warning: variable ‘done’ set but not used [-Wunused-but-set-variable] 2243 | Boolean done, started, wasa_null, hada_null; | ^~~~ edutil.c: In function ‘IndexedSeqFeatsCopy’: edutil.c:2400:16: warning: variable ‘region’ set but not used [-Wunused-but-set-variable] 2400 | ValNodePtr region; | ^~~~~~ edutil.c: In function ‘SeqFeatsCopy’: edutil.c:2504:16: warning: variable ‘region’ set but not used [-Wunused-but-set-variable] 2504 | ValNodePtr region; | ^~~~~~ edutil.c: In function ‘SeqLocInsert’: edutil.c:3686:10: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 3686 | Int4 diff, numpnt, i, tpos; | ^~~~ edutil.c: In function ‘SeqEdRecreateDeletedFeats’: edutil.c:4212:19: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 4212 | SeqFeatPtr sfp; | ^~~ edutil.c: In function ‘SeqEdSeqLocInsert’: edutil.c:4512:8: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 4512 | Int4 diff, numpnt, i, tpos; | ^~~~ edutil.c: In function ‘SeqEdSeqLocDelete’: edutil.c:5069:10: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 5069 | Int4 diff; | ^~~~ edutil.c: In function ‘SeqEdInsertAdjustFeat’: edutil.c:5300:7: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 5300 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c: In function ‘SeqEdDeleteFromBsp’: edutil.c:6485:11: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6485 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c:6548:11: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 6548 | && sfp->data.choice == SEQFEAT_CDREGION) edutil.c:6437:21: warning: variable ‘merge_mode’ set but not used [-Wunused-but-set-variable] 6437 | Boolean merge_mode; | ^~~~~~~~~~ edutil.c:6428:21: warning: variable ‘feats_altered’ set but not used [-Wunused-but-set-variable] 6428 | Boolean feats_altered = FALSE; | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from asn2ff1.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff1.c: In function ‘asn2ff_print’: asn2ff1.c:289:25: warning: unused variable ‘dsp’ [-Wunused-variable] 289 | DescrStructPtr dsp = NULL; | ^~~ asn2ff1.c: In function ‘Asn2ffJobCreate’: asn2ff1.c:351:25: warning: unused variable ‘itemID’ [-Wunused-variable] 351 | Uint4 itemID = 0; | ^~~~~~ asn2ff1.c: In function ‘SeqEntryToEntrez’: asn2ff1.c:498:41: warning: unused variable ‘slp’ [-Wunused-variable] 498 | SeqLocPtr slp = NULL; | ^~~ asn2ff1.c: In function ‘SeqLocToFlat’: asn2ff1.c:1518:26: warning: unused variable ‘itemID’ [-Wunused-variable] 1518 | Uint4 itemID=0; | ^~~~~~ asn2ff1.c: In function ‘asn2ff_setup’: asn2ff1.c:1579:19: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 1579 | BioseqPtr bsp; | ^~~ asn2ff1.c: In function ‘PrintStatusLine’: asn2ff1.c:2197:36: warning: unused variable ‘ptr’ [-Wunused-variable] 2197 | CharPtr u, ptr=NULL; | ^~~ asn2ff1.c: In function ‘asn2gb_setup’: asn2ff1.c:2403:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2403 | if (ajp->genome_view && gbp->map == FALSE || ajp->contig_view) { asn2ff1.c: At top level: asn2ff1.c:2189:13: warning: ‘PrintStatusLine’ defined but not used [-Wunused-function] 2189 | static void PrintStatusLine(Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~~~~~~ asn2ff1.c:2171:16: warning: ‘find_user_object’ defined but not used [-Wunused-function] 2171 | static Boolean find_user_object(BioseqPtr bsp) | ^~~~~~~~~~~~~~~~ asn2ff1.c:816:19: warning: ‘SeqEntryToLinkStrEx’ defined but not used [-Wunused-function] 816 | static LinkStrPtr SeqEntryToLinkStrEx(Asn2ffJobPtr ajp, SeqEntryPtr sep, LinkStrPtr lsp, Uint1 format) | ^~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from asn2ff1.c:45: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff1.c: In function ‘print_taxinfo’: asn2ff1.c:4356:33: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 4356 | sprintf(tmp, "%d", gcode); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘print_taxinfo’ at asn2ff1.c:4356:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff1.c: In function ‘asn2embl_setup’: asn2ff1.c:2753:36: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized] 2753 | for (index=0; index< max; index++) { | ~~~~~^~~~~ asn2ff1.c:2642:21: note: ‘max’ was declared here 2642 | Int4 index, max, total, pub_num, seqblks_num; | ^~~ asn2ff1.c: In function ‘asn2gp_setup’: asn2ff1.c:2942:45: warning: ‘feat_num’ may be used uninitialized [-Wmaybe-uninitialized] 2942 | for (index=0; index < feat_num; index++) { | ~~~~~~^~~~~~~~~~ asn2ff1.c:2795:14: note: ‘feat_num’ was declared here 2795 | Int4 feat_num; | ^~~~~~~~ asn2ff1.c: In function ‘SeqEntryToGBFlatNoSeq’: asn2ff1.c:1307:20: warning: ‘rsult’ may be used uninitialized [-Wmaybe-uninitialized] 1307 | return rsult; | ^~~~~ asn2ff1.c:1292:19: note: ‘rsult’ was declared here 1292 | Boolean rsult; | ^~~~~ asn2ff1.c: In function ‘PrintSequence’: asn2ff1.c:5218:67: warning: ‘%9ld’ directive writing between 9 and 11 bytes into a region of size 10 [-Wformat-overflow=] 5218 | sprintf(num_ptr, "%9ld", (long) (total+1 - loc_start)); | ^~~~ asn2ff1.c:5218:66: note: directive argument in the range [-2147483648, 2147483647] 5218 | sprintf(num_ptr, "%9ld", (long) (total+1 - loc_start)); | ^~~~~~ In function ‘sprintf’, inlined from ‘PrintSequence’ at asn2ff1.c:5218:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 10 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from asn2ff2.c:216: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff2.c: In function ‘GetStrForBankit’: asn2ff2.c:518:33: warning: unused variable ‘i’ [-Wunused-variable] 518 | Int2 i=0, ptrlen = 0; | ^ asn2ff2.c: In function ‘GetCommentByChoice’: asn2ff2.c:769:41: warning: unused variable ‘string’ [-Wunused-variable] 769 | CharPtr buf = NULL, ptr = NULL, string=NULL, new_string=NULL, str=NULL; | ^~~~~~ asn2ff2.c: In function ‘GP_GetSeqDescrComms’: asn2ff2.c:1163:17: warning: unused variable ‘got_comment’ [-Wunused-variable] 1163 | Boolean got_comment=FALSE; | ^~~~~~~~~~~ asn2ff2.c: At top level: asn2ff2.c:1358:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 1358 | static ChoicePID(SeqIdPtr sid) | ^~~~~~~~~ asn2ff2.c: In function ‘GetGibbsqCommentLength’: asn2ff2.c:1600:14: warning: unused variable ‘gibbsq’ [-Wunused-variable] 1600 | Int4 gibbsq=0, total; | ^~~~~~ asn2ff2.c: In function ‘GatherDescrByChoice’: asn2ff2.c:1864:15: warning: variable ‘bspID’ set but not used [-Wunused-but-set-variable] 1864 | Uint2 bspID; | ^~~~~ asn2ff2.c: At top level: asn2ff2.c:1190:16: warning: ‘GetSPBlock’ defined but not used [-Wunused-function] 1190 | static CharPtr GetSPBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~ asn2ff2.c:680:16: warning: ‘GetEvidence’ defined but not used [-Wunused-function] 680 | static CharPtr GetEvidence(Asn2ffJobPtr ajp, GBEntryPtr gbp) | ^~~~~~~~~~~ asn2ff2.c:232:16: warning: ‘has_comment’ defined but not used [-Wunused-variable] 232 | static Boolean has_comment; | ^~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from asn2ff2.c:218: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff2.c: In function ‘GetCommentByChoice’: asn2ff2.c:829:36: warning: ‘is_other’ may be used uninitialized [-Wmaybe-uninitialized] 829 | if (is_other == TRUE && mfp->completeness) { | ^ asn2ff2.c:772:17: note: ‘is_other’ was declared here 772 | Boolean is_other; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff3.c:39: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff3.c: In function ‘PutGeneFirst’: asn2ff3.c:1073:33: warning: unused variable ‘qual_temp’ [-Wunused-variable] 1073 | GBQualPtr gbqual, qual, qual_temp=NULL, qual_gene=NULL; | ^~~~~~~~~ asn2ff3.c:1072:17: warning: unused variable ‘still_looking’ [-Wunused-variable] 1072 | Boolean still_looking=TRUE; | ^~~~~~~~~~~~~ asn2ff3.c: In function ‘mRNAEvidenceComment’: asn2ff3.c:1157:33: warning: unused variable ‘Locus_id’ [-Wunused-variable] 1157 | Int4 Locus_id = 0; | ^~~~~~~~ asn2ff3.c: In function ‘Add_gene_id’: asn2ff3.c:2717:31: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘Nlm_VoidPtr’ {aka ‘void *’} [-Wformat=] 2717 | sprintf(val, "GeneID:%s", vnp->data.ptrvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | char * Nlm_VoidPtr {aka void *} | %p asn2ff3.c: In function ‘Add_trid’: asn2ff3.c:3123:16: warning: unused variable ‘gi’ [-Wunused-variable] 3123 | BIG_ID gi = -1; | ^~ asn2ff3.c: At top level: asn2ff3.c:2702:13: warning: ‘Add_gene_id’ defined but not used [-Wunused-function] 2702 | static void Add_gene_id (GeneStructPtr gsp, SeqFeatPtr sfp_out) | ^~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff3.c: In function ‘Add_dbxref’: asn2ff3.c:269:24: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 269 | if (val[0] != '\0') { | ~~~^~~ asn2ff3.c:216:17: note: ‘val’ was declared here 216 | CharPtr val; | ^~~ asn2ff3.c: In function ‘GettRNAaa’: asn2ff3.c:1618:28: warning: ‘seq_code’ may be used uninitialized [-Wmaybe-uninitialized] 1618 | if ((table=SeqCodeTableFind (seq_code)) != NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2ff3.c:1596:15: note: ‘seq_code’ was declared here 1596 | Uint1 seq_code; | ^~~~~~~~ In file included from ../include/ncbi.h:62: asn2ff3.c: In function ‘mRNAEvidenceComment’: ../include/ncbistr.h:331:25: warning: ‘ne_name’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen asn2ff3.c:1153:53: note: ‘ne_name’ was declared here 1153 | CharPtr method = NULL, ptr, ne_name; | ^~~~~~~ asn2ff3.c: In function ‘ConvertToNAImpFeat’: asn2ff3.c:2254:51: warning: ‘%ld’ directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=] 2254 | sprintf(buf_ptr, "%ld", (long) (cdr->frame)); | ^~~ asn2ff3.c:2254:50: note: directive argument in the range [1, 255] 2254 | sprintf(buf_ptr, "%ld", (long) (cdr->frame)); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ConvertToNAImpFeat’ at asn2ff3.c:2254:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 2 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff4.c:273: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff4.c: In function ‘FlatLocPoint’: asn2ff4.c:437:22: warning: variable ‘order’ set but not used [-Wunused-but-set-variable] 437 | static Uint1 order[NUM_SEQID]; | ^~~~~ asn2ff4.c: In function ‘FlatLocElement’: asn2ff4.c:778:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 778 | if (ASN2FF_SHOW_ERROR_MSG == TRUE) | ^~ asn2ff4.c:781:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 781 | break; | ^~~~~ asn2ff4.c: In function ‘do_FlatLoc’: asn2ff4.c:1122:28: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1122 | if ( ! FlatVirtLoc( bsp, slp)) | ^ asn2ff4.c: At top level: asn2ff4.c:1347:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 1347 | static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2) | ^~~~~~~~~~ asn2ff4.c: In function ‘CreateImpFeatFromProt’: asn2ff4.c:1659:33: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 1659 | GeneRefPtr grp; | ^~~ asn2ff4.c: In function ‘is_embl’: asn2ff4.c:2069:43: warning: the comparison will always evaluate as ‘false’ for the address of ‘accession’ will never be NULL [-Waddress] 2069 | if (gbp == NULL || gbp->accession == NULL) | ^~ ../include/asn2ffg.h:339:14: note: ‘accession’ declared here 339 | Char accession[60]; /* primary accession */ | ^~~~~~~~~ asn2ff4.c: In function ‘MatchNAGeneToFeat’: asn2ff4.c:2196:25: warning: variable ‘nsp’ set but not used [-Wunused-but-set-variable] 2196 | NoteStructPtr nsp; /* UNUSED */ | ^~~ asn2ff4.c: In function ‘MatchAAGeneToFeat’: asn2ff4.c:2367:33: warning: variable ‘nsp’ set but not used [-Wunused-but-set-variable] 2367 | NoteStructPtr nsp; /* UNUSED */ | ^~~ asn2ff4.c: In function ‘SortOrganizeFeat’: asn2ff4.c:2457:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2457 | if (ofp == NULL) | ^~ asn2ff4.c:2459:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2459 | if (ofp->sfpListsize > 0 && ofp->sortListsize < ofp->sfpListsize) { | ^~ asn2ff4.c: In function ‘OrganizeSeqFeat’: asn2ff4.c:2578:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2578 | if (ajp->ignore_top) | ^~ asn2ff4.c:2580:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2580 | gsc.seglevels = 1; | ^~~ asn2ff4.c: In function ‘GetSeqFeat’: asn2ff4.c:2660:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘locus’ will never be NULL [-Waddress] 2660 | if (gbp->locus) { | ^~~ ../include/asn2ffg.h:338:14: note: ‘locus’ declared here 338 | Char locus[25]; /* locus */ | ^~~~~ asn2ff4.c:2664:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘accession’ will never be NULL [-Waddress] 2664 | if (gbp->accession) { | ^~~ ../include/asn2ffg.h:339:14: note: ‘accession’ declared here 339 | Char accession[60]; /* primary accession */ | ^~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h: At top level: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff4.c: In function ‘CheckNewSfpLoc’: asn2ff4.c:1766:13: warning: ‘slp’ may be used uninitialized [-Wmaybe-uninitialized] 1766 | if (SeqIdForSameBioseq(SeqLocId(slp), bsp->id)) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2ff4.c:1761:19: note: ‘slp’ was declared here 1761 | SeqLocPtr slp, slp1 = NULL; | ^~~ asn2ff4.c: In function ‘CreateImpFeatFromProt’: asn2ff4.c:1723:39: warning: ‘%d’ directive writing between 1 and 3 bytes into a region of size 2 [-Wformat-overflow=] 1723 | sprintf(buf, "%d", cdr->frame); | ^~ asn2ff4.c:1723:38: note: directive argument in the range [1, 255] 1723 | sprintf(buf, "%d", cdr->frame); | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘CreateImpFeatFromProt’ at asn2ff4.c:1723:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 2 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff4.c: In function ‘FlatLocHalfCaret’: asn2ff4.c:388:63: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 2 and 22 [-Wformat-overflow=] 388 | sprintf(localbuf,"(%ld.%ld)..(%ld.%ld)", | ^~~ asn2ff4.c:388:50: note: directive argument in the range [-2147483648, 2147483647] 388 | sprintf(localbuf,"(%ld.%ld)..(%ld.%ld)", | ^~~~~~~~~~~~~~~~~~~~~~ asn2ff4.c:388:50: note: directive argument in the range [-2147483648, 2147483647] In function ‘sprintf’, inlined from ‘FlatLocHalfCaret’ at asn2ff4.c:388:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 53 bytes into a destination of size 30 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from asn2ff5.c:177: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff5.c: In function ‘format_cit_sub’: asn2ff5.c:1023:78: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1023 | format == EMBLPEPT_FMT && afp->choice == 1) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ asn2ff5.c:926:41: warning: variable ‘need_space’ set but not used [-Wunused-but-set-variable] 926 | Boolean need_comma = FALSE, /*UNUSED*/need_space = TRUE; | ^~~~~~~~~~ asn2ff5.c: In function ‘format_thesis’: asn2ff5.c:1213:27: warning: variable ‘embl_format’ set but not used [-Wunused-but-set-variable] 1213 | Boolean /*UNUSED*/embl_format = FALSE; | ^~~~~~~~~~~ asn2ff5.c: In function ‘format_book’: asn2ff5.c:1296:17: warning: variable ‘embl_format’ set but not used [-Wunused-but-set-variable] 1296 | Boolean embl_format = FALSE; | ^~~~~~~~~~~ asn2ff5.c: In function ‘format_jourarticle’: asn2ff5.c:1680:28: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1680 | if (ip->pages != NULL) | ^ asn2ff5.c: In function ‘StripParanthesis’: asn2ff5.c:2124:33: warning: value computed is not used [-Wunused-value] 2124 | temp++; *ptr_in++; | ^~~~~~~~~ asn2ff5.c: In function ‘PostARefErrMessage’: asn2ff5.c:3005:27: warning: variable ‘ignore_this’ set but not used [-Wunused-but-set-variable] 3005 | Boolean /*UNUSED*/ignore_this, submit=FALSE, error; | ^~~~~~~~~~~ asn2ff5.c: At top level: asn2ff5.c:188:26: warning: ‘GetSubmitterName’ declared ‘static’ but never defined [-Wunused-function] 188 | static CharPtr /*UNUSED*/GetSubmitterName PROTO ((Uint1 format, ValNodePtr pub)); | ^~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff5.c: In function ‘CheckPubs’: asn2ff5.c:2768:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 2768 | if (status < 0) | ^ asn2ff5.c:2746:24: note: ‘status’ was declared here 2746 | Int2 retval=0, status; | ^~~~~~ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1121:40: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1121 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1121:37: note: directive argument in the range [1, 2147483647] 1121 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘format_patent’ at asn2ff5.c:1121:4, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1115:40: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1115 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1115:37: note: directive argument in the range [1, 2147483647] 1115 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘format_patent’ at asn2ff5.c:1115:4, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘format_patent’, inlined from ‘FlatJournal’ at asn2ff5.c:827:17: asn2ff5.c:1140:31: warning: ‘afp’ may be used uninitialized [-Wmaybe-uninitialized] 1140 | if (ap == NULL || afp == NULL) { | ^ asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1051:18: note: ‘afp’ was declared here 1051 | AffilPtr afp; | ^~~ In file included from ../include/ncbi.h:62: In function ‘format_general’, inlined from ‘FlatJournal’ at asn2ff5.c:844:17: ../include/ncbistr.h:349:25: warning: ‘temp’ may be used uninitialized [-Wmaybe-uninitialized] 349 | #define StringMove Nlm_StringMove asn2ff5.c: In function ‘FlatJournal’: asn2ff5.c:1946:23: note: ‘temp’ was declared here 1946 | CharPtr affil=NULL, temp, dup_pages=NULL, retval=NULL; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2ff6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ff6.h:134, from asn2ff6.c:347: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff6.c: In function ‘AddGBQual’: asn2ff6.c:1327:25: warning: variable ‘note’ set but not used [-Wunused-but-set-variable] 1327 | GBQualPtr curq, note = NULL; | ^~~~ asn2ff6.c: In function ‘FlatOrganelle’: asn2ff6.c:1483:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1483 | if (! retval ) | ^~ asn2ff6.c:1486:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1486 | break; | ^~~~~ asn2ff6.c: In function ‘BioseqGetGBDivCodeEx’: asn2ff6.c:1700:30: warning: variable ‘diff’ set but not used [-Wunused-but-set-variable] 1700 | Int2 tech, /*UNUSED*/diff, retval = 0; | ^~~~ asn2ff6.c: In function ‘GR_PrintPubs’: asn2ff6.c:2297:48: warning: unused variable ‘stop’ [-Wunused-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~ asn2ff6.c:2297:39: warning: unused variable ‘start’ [-Wunused-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~~ asn2ff6.c:2297:20: warning: variable ‘pmid’ set but not used [-Wunused-but-set-variable] 2297 | Int4 muid, pmid, pat_seqid=0, start=0, stop=0; | ^~~~ asn2ff6.c:2296:17: warning: unused variable ‘descr’ [-Wunused-variable] 2296 | CharPtr descr = NULL; | ^~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2786:24: warning: variable ‘base_locus_max’ set but not used [-Wunused-but-set-variable] 2786 | Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits; | ^~~~~~~~~~~~~~ asn2ff6.c: In function ‘ValidateOtherAccession’: asn2ff6.c:2886:36: warning: unused variable ‘FiveNum’ [-Wunused-variable] 2886 | Boolean FirstLetter=FALSE, FiveNum = FALSE; | ^~~~~~~ asn2ff6.c:2886:17: warning: unused variable ‘FirstLetter’ [-Wunused-variable] 2886 | Boolean FirstLetter=FALSE, FiveNum = FALSE; | ^~~~~~~~~~~ asn2ff6.c: In function ‘AddExtraAccessions’: asn2ff6.c:3498:27: warning: variable ‘ncbi’ set but not used [-Wunused-but-set-variable] 3498 | Boolean /*UNUSED*/ncbi = FALSE; | ^~~~ asn2ff6.c: At top level: asn2ff6.c:2883:13: warning: ‘ValidateOtherAccession’ defined but not used [-Wunused-function] 2883 | static Int2 ValidateOtherAccession(CharPtr new_buf, CharPtr orig_buf) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2866:61: warning: ‘%ld’ directive writing between 1 and 6 bytes into a region of size 4 [-Wformat-overflow=] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^~~ asn2ff6.c:2866:60: note: directive argument in the range [-32768, 32767] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ValidateLocus’ at asn2ff6.c:2866:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 7 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2ff6.c: In function ‘ValidateLocus’: asn2ff6.c:2866:54: warning: ‘exp’ may be used uninitialized [-Wmaybe-uninitialized] 2866 | sprintf(buf_ext+num_of_digits-exp, "%ld", (long) num_seg); | ^ asn2ff6.c:2786:51: note: ‘exp’ was declared here 2786 | Int2 /*UNUSED*/base_locus_max, buf_index, exp, length, num_of_digits; | ^~~ asn2ff6.c: In function ‘MakeBaseLocusAwp’: asn2ff6.c:3093:45: warning: ‘num_of_digits’ may be used uninitialized [-Wmaybe-uninitialized] 3093 | base_locus_max = MAX_LOCUS_NAME_LEN - num_of_digits; asn2ff6.c:3070:56: note: ‘num_of_digits’ was declared here 3070 | Int2 index, length, base_locus_max, name_len, num_of_digits, num_seg; | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb1.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb1.c: In function ‘IsWholeWordSubstr’: asn2gnb1.c:2202:19: warning: variable ‘right’ set but not used [-Wunused-but-set-variable] 2202 | Boolean left, right; | ^~~~~ asn2gnb1.c: In function ‘s_LocusGetBaseName’: asn2gnb1.c:2350:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 2350 | else | ^~~~ asn2gnb1.c:2352:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 2352 | newLength = segNameLen - deleteChars; | ^~~~~~~~~ asn2gnb1.c: In function ‘DoOneSection’: asn2gnb1.c:2522:24: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 2522 | IntAsn2gbSectPtr iasp; | ^~~~ asn2gnb1.c:2514:24: warning: variable ‘bkmask’ set but not used [-Wunused-but-set-variable] 2514 | BlockMask bkmask; | ^~~~~~ asn2gnb1.c: In function ‘Count2Seg’: asn2gnb1.c:3438:18: warning: variable ‘to’ set but not used [-Wunused-but-set-variable] 3438 | Int4 to; | ^~ asn2gnb1.c:3436:18: warning: variable ‘parent’ set but not used [-Wunused-but-set-variable] 3436 | BioseqPtr parent; | ^~~~~~ asn2gnb1.c: At top level: asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] 3714 | static ModeFlags flagTable [] = { | ^ asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c:3714:33: warning: missing braces around initializer [-Wmissing-braces] asn2gnb1.c: In function ‘SeqIdWriteForTable’: asn2gnb1.c:5808:13: warning: variable ‘pdb’ set but not used [-Wunused-but-set-variable] 5808 | pdb = NULL, general = NULL, gi = NULL; | ^~~ asn2gnb1.c:5807:40: warning: variable ‘patent’ set but not used [-Wunused-but-set-variable] 5807 | SeqIdPtr accn = NULL, local = NULL, patent = NULL, | ^~~~~~ In file included from ../include/ncbi.h:58: asn2gnb1.c: In function ‘DoImmediateFormat’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb1.c:6951:19: note: in expansion of macro ‘MAX’ 6951 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb1.c:6930:20: warning: variable ‘is_www’ set but not used [-Wunused-but-set-variable] 6930 | Boolean is_www; | ^~~~~~ asn2gnb1.c: In function ‘asn2gnbk_format’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb1.c:7072:19: note: in expansion of macro ‘MAX’ 7072 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb1.c: In function ‘asn2gnbk_cleanup’: asn2gnb1.c:7118:21: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 7118 | IntAsn2gbSectPtr iasp; | ^~~~ asn2gnb1.c: In function ‘SeqEntryToGnbk’: asn2gnb1.c:7304:22: warning: variable ‘userdata’ set but not used [-Wunused-but-set-variable] 7304 | Pointer userdata = NULL; | ^~~~~~~~ asn2gnb1.c:7299:22: warning: variable ‘gbseq’ set but not used [-Wunused-but-set-variable] 7299 | GBSeqPtr gbseq = NULL; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb1.c:58: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb1.c: In function ‘PrintFtableIntervals’: asn2gnb1.c:5463:28: warning: ‘ ’ directive writing 1 byte into a region of size between 0 and 62 [-Wformat-overflow=] 5463 | sprintf (str, "%s\t%s\t%s\n", str1, str2, label); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintFtableIntervals’ at asn2gnb1.c:5463:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 4 or more bytes (assuming 66) into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb1.c: In function ‘PrintFtableIntervals’: asn2gnb1.c:5487:30: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5487 | sprintf (str, "%s\t%s\n", str1, str2); | ^ In function ‘sprintf’, inlined from ‘PrintFtableIntervals’ at asn2gnb1.c:5487:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 65 bytes into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb2.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb2.c: In function ‘s_LocusAddSuffix’: asn2gnb2.c:217:11: warning: variable ‘ch’ set but not used [-Wunused-but-set-variable] 217 | Char ch; | ^~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1361:66: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1361 | } else if ((moltype >= 2 && moltype <= 8) || moltype >= 10 && moltype <= 11) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘IsSuccessor’: asn2gnb2.c:1742:15: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1742 | while (accp != '\0' && prevp != '\0') { | ^~ asn2gnb2.c:1742:10: note: did you mean to dereference the pointer? 1742 | while (accp != '\0' && prevp != '\0') { | ^ asn2gnb2.c:1742:34: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1742 | while (accp != '\0' && prevp != '\0') { | ^~ asn2gnb2.c:1742:28: note: did you mean to dereference the pointer? 1742 | while (accp != '\0' && prevp != '\0') { | ^ asn2gnb2.c: In function ‘IsProjectAccn’: asn2gnb2.c:1767:38: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue; | ^~ asn2gnb2.c:1767:34: note: did you mean to dereference the pointer? 1767 | for (ptr = acc, letters = 0; ptr != '\0' && IS_ALPHA(*ptr); ++ptr, ++letters) continue; | ^ asn2gnb2.c: In function ‘AddDblinkBlock’: asn2gnb2.c:2892:22: warning: variable ‘parentID’ set but not used [-Wunused-but-set-variable] 2892 | Int4 parentID; | ^~~~~~~~ asn2gnb2.c: In function ‘AddSPBlock’: asn2gnb2.c:3409:14: warning: implicit declaration of function ‘PrintDate’ [-Wimplicit-function-declaration] 3409 | string = PrintDate (spb->created); | ^~~~~~~~~ asn2gnb2.c:3409:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3409 | string = PrintDate (spb->created); | ^ asn2gnb2.c:3417:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3417 | string = PrintDate (spb->sequpd); | ^ asn2gnb2.c:3424:12: warning: assignment to ‘Nlm_CharPtr’ {aka ‘char *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 3424 | string = PrintDate (spb->annotupd); | ^ asn2gnb2.c: In function ‘AddSourceOrganismBlock’: asn2gnb2.c:5056:22: warning: variable ‘common’ set but not used [-Wunused-but-set-variable] 5056 | CharPtr common; | ^~~~~~ asn2gnb2.c: In function ‘GetRefsOnBioseq’: asn2gnb2.c:5893:22: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 5893 | Uint1 strand; | ^~~~~~ asn2gnb2.c:5890:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 5890 | Boolean split; | ^~~~~ asn2gnb2.c:5884:22: warning: variable ‘right’ set but not used [-Wunused-but-set-variable] 5884 | Int4 right; | ^~~~~ asn2gnb2.c:5878:22: warning: variable ‘left’ set but not used [-Wunused-but-set-variable] 5878 | Int4 left; | ^~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:239:24: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 6 [-Wformat-overflow=] 239 | sprintf(segCountStr,"%d",awp->numsegs); | ^~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:239:23: note: directive argument in the range [2, 2147483647] 239 | sprintf(segCountStr,"%d",awp->numsegs); | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:239:3, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:244:25: warning: ‘%0*d’ directive writing between 1 and 32768 bytes into a region of size 4 [-Wformat-overflow=] 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg); | ^~~~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:244:23: note: directive argument in the range [0, 65535] 244 | sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg); | ^~~~~~~ In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:244:5, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 32770 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:246:24: warning: ‘%0*d’ directive writing between 1 and 32768 bytes into a region of size 5 [-Wformat-overflow=] 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg); | ^~~~ In function ‘s_LocusAddSuffix’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: asn2gnb2.c:246:23: note: directive argument in the range [0, 65535] 246 | sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg); | ^~~~~~ In function ‘sprintf’, inlined from ‘s_LocusAddSuffix’ at asn2gnb2.c:246:5, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1190:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1514:48: warning: ‘" title="Jump to the comment...’ directive writing 69 bytes into a region of size between 66 and 106 [-Wformat-overflow=] 1514 | sprintf (sect, "
  • Comment
    • ", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1514:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 92 and 132 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1518:46: warning: ‘" title="Jump to the feature...’ directive writing 68 bytes into a region of size between 66 and 106 [-Wformat-overflow=] 1518 | sprintf (sect, "
  • Features
    • ", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1518:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 91 and 131 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1527:117: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1527 | sprintf (sect, "
  • Genome
    • ", | ^ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1527:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 89 and 129 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1532:117: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1532 | sprintf (sect, "
  • Contig
    • ", | ^ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1532:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 89 and 129 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1579:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 68 and 77 [-Wformat-overflow=] 1579 | sprintf (sect, "
  • Next
    • ", (long) nextGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1579:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 67 and 203 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1587:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 67 and 77 [-Wformat-overflow=] 1587 | sprintf (sect, "
  • Next
    • ", (long) awp->nextGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1587:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 67 and 204 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1608:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 67 and 77 [-Wformat-overflow=] 1608 | sprintf (sect, "
  • Previous
    • ", (long) awp->prevGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1608:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 71 and 208 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb2.c: In function ‘AddLocusBlock’: asn2gnb2.c:1600:81: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 68 and 77 [-Wformat-overflow=] 1600 | sprintf (sect, "
  • Previous
    • ", (long) prevGi, seqid); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘AddLocusBlock’ at asn2gnb2.c:1600:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 71 and 207 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb3.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb3.c: In function ‘GetStatusForRefTrack’: asn2gnb3.c:796:22: warning: variable ‘urf’ set but not used [-Wunused-but-set-variable] 796 | UserFieldPtr ufp, urf = NULL; | ^~~ asn2gnb3.c: In function ‘AddCommentBlock’: asn2gnb3.c:2656:22: warning: variable ‘is_wgs’ set but not used [-Wunused-but-set-variable] 2656 | Boolean is_wgs = FALSE; | ^~~~~~ asn2gnb3.c: In function ‘GetSourcesOnBioseq’: asn2gnb3.c:5472:22: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 5472 | Uint1 strand; | ^~~~~~ asn2gnb3.c:5470:22: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5470 | Int4 start; | ^~~~~ asn2gnb3.c:5468:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 5468 | Boolean split; | ^~~~~ asn2gnb3.c: In function ‘AddSourceFeatBlock’: asn2gnb3.c:5989:22: warning: unused variable ‘sip’ [-Wunused-variable] 5989 | SeqIdPtr sip; | ^~~ asn2gnb3.c: In function ‘GetFeatsOnCdsProduct’: asn2gnb3.c:6446:22: warning: variable ‘isRefSeq’ set but not used [-Wunused-but-set-variable] 6446 | Boolean isRefSeq; | ^~~~~~~~ asn2gnb3.c: In function ‘GetRemoteFeatsOnCdsProduct’: asn2gnb3.c:6595:20: warning: variable ‘lastsfp’ set but not used [-Wunused-but-set-variable] 6595 | SeqFeatPtr lastsfp; | ^~~~~~~ asn2gnb3.c:6594:20: warning: variable ‘lastsap’ set but not used [-Wunused-but-set-variable] 6594 | SeqAnnotPtr lastsap; | ^~~~~~~ asn2gnb3.c:6593:20: warning: variable ‘lastright’ set but not used [-Wunused-but-set-variable] 6593 | Int4 lastright; | ^~~~~~~~~ asn2gnb3.c:6592:20: warning: variable ‘lastleft’ set but not used [-Wunused-but-set-variable] 6592 | Int4 lastleft; | ^~~~~~~~ asn2gnb3.c:6591:20: warning: variable ‘isRefSeq’ set but not used [-Wunused-but-set-variable] 6591 | Boolean isRefSeq; | ^~~~~~~~ asn2gnb3.c: In function ‘GetFeatsOnBioseq’: asn2gnb3.c:6895:22: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 6895 | Int4 start; | ^~~~~ asn2gnb3.c:6866:22: warning: variable ‘icp’ set but not used [-Wunused-but-set-variable] 6866 | IntCdsBlockPtr icp; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb3.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb3.c:1582:16: warning: ‘nsWGSGapsString’ defined but not used [-Wunused-variable] 1582 | static CharPtr nsWGSGapsString = "The strings of n's in this record represent gaps between contigs or uncallable bases."; | ^~~~~~~~~~~~~~~ asn2gnb3.c:1581:16: warning: ‘nsAreGapsString’ defined but not used [-Wunused-variable] 1581 | static CharPtr nsAreGapsString = "The strings of n's in this record represent gaps between contigs, and the length of each string corresponds to the length of the gap."; | ^~~~~~~~~~~~~~~ asn2gnb3.c: In function ‘AddCommentBlock’: asn2gnb3.c:3429:29: warning: ‘nm’ may be used uninitialized [-Wmaybe-uninitialized] 3429 | if (IS_protdb_accession (nm)) { | ^~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb3.c:2676:22: note: ‘nm’ was declared here 2676 | CharPtr nm; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb4.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockQuals’: asn2gnb4.c:3723:50: warning: "/*" within comment [-Wcomment] 3723 | StringChr (str + 1, '(') == NULL /* && StringChr (str, ',') != NULL */) { | asn2gnb4.c:3101:24: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 3101 | Boolean split; | ^~~~~ asn2gnb4.c:3042:24: warning: variable ‘at_end’ set but not used [-Wunused-but-set-variable] 3042 | Boolean at_end = FALSE; | ^~~~~~ asn2gnb4.c: In function ‘FF_asn2gb_www_featkey_Ex’: asn2gnb4.c:5325:16: warning: variable ‘prefix’ set but not used [-Wunused-but-set-variable] 5325 | CharPtr prefix = "?"; | ^~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockEx’: asn2gnb4.c:6572:22: warning: variable ‘split’ set but not used [-Wunused-but-set-variable] 6572 | Boolean split; | ^~~~~ In file included from ../include/ncbi.h:58: asn2gnb4.c: In function ‘DoImmediateRemoteFeatureFormat’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb4.c:8796:19: note: in expansion of macro ‘MAX’ 8796 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ asn2gnb4.c: In function ‘FormatFeatureQuals’: ../include/ncbistd.h:255:29: warning: comparison between ‘enum ’ and ‘enum ’ [-Wenum-compare] 255 | #define MAX(a,b) ((a)>=(b)?(a):(b)) | ^~ asn2gnb4.c:8869:19: note: in expansion of macro ‘MAX’ 8869 | max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb4.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb4.c: In function ‘FormatFeatureBlockEx’: asn2gnb4.c:7695:26: warning: ‘sep’ may be used uninitialized [-Wmaybe-uninitialized] 7695 | oldscope = SeqEntrySetScope (sep); | ^~~~~~~~~~~~~~~~~~~~~~ asn2gnb4.c:6566:22: note: ‘sep’ was declared here 6566 | SeqEntryPtr sep; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb5.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb5.c: In function ‘FormatCitBookArt’: asn2gnb5.c:2108:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2108 | ValNodePtr vnp; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb5.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb5.c: In function ‘FormatReferenceBlock’: asn2gnb5.c:2553:22: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2553 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~ In function ‘FormatCitPat’, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: asn2gnb5.c:2553:19: note: directive argument in the range [1, 2147483647] 2553 | sprintf(buf,"%s%ld ", " ", (long) pat_seqid); | ^~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FormatCitPat’ at asn2gnb5.c:2553:7, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gnb5.c: In function ‘FormatReferenceBlock’: asn2gnb5.c:2550:22: warning: ‘%ld’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 2550 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~ In function ‘FormatCitPat’, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: asn2gnb5.c:2550:19: note: directive argument in the range [1, 2147483647] 2550 | sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘FormatCitPat’ at asn2gnb5.c:2550:7, inlined from ‘GetPubJournal’ at asn2gnb5.c:2983:21, inlined from ‘FormatReferenceBlock’ at asn2gnb5.c:3931:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 14 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2gnb6.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gnb6.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gnb6.c: In function ‘FlatLocElement’: asn2gnb6.c:2546:27: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2546 | if (sintp->to > 0 && | ~~~~~~~~~~~~~~^~ 2547 | (sintp->to != sintp->from || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2548 | sintp->if_from != NULL || | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2549 | sintp->if_to != NULL) || | ~~~~~~~~~~~~~~~~~~~~~ asn2gnb6.c: In function ‘FormatContigBlock’: asn2gnb6.c:5701:20: warning: variable ‘dspnext’ set but not used [-Wunused-but-set-variable] 5701 | DeltaSeqPtr dspnext; | ^~~~~~~ asn2gnb6.c: In function ‘ProcessGapSpecialFormat’: asn2gnb6.c:6041:13: warning: unused variable ‘sip’ [-Wunused-variable] 6041 | SeqIdPtr sip; | ^~~ asn2gnb6.c: In function ‘FormatSequenceBlock’: asn2gnb6.c:6168:21: warning: variable ‘iasp’ set but not used [-Wunused-but-set-variable] 6168 | IntAsn2gbSectPtr iasp; | ^~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2gnb6.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asn2gnb6.c:76:16: warning: ‘link_lat_lon’ defined but not used [-Wunused-variable] 76 | static CharPtr link_lat_lon = "https://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html?"; | ^~~~~~~~~~~~ asn2gnb6.c: In function ‘FormatBasecountBlock’: asn2gnb6.c:5365:58: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 10 and 50 [-Wformat-overflow=] 5365 | sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;", | ^~~ asn2gnb6.c:5365:19: note: directive argument in the range [-2147483648, 2147483647] 5365 | sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2gnb6.c:5365:19: note: directive argument in the range [-2147483648, 2147483647] In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FormatBasecountBlock’ at asn2gnb6.c:5365:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 44 and 104 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ftusrstr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ftusrstr.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gbfeat.c gbfeat.c: In function ‘CkLabelType’: gbfeat.c:1465:47: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1465 | for (str = bptr; *str != '\0' && IS_ALPHA(*str) || IS_DIGIT(*str) x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gbftglob.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gbparint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/parsegb.h:57, from gbparint.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gbparint.c: In function ‘Nlm_gbparselex’: gbparint.c:2134:24: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2134 | if (*current_col != '\0') | ^ gbparint.c: In function ‘Nlm_gbparselex_ver’: gbparint.c:2520:24: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2520 | if (*current_col != '\0') | ^ gbparint.c: In function ‘Nlm_gbparselex’: gbparint.c:1903:9: warning: array subscript 0 is outside array bounds of ‘char[0:]’ [-Warray-bounds=] 1903 | *(current_col +1) = Saved_ch; | ^~~~~~~~~~~~~~~~~ cc1: note: source object is likely at address zero gbparint.c: In function ‘Nlm_gbparselex_ver’: gbparint.c:1903:9: warning: array subscript 0 is outside array bounds of ‘char[0:]’ [-Warray-bounds=] 1903 | *(current_col +1) = Saved_ch; | ^~~~~~~~~~~~~~~~~ cc1: note: source object is likely at address zero x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF utilpars.c utilpars.c:112:39: warning: missing braces around initializer [-Wmissing-braces] 112 | ParFlat_AA_array[ParFlat_TOTAL_AA] = { | ^ 113 | "Ala", 'A', | { } 114 | "Asx", 'B', | { } 115 | "Cys", 'C', | { } 116 | "Asp", 'D', | { } 117 | "Glu", 'E', | { } 118 | "Phe", 'F', | { } 119 | "Gly", 'G', | { } 120 | "His", 'H', | { } 121 | "Ile", 'I', | { } 122 | "Xle", 'J', /* was - notice no 'J', breaks naive meaning of index -Karl */ | { } 123 | "Lys", 'K', | { } 124 | "Leu", 'L', | { } 125 | "Met", 'M', | { } 126 | "Asn", 'N', | { } 127 | "Pyl", 'O', /* was - no 'O' */ | { } 128 | "Pro", 'P', | { } 129 | "Gln", 'Q', | { } 130 | "Arg", 'R', | { } 131 | "Ser", 'S', | { } 132 | "Thr", 'T', | { } 133 | "Val", 'V', | { } 134 | "Trp", 'W', | { } 135 | "Sec", 'U', /* was - not in iupacaa */ | { } 136 | "Xxx", 'X', | { } 137 | "Tyr", 'Y', | { } 138 | "Glx", 'Z', | { } 139 | "TERM", '*', /* not in iupacaa */ /*changed by Tatiana 06.07.95?`*/ | { } 140 | "OTHER", 'X'}; | { } x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF utilpub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from utilpub.c:13: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ utilpub.c: In function ‘FindCit’: utilpub.c:998:43: warning: variable ‘ifp’ set but not used [-Wunused-but-set-variable] 998 | ImpFeatPtr /*UNUSED*/ifp; | ^~~ utilpub.c: In function ‘ChangeCitQual’: utilpub.c:1053:72: warning: variable ‘pub’ set but not used [-Wunused-but-set-variable] 1053 | ValNodePtr vnp, pubset = NULL, pub_min, /*UNUSED*/pub; | ^~~ utilpub.c:1052:41: warning: variable ‘descr’ set but not used [-Wunused-but-set-variable] 1052 | ValNodePtr PNTR vnpp, /*UNUSED*/descr; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ffprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asn2ffg.h:200, from ../include/asn2ffp.h:48, from ffprint.c:127: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ffprint.c: In function ‘FFBSPrint’: ffprint.c:347:19: warning: unused variable ‘byte_sp’ [-Wunused-variable] 347 | ByteStorePtr byte_sp = NULL; | ^~~~~~~ ffprint.c: At top level: ffprint.c:420:16: warning: ‘ff_print_insert’ defined but not used [-Wunused-function] 420 | static CharPtr ff_print_insert(CharPtr str, CharPtr ins) | ^~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF wprint.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from wprint.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ wprint.c: In function ‘LocPrintGenome’: wprint.c:1696:21: warning: unused variable ‘sep’ [-Wunused-variable] 1696 | SeqEntryPtr sep = NULL; | ^~~ wprint.c:1695:37: warning: unused variable ‘b’ [-Wunused-variable] 1695 | BioseqPtr bsp = NULL, b = NULL; | ^ wprint.c:1695:25: warning: unused variable ‘bsp’ [-Wunused-variable] 1695 | BioseqPtr bsp = NULL, b = NULL; | ^~~ wprint.c:1692:52: warning: unused variable ‘temp’ [-Wunused-variable] 1692 | static Char buf[14], val[166], temp[166]; | ^~~~ wprint.c: At top level: wprint.c:79:13: warning: ‘link_gdb_map’ defined but not used [-Wunused-variable] 79 | static Char link_gdb_map[MAX_WWWBUF]; | ^~~~~~~~~~~~ wprint.c:77:13: warning: ‘link_pir’ defined but not used [-Wunused-variable] 77 | static Char link_pir[MAX_WWWBUF]; | ^~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from wprint.c:51: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ wprint.c: In function ‘PrintDate’: wprint.c:188:41: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 188 | sprintf(day, "%d", (int) (date -> data[3] )); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintDate’ at wprint.c:188:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4 bytes into a destination of size 3 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ wprint.c: In function ‘www_db_xref’: wprint.c:969:48: warning: ‘%d’ directive writing between 1 and 6 bytes into a region of size between 4 and 9 [-Wformat-overflow=] 969 | sprintf(id, "%d%d", id1, id2); | ^~ In function ‘www_db_xref’, inlined from ‘www_db_xref’ at wprint.c:679:28: wprint.c:969:45: note: directive argument in the range [-32768, 32767] 969 | sprintf(id, "%d%d", id1, id2); | ^~~~~~ In function ‘sprintf’, inlined from ‘www_db_xref’ at wprint.c:969:5, inlined from ‘www_db_xref’ at wprint.c:679:28: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ../include/ncbi.h:62: wprint.c: In function ‘www_xref’: ../include/ncbistr.h:331:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1358:20: note: ‘link’ was declared here 1358 | CharPtr s, link, prefix, ss; | ^~~~ ../include/ncbistr.h:331:25: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1358:26: note: ‘prefix’ was declared here 1358 | CharPtr s, link, prefix, ss; | ^~~~~~ wprint.c: In function ‘www_xref_button’: ../include/ncbistr.h:331:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1398:20: note: ‘link’ was declared here 1398 | CharPtr s, link, prefix, ss; | ^~~~ ../include/ncbistr.h:331:25: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen wprint.c:1398:26: note: ‘prefix’ was declared here 1398 | CharPtr s, link, prefix, ss; | ^~~~~~ wprint.c: In function ‘PrintSPBlock’: wprint.c:1570:41: warning: ‘s’ may be used uninitialized [-Wmaybe-uninitialized] 1570 | AddLink(s); | ^~~~~~~~~~ wprint.c:1443:31: note: ‘s’ was declared here 1443 | CharPtr link, prefix, s; | ^ In function ‘sprintf’, inlined from ‘PrintSPBlock’ at wprint.c:1601:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘prefix’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ wprint.c: In function ‘PrintSPBlock’: wprint.c:1443:23: note: ‘prefix’ was declared here 1443 | CharPtr link, prefix, s; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF satutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/satutil.h:12, from satutil.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ satutil.c: In function ‘CopyFeatureFromAlign’: satutil.c:1011:17: warning: variable ‘check_gap’ set but not used [-Wunused-but-set-variable] 1011 | Boolean check_gap; | ^~~~~~~~~ satutil.c: At top level: satutil.c:168:16: warning: ‘bk_map_one_location’ defined but not used [-Wunused-function] 168 | static Boolean bk_map_one_location(SeqLocPtr source_loc, SeqAlignPtr align, SeqIdPtr target_sip, Boolean check_gap, Int4Ptr r_start, Int4Ptr r_stop, SeqLocPtr PNTR head_slp) | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from seqmgr.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqmgr.c: In function ‘SeqEntrySetScope’: seqmgr.c:311:13: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 311 | Boolean found; | ^~~~~ seqmgr.c: In function ‘ClearBioseqFindCache’: seqmgr.c:897:14: warning: variable ‘smp’ set but not used [-Wunused-but-set-variable] 897 | SeqMgrPtr smp; | ^~~ seqmgr.c: In function ‘GetUniGeneIDForSeqId’: seqmgr.c:3676:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3676 | if(StringCmp(db_tag->db, "BSNR") == 0) | ^~ seqmgr.c:3678:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3678 | if(StringCmp(db_tag->db, "HUMGEN") == 0) | ^~ seqmgr.c: In function ‘SeqMgrGetExtraDataForOmdp’: seqmgr.c:3736:14: warning: variable ‘omp’ set but not used [-Wunused-but-set-variable] 3736 | ObjMgrPtr omp; | ^~~ seqmgr.c: In function ‘CheckForTransSplice’: seqmgr.c:5657:14: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 5657 | SeqLocPtr prev, tmp; | ^~~~ seqmgr.c: In function ‘SeqEntryAsnOut’: seqmgr.c:11799:41: warning: variable ‘aopp_desc’ set but not used [-Wunused-but-set-variable] 11799 | AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL; | ^~~~~~~~~ seqmgr.c:11799:23: warning: variable ‘aopp_feat’ set but not used [-Wunused-but-set-variable] 11799 | AsnOptionPtr aopp_feat = NULL, aopp_desc = NULL; | ^~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from seqmgr.c:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from objmgr.c:51: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmgr.c: In function ‘ObjMgrReapOne’: objmgr.c:2727:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2727 | if (omp->reaping) /* protect against recursion caused by ObjMgrSendMsg */ | ^~ objmgr.c:2730:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2730 | lowest = UINT4_MAX; | ^~~~~~ objmgr.c: In function ‘ObjMgrDeSelectStructFunc’: objmgr.c:3767:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3767 | if (next != NULL) | ^~ objmgr.c:3770:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3770 | ObjMgrSendDeSelMsg (omp, ssp->entityID, ssp->itemID, ssp->itemtype, ssp->regiontype, ssp->region); | ^~~~~~~~~~~~~~~~~~ objmgr.c: In function ‘ObjMgrSelectFunc2’: objmgr.c:4031:22: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 4031 | Boolean retval = FALSE; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gather.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from gather.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gather.c: In function ‘AttachDataProc’: gather.c:4827:30: warning: variable ‘into_seqentry’ set but not used [-Wunused-but-set-variable] 4827 | Boolean no_good = FALSE, into_seqentry = FALSE; | ^~~~~~~~~~~~~ In file included from ../include/ncbi.h:59: gather.c: In function ‘GatherSeqFeat’: ../include/ncbimem.h:232:23: warning: ‘lrdp’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree gather.c:1404:38: note: ‘lrdp’ was declared here 1404 | GatherRangePtr rdp = NULL, trdp, lrdp; | ^~~~ gather.c:1527:32: warning: ‘max_interval’ may be used uninitialized [-Wmaybe-uninitialized] 1527 | if (ctr >= max_interval) | ^ gather.c:1407:15: note: ‘max_interval’ was declared here 1407 | Int2 ctr, max_interval, i, numcheck, j; | ^~~~~~~~~~~~ gather.c: In function ‘gather_align_data’: gather.c:2441:70: warning: ‘mag_val’ may be used uninitialized [-Wmaybe-uninitialized] 2441 | t_range.right = t_range.left+len / mag_val -1; | ~~~~^~~~~~~~~ gather.c:2218:10: note: ‘mag_val’ was declared here 2218 | Int4 mag_val; /*the magnification value */ | ^~~~~~~ gather.c:2450:34: warning: ‘master_loc’ may be used uninitialized [-Wmaybe-uninitialized] 2450 | c_stop = SeqLocStop(master_loc); | ^~~~~~~~~~~~~~~~~~~~~~ gather.c:2219:15: note: ‘master_loc’ was declared here 2219 | SeqLocPtr master_loc, m_loc; | ^~~~~~~~~~ gather.c: In function ‘GatherBioseqFunc’: gather.c:3307:53: warning: ‘tlen’ may be used uninitialized [-Wmaybe-uninitialized] 3307 | rdp->right = offset + tlen - 1; | ~~~~~~~^~~~~~ gather.c:3022:35: note: ‘tlen’ was declared here 3022 | Int4 offset, toffset, seglen, tlen; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF accmmdbs.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from accmmdbs.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF acccn3ds.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from acccn3ds.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF lsqfetch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from ../include/lsqfetch.h:110, from lsqfetch.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ lsqfetch.c: In function ‘ChangeLocalToGenbank’: lsqfetch.c:1403:21: warning: ‘%s’ directive writing up to 40 bytes into a region of size 38 [-Wformat-overflow=] 1403 | sprintf (tmp, "gb|%s", id); | ^~ ~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ChangeLocalToGenbank’ at lsqfetch.c:1403:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 4 and 44 bytes into a destination of size 41 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF findrepl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from findrepl.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF codon.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/codon.h:61, from codon.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ codon.c: In function ‘make_cds_paragraph’: codon.c:262:14: warning: variable ‘space_len’ set but not used [-Wunused-but-set-variable] 262 | Int4 space_len, i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF jzcoll.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from jzcoll.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ jzcoll.c: In function ‘load_default_matrix’: jzcoll.c:99:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 99 | ss[pchars[i]][pchars[j]] = webb_blosum62[i][j]; | ~~~~~~^~~ jzcoll.c:99:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 99 | ss[pchars[i]][pchars[j]] = webb_blosum62[i][j]; | ~~~~~~^~~ jzcoll.c:101:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 101 | ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4; | ~~~~~~^~~ jzcoll.c:101:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 101 | ss[pchars[i]]['*'] = ss['*'][pchars[i]] = -4; | ~~~~~~^~~ jzcoll.c: In function ‘GetUseThisGi’: jzcoll.c:143:17: warning: unused variable ‘retval’ [-Wunused-variable] 143 | Boolean retval=FALSE; | ^~~~~~ jzcoll.c: In function ‘buffer_for_feature’: jzcoll.c:514:14: warning: unused variable ‘i’ [-Wunused-variable] 514 | Int2 i=0; | ^ jzcoll.c: In function ‘ProcessTextInsertion’: jzcoll.c:878:14: warning: variable ‘last_ins’ set but not used [-Wunused-but-set-variable] 878 | Int4 last_ins; | ^~~~~~~~ jzcoll.c: In function ‘satcollfunc’: jzcoll.c:1748:27: warning: the comparison will always evaluate as ‘false’ for the address of ‘features’ will never be NULL [-Waddress] 1748 | if(csop->features == NULL && afp->all_feature == FALSE) | ^~ ../include/jzcoll.h:206:17: note: ‘features’ declared here 206 | Boolean features[FEATDEF_ANY]; /*for filtering unwanted features*/ | ^~~~~~~~ jzcoll.c:1723:19: warning: variable ‘head’ set but not used [-Wunused-but-set-variable] 1723 | SeqLocPtr head; | ^~~~ jzcoll.c:1721:15: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 1721 | Uint1 strand; | ^~~~~~ jzcoll.c:1720:14: warning: variable ‘current_pos’ set but not used [-Wunused-but-set-variable] 1720 | Int4 current_pos; | ^~~~~~~~~~~ jzcoll.c:1714:19: warning: unused variable ‘slp’ [-Wunused-variable] 1714 | SeqLocPtr slp = NULL; | ^~~ jzcoll.c: In function ‘coll_align_data’: jzcoll.c:2631:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 2631 | sprintf(buf, "%d", gilist->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld jzcoll.c: In function ‘collect_anpnode_with_option’: jzcoll.c:3053:20: warning: unused variable ‘prev’ [-Wunused-variable] 3053 | ValNodePtr prev = NULL; | ^~~~ jzcoll.c: In function ‘ck_seqfeat_extra’: jzcoll.c:3414:17: warning: unused variable ‘has_gb’ [-Wunused-variable] 3414 | Boolean has_gb = FALSE, has_med = FALSE; | ^~~~~~ jzcoll.c: In function ‘collseqfunc’: jzcoll.c:3768:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3768 | if(omtp->labelfunc !=NULL) | ^~ jzcoll.c:3770:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3770 | fnp->landmark = check_feature_for_landmark(chp->thislabel, chp->gdata, sfp, gcp, chp->priority); | ^~~ jzcoll.c: In function ‘load_open_close_sts_mark’: jzcoll.c:4010:17: warning: variable ‘collected’ set but not used [-Wunused-but-set-variable] 4010 | Boolean collected = FALSE; | ^~~~~~~~~ jzcoll.c: In function ‘FeatNodeCompProc’: jzcoll.c:4225:22: warning: variable ‘gr2’ set but not used [-Wunused-but-set-variable] 4225 | GatherRange gr1, gr2; | ^~~ jzcoll.c:4225:17: warning: variable ‘gr1’ set but not used [-Wunused-but-set-variable] 4225 | GatherRange gr1, gr2; | ^~~ jzcoll.c: At top level: jzcoll.c:2316:16: warning: ‘stop_collecting_alignment’ defined but not used [-Wunused-function] 2316 | static Boolean stop_collecting_alignment(ValNodePtr anp_list, Int4 max_num) | ^~~~~~~~~~~~~~~~~~~~~~~~~ jzcoll.c:1654:16: warning: ‘collect_sequence_label’ defined but not used [-Wunused-function] 1654 | static Boolean collect_sequence_label(Uint1 format) | ^~~~~~~~~~~~~~~~~~~~~~ jzcoll.c: In function ‘load_text.isra.0’: jzcoll.c:421:41: warning: ‘smtp’ may be used uninitialized [-Wmaybe-uninitialized] 421 | stdaa_res = SeqMapTableConvert(smtp, m_res); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jzcoll.c:274:20: note: ‘smtp’ was declared here 274 | SeqMapTablePtr smtp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF jzmisc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/jzmisc.h:86, from jzmisc.c:23: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF maputil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from maputil.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ maputil.c: In function ‘load_gene_list’: maputil.c:690:15: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 690 | Uint1 val; | ^~~ maputil.c: In function ‘gmarkfunc’: maputil.c:985:20: warning: variable ‘syn’ set but not used [-Wunused-but-set-variable] 985 | ValNodePtr syn = NULL; | ^~~ maputil.c: In function ‘get_location_for_query’: maputil.c:1265:1: warning: function may return address of local variable [-Wreturn-local-addr] 1265 | } | ^ maputil.c:1190:16: note: declared here 1190 | SeqLoc sl; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mconsist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/mconsist.h:4, from mconsist.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF macroapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from macroapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ macroapi.c: In function ‘AdvancedStringCompare’: macroapi.c:4463:23: warning: variable ‘init_target_match_len’ set but not used [-Wunused-but-set-variable] 4463 | Int4 len1, len2, init_target_match_len = 0, target_match_len = 0; | ^~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘RemoveGBQualMatch’: macroapi.c:6981:27: warning: variable ‘does_match’ set but not used [-Wunused-but-set-variable] 6981 | Boolean rval = FALSE, does_match, do_remove; | ^~~~~~~~~~ macroapi.c: In function ‘ParseCodonsRecognizedFromCommaDelimitedList’: macroapi.c:7726:41: warning: pointer targets in passing argument 1 of ‘ExpandWobbleCodon’ differ in signedness [-Wpointer-sign] 7726 | wobble_list = ExpandWobbleCodon(codon); | ^~~~~ | | | Nlm_Uint1 * {aka unsigned char *} macroapi.c:7636:46: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} 7636 | static ValNodePtr ExpandWobbleCodon (CharPtr codon) macroapi.c: In function ‘GetQualFromFeatureAnyType’: macroapi.c:8537:8: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 8536 | if (str == NULL | ~~~~~~~~~~~ 8537 | && (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:8681:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 8681 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘SetNameInPrimerList’: macroapi.c:10682:21: warning: variable ‘prev_pp’ set but not used [-Wunused-but-set-variable] 10682 | PCRPrimerPtr pp, prev_pp = NULL; | ^~~~~~~ macroapi.c: In function ‘SetSeqInPrimerList’: macroapi.c:10703:21: warning: variable ‘prev_pp’ set but not used [-Wunused-but-set-variable] 10703 | PCRPrimerPtr pp, prev_pp = NULL; | ^~~~~~~ macroapi.c: In function ‘GetGenomeProjectIdFromBioseq’: macroapi.c:12881:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12881 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘RemoveGenomeProjectIdFromBioseq’: macroapi.c:12916:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12916 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘SetGenomeProjectIdOnBioseq’: macroapi.c:12957:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12957 | sprintf (buf, "%d", ufp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘GetPubFieldFromPub’: macroapi.c:15043:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15043 | sprintf (str, "%d", the_pub->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘GetCitListsForSeqEntry’: macroapi.c:15825:19: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 15825 | Uint2 entityID; | ^~~~~~~~ macroapi.c:15823:19: warning: variable ‘okay’ set but not used [-Wunused-but-set-variable] 15823 | Boolean okay; | ^~~~ macroapi.c: In function ‘GetPubclassQualFromPub’: macroapi.c:18324:11: warning: unused variable ‘str’ [-Wunused-variable] 18324 | CharPtr str = NULL; | ^~~ macroapi.c: In function ‘GetPubMLStatus’: macroapi.c:18681:14: warning: variable ‘csp’ set but not used [-Wunused-but-set-variable] 18681 | CitSubPtr csp; | ^~~ macroapi.c: In function ‘CollectDBLinkObjectsForApply’: macroapi.c:20029:72: warning: unused variable ‘tmp_tail’ [-Wunused-variable] 20029 | ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp; | ^~~~~~~~ macroapi.c:20029:55: warning: unused variable ‘tmp_list’ [-Wunused-variable] 20029 | ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp; | ^~~~~~~~ macroapi.c: In function ‘DoConvertActionToObjectListEx’: macroapi.c:20844:20: warning: unused variable ‘already_added’ [-Wunused-variable] 20844 | Boolean already_added, field_change; | ^~~~~~~~~~~~~ macroapi.c: In function ‘ApplyPartial5SetActionToSeqFeat’: macroapi.c:25749:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25749 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘ApplyPartial3SetActionToSeqFeat’: macroapi.c:25872:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25872 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘ApplyPartialBothSetActionToSeqFeat’: macroapi.c:25939:16: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 25939 | Uint1 strand; | ^~~~~~ macroapi.c: In function ‘FindPosBeforeFeat’: macroapi.c:26236:15: warning: variable ‘regulator’ set but not used [-Wunused-but-set-variable] 26236 | SeqFeatPtr regulator = NULL, candidate; | ^~~~~~~~~ macroapi.c: In function ‘PerformAutofixInSeqEntry’: macroapi.c:29471:8: warning: unused variable ‘num_created’ [-Wunused-variable] 29471 | Int4 num_created = 0; | ^~~~~~~~~~~ macroapi.c: In function ‘AddFileDescriptors’: macroapi.c:29871:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 29871 | while (sdp = SeqDescAsnRead (aip, NULL)) { | ^~~ macroapi.c: In function ‘ApplyMacroToSeqEntryExEx’: macroapi.c:31907:28: warning: too many arguments for format [-Wformat-extra-args] 31907 | fprintf (log_fp, "Instantiated protein titles\n", num); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘PreprocessAddDescriptorListMacro’: macroapi.c:32020:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 32020 | while (sdp = SeqDescAsnRead (aip, NULL)) { | ^~~ macroapi.c: In function ‘FieldTypeFromString’: macroapi.c:32370:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 32370 | if (ft == NULL && StringsAreEquivalent(str, "location") || StringsAreEquivalent(str, "genome")) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘SummarizeRemoveOutsideAction’: macroapi.c:32939:11: warning: unused variable ‘case_insensitive’ [-Wunused-variable] 32939 | CharPtr case_insensitive = " (case insensitive)"; | ^~~~~~~~~~~~~~~~ macroapi.c: In function ‘GetObjectTableForTabTable’: macroapi.c:37508:63: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 37508 | ValNodePtr obj_table = NULL, obj_row, last_obj = NULL, tmp, last = NULL; | ^~~~ macroapi.c: In function ‘FormatMultipleDestinationErrorMessage’: macroapi.c:37987:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 37987 | sprintf (buf, "%d", vnp->data.intvalue + 1); | ~^ ~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macroapi.c: In function ‘CheckObjTableForExistingText’: macroapi.c:38084:14: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 38084 | Uint2 entityID; | ^~~~~~~~ macroapi.c: In function ‘FixSuspectProductNamesInEntrezGene’: macroapi.c:40352:18: warning: variable ‘prefix’ set but not used [-Wunused-but-set-variable] 40352 | CharPtr prefix = NULL; | ^~~~~~ In file included from ../include/tax3api.h:51, from macroapi.c:67: ../include/objtax3.h: At top level: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ macroapi.c:37233:16: warning: ‘IsFieldTypeProteinDesc’ defined but not used [-Wunused-function] 37233 | static Boolean IsFieldTypeProteinDesc (FieldTypePtr ft) | ^~~~~~~~~~~~~~~~~~~~~~ macroapi.c:27097:13: warning: ‘GetDescriptorTypeFromDescriptorChoice’ defined but not used [-Wunused-function] 27097 | static Int4 GetDescriptorTypeFromDescriptorChoice (Uint1 descriptor_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:21298:13: warning: ‘GetFieldsFromAECR’ defined but not used [-Wunused-function] 21298 | static void GetFieldsFromAECR (AECRActionPtr act, FieldTypePtr PNTR pField, ValNodePtr PNTR pFieldPair) | ^~~~~~~~~~~~~~~~~ macroapi.c:20787:16: warning: ‘NoFieldChange’ defined but not used [-Wunused-function] 20787 | static Boolean NoFieldChange (CharPtr new_val, ValNodePtr vnp, FieldTypePtr field_from, StringConstraintPtr scp, BatchExtraPtr batch_extra) | ^~~~~~~~~~~~~ macroapi.c:16014:13: warning: ‘InitBatchExtraForAECRActionAndObjectList’ defined but not used [-Wunused-function] 16014 | static void InitBatchExtraForAECRActionAndObjectList (BatchExtraPtr batch_extra, AECRActionPtr action, ValNodePtr object_list) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:10389:16: warning: ‘HasMultiplePrimerSets’ defined but not used [-Wunused-function] 10389 | static Boolean HasMultiplePrimerSets (CharPtr value) | ^~~~~~~~~~~~~~~~~~~~~ macroapi.c:5482:16: warning: ‘DoesLocationMatchConstraint’ defined but not used [-Wunused-function] 5482 | static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:4590:13: warning: ‘TestAdvancedStringMatch’ defined but not used [-Wunused-function] 4590 | static void TestAdvancedStringMatch (void) | ^~~~~~~~~~~~~~~~~~~~~~~ macroapi.c:2806:13: warning: ‘OriginFromOriginName’ defined but not used [-Wunused-function] 2806 | static Int4 OriginFromOriginName (CharPtr origin_name) | ^~~~~~~~~~~~~~~~~~~~ macroapi.c:1200:16: warning: ‘IsObjectAppropriateForFieldPair’ defined but not used [-Wunused-function] 1200 | static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘GetSourceQualFromBioSource’: macroapi.c:11021:20: warning: ‘subfield’ may be used uninitialized [-Wmaybe-uninitialized] 11021 | if (subfield == 0) { | ^ macroapi.c:10957:8: note: ‘subfield’ was declared here 10957 | Int4 subfield; | ^~~~~~~~ macroapi.c: In function ‘GetMultipleSourceQualsFromBioSource’: macroapi.c:11169:18: warning: ‘subfield’ may be used uninitialized [-Wmaybe-uninitialized] 11169 | if (subfield == 0) { | ^ macroapi.c:11101:8: note: ‘subfield’ was declared here 11101 | Int4 subfield; | ^~~~~~~~ macroapi.c: In function ‘RemoveSourceQualFromBioSource’: macroapi.c:11355:18: warning: ‘subfield’ may be used uninitialized [-Wmaybe-uninitialized] 11355 | if (subfield == 0) { | ^ macroapi.c:11278:50: note: ‘subfield’ was declared here 11278 | Int4 orgmod_subtype = -1, subsrc_subtype = -1, subfield; | ^~~~~~~~ In function ‘ReadNameFromString’, inlined from ‘ReadNameListFromString’ at macroapi.c:14060:9: macroapi.c:14037:14: warning: ‘ch_r1’ may be used uninitialized [-Wmaybe-uninitialized] 14037 | *p_repl1 = ch_r1; | ~~~~~~~~~^~~~~~~ macroapi.c: In function ‘ReadNameListFromString’: macroapi.c:13946:11: note: ‘ch_r1’ was declared here 13946 | Char ch_r1, ch_r2, ch_r3; | ^~~~~ macroapi.c: In function ‘AlsoChangeMrnaForObject’: macroapi.c:20637:10: warning: ‘mrna’ may be used uninitialized [-Wmaybe-uninitialized] 20637 | if (mrna != NULL) { | ^ macroapi.c:20618:19: note: ‘mrna’ was declared here 20618 | SeqFeatPtr sfp, mrna, cds; | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘fprintf’, inlined from ‘ApplyMacroToSeqEntryExEx’ at macroapi.c:31907:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: ‘num’ may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ macroapi.c: In function ‘ApplyMacroToSeqEntryExEx’: macroapi.c:31469:37: note: ‘num’ was declared here 31469 | Int4 num_AECR = 0, num_parse = 0, num; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salpedit.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salpedit.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpedit.c: In function ‘SeqAlignInsert’: salpedit.c:162:19: warning: variable ‘ssp’ set but not used [-Wunused-but-set-variable] 162 | StdSegPtr ssp; | ^~~ salpedit.c:161:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 161 | DenseDiagPtr ddp; | ^~~ salpedit.c: At top level: salpedit.c:4120:18: warning: ‘build_slp_for_gcontig’ defined but not used [-Wunused-function] 4120 | static SeqLocPtr build_slp_for_gcontig (BioseqPtr gcontig_bsp, SeqIdPtr gcontig_sip) | ^~~~~~~~~~~~~~~~~~~~~ salpedit.c:4073:17: warning: ‘get_best_id’ defined but not used [-Wunused-function] 4073 | static SeqIdPtr get_best_id(BioseqPtr bsp) | ^~~~~~~~~~~ salpedit.c:4046:16: warning: ‘second_seq_has_gap’ defined but not used [-Wunused-function] 4046 | static Boolean second_seq_has_gap(BioseqPtr s_bsp) | ^~~~~~~~~~~~~~~~~~ salpedit.c:4016:18: warning: ‘dup_mul_locs’ defined but not used [-Wunused-function] 4016 | static SeqLocPtr dup_mul_locs(SeqLocPtr slp) | ^~~~~~~~~~~~ salpedit.c:3968:18: warning: ‘create_fake_bioseq’ defined but not used [-Wunused-function] 3968 | static BioseqPtr create_fake_bioseq(SeqLocPtr seq_loc, CharPtr fake_name) | ^~~~~~~~~~~~~~~~~~ salpedit.c:3937:13: warning: ‘reverse_seqloc’ defined but not used [-Wunused-function] 3937 | static void reverse_seqloc (SeqLocPtr s_loc) | ^~~~~~~~~~~~~~ salpedit.c:3850:13: warning: ‘save_output’ defined but not used [-Wunused-function] 3850 | static void save_output (SeqIdPtr sip, CharPtr f_name, SeqAlignPtr align) | ^~~~~~~~~~~ salpedit.c:3836:13: warning: ‘get_align_list_len’ defined but not used [-Wunused-function] 3836 | static Int4 get_align_list_len(SeqAlignPtr align) | ^~~~~~~~~~~~~~~~~~ salpedit.c:2939:20: warning: ‘open_annot’ defined but not used [-Wunused-function] 2939 | static SeqAnnotPtr open_annot(CharPtr f_name) | ^~~~~~~~~~ salpedit.c:2835:13: warning: ‘SeqAnnotWrite’ defined but not used [-Wunused-function] 2835 | static void SeqAnnotWrite(SeqAlignPtr align) | ^~~~~~~~~~~~~ salpedit.c:2653:16: warning: ‘FigureAlignRange’ defined but not used [-Wunused-function] 2653 | static Boolean FigureAlignRange(SeqAlignPtr align, SeqLocPtr m_loc, SeqLocPtr s_loc) | ^~~~~~~~~~~~~~~~ salpedit.c:1665:16: warning: ‘free_diag_in_list’ defined but not used [-Wunused-function] 1665 | static Boolean free_diag_in_list(ValNodePtr ddp_list, DenseDiagPtr ddp) | ^~~~~~~~~~~~~~~~~ salpedit.c:1605:16: warning: ‘is_overlap’ defined but not used [-Wunused-function] 1605 | static Boolean is_overlap(BoolPtr status, Int4 from, Int4 len) | ^~~~~~~~~~ salpedit.c:1560:13: warning: ‘filter_wrong_orientation’ defined but not used [-Wunused-function] 1560 | static void filter_wrong_orientation (SeqAlignPtr align, Boolean same_orient) | ^~~~~~~~~~~~~~~~~~~~~~~~ salpedit.c:1479:16: warning: ‘filter_this_seg’ defined but not used [-Wunused-function] 1479 | static Boolean filter_this_seg (DenseDiagPtr curr, DenseDiagPtr PNTR h_list, Int2 order) | ^~~~~~~~~~~~~~~ salpedit.c:1422:16: warning: ‘convert_ddp_to_array’ defined but not used [-Wunused-function] 1422 | static Int4Ptr convert_ddp_to_array (ValNodePtr ddp_list, Uint1 strand, Int2 s_order, Int4Ptr p_num) | ^~~~~~~~~~~~~~~~~~~~ salpedit.c:1387:14: warning: ‘has_too_much_overlap’ defined but not used [-Wunused-function] 1387 | static Uint1 has_too_much_overlap (Int4 start_1, Int4 stop_1, Int4 start_2, Int4 stop_2) | ^~~~~~~~~~~~~~~~~~~~ salpedit.c:1281:13: warning: ‘attach_new_align’ defined but not used [-Wunused-function] 1281 | static void attach_new_align(SeqAlignPtr new_salp, SeqAlignPtr PNTR old) { | ^~~~~~~~~~~~~~~~ salpedit.c:1169:20: warning: ‘JZSeqAlignMerge’ defined but not used [-Wunused-function] 1169 | static SeqAlignPtr JZSeqAlignMerge(SeqAlignPtr f_align, SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr t_align) | ^~~~~~~~~~~~~~~ salpedit.c:254:16: warning: ‘is_gap_segment’ defined but not used [-Wunused-function] 254 | static Boolean is_gap_segment(Int4Ptr c_starts, Int2 dim) | ^~~~~~~~~~~~~~ salpedit.c:158:20: warning: ‘SeqAlignInsert’ defined but not used [-Wunused-function] 158 | static SeqAlignPtr SeqAlignInsert(SeqIdPtr from_id, Int4 from, Int4 to, Uint1 strand, SeqIdPtr to_id, Int4 pos, SeqAlignPtr head, Boolean merge, Boolean add_insertion) | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salpstat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salpstat.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpstat.c: In function ‘DenseSegStats’: salpstat.c:310:10: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 310 | if(dsp && (((mmatches || mmismatches) && bsp_1 && bsp_2)) || !(mmatches || mmismatches)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c: In function ‘SeqAlignScoreFix’: salpstat.c:162:27: warning: ‘sp_last’ may be used uninitialized [-Wmaybe-uninitialized] 162 | sp_last->next = (ScorePtr) MemNew(sizeof(Score)); salpstat.c:121:20: note: ‘sp_last’ was declared here 121 | ScorePtr sp=NULL,sp_last; | ^~~~~~~ salpstat.c: In function ‘DenseSegStats’: salpstat.c:345:23: warning: ‘spp_1’ may be used uninitialized [-Wmaybe-uninitialized] 345 | SeqPortSeek(spp_1,start_1,SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c:307:14: note: ‘spp_1’ was declared here 307 | SeqPortPtr spp_1, spp_2; | ^~~~~ salpstat.c:352:23: warning: ‘spp_2’ may be used uninitialized [-Wmaybe-uninitialized] 352 | SeqPortSeek(spp_2,start_2,SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpstat.c:307:21: note: ‘spp_2’ was declared here 307 | SeqPortPtr spp_1, spp_2; | ^~~~~ salpstat.c: In function ‘SeqAlignWindowScoreFN’: salpstat.c:2038:45: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 2038 | residue_score[pos]=score; | ~~~~~~~~~~~~~~~~~~^~~~~~ salpstat.c:1915:8: note: ‘score’ was declared here 1915 | Int4 score,win_score,gap_score; | ^~~~~ salpstat.c: In function ‘SeqAlignWindowScore’: salpstat.c:2214:12: warning: ‘scoreptr’ may be used uninitialized [-Wmaybe-uninitialized] 2214 | return scoreptr; | ^~~~~~~~ salpstat.c:2142:16: note: ‘scoreptr’ was declared here 2142 | FloatHiPtr scoreptr; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salpacc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salpacc.h:33, from salpacc.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpacc.c: In function ‘SeqAlignStrand’: salpacc.c:334:20: warning: unused variable ‘this_strand’ [-Wunused-variable] 334 | Uint1Ptr this_strand=Seq_strand_unknown; | ^~~~~~~~~~~ salpacc.c: In function ‘SeqAlignStop’: salpacc.c:561:13: warning: ‘this_stop’ may be used uninitialized [-Wmaybe-uninitialized] 561 | if(this_stop!=-1) | ^ salpacc.c:545:12: note: ‘this_stop’ was declared here 545 | Int4 this_stop; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salprop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salprop.h:46, from salprop.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salprop.c: In function ‘CopySeqLocFromSeqAlign’: salprop.c:398:13: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 398 | else | ^~~~ salprop.c:401:16: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 401 | if(crp != NULL) /*for coding region features*/ | ^~ salprop.c:291:12: warning: variable ‘check_gap’ set but not used [-Wunused-but-set-variable] 291 | Boolean check_gap; | ^~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:867:43: warning: the comparison will always evaluate as ‘true’ for the address of ‘label’ will never be NULL [-Waddress] 867 | if (af.protName==NULL && sesp->label) | ^~ ../include/salsa.h:171:20: note: ‘label’ declared here 171 | Char label[101]; | ^~~~~ salprop.c: In function ‘FeatListToProp’: salprop.c:1336:20: warning: variable ‘feat_itemID’ set but not used [-Wunused-but-set-variable] 1336 | Uint4 feat_itemID; | ^~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from salprop.c:46: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ../include/salprop.h:50:16: warning: ‘GBFeat’ defined but not used [-Wunused-variable] 50 | static CharPtr GBFeat[number_GBFeat] = { | ^~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:861:40: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 861 | if ((val2=is_id_unique (entityID, SeqLocId(sfp->product)))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c:785:20: note: ‘entityID’ was declared here 785 | Uint2 entityID; | ^~~~~~~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:737:12: warning: ‘ppp.p3’ may be used uninitialized [-Wmaybe-uninitialized] 737 | SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:679:17: note: ‘ppp.p3’ was declared here 679 | ParTials ppp; | ^~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:711:6: warning: ‘sfp’ may be used uninitialized [-Wmaybe-uninitialized] 711 | if (sfp != NULL) | ^ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:674:17: note: ‘sfp’ was declared here 674 | SeqFeatPtr sfp; | ^~~ In function ‘CheckPartialInterval’, inlined from ‘ApplyBioFeatToSeqEntry’ at salprop.c:731:12, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:620:11: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 620 | j = stop - SeqLocStop(sfp_location); | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:514:17: note: ‘stop’ was declared here 514 | stop, | ^~~~ In function ‘ApplyBioFeatToSeqEntry’, inlined from ‘ApplyNewSeqFeat’ at salprop.c:911:27: salprop.c:733:24: warning: ‘ppp.p5’ may be used uninitialized [-Wmaybe-uninitialized] 733 | if (!sfp_p5 && ppp.p5) | ~~~~~~~~^~~~~~~~~ salprop.c: In function ‘ApplyNewSeqFeat’: salprop.c:679:17: note: ‘ppp.p5’ was declared here 679 | ParTials ppp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salsap.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salsap.h:57, from salsap.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salsap.c: In function ‘DenseDiagToDenseSegFunc’: salsap.c:2912:30: warning: variable ‘slpstop2’ set but not used [-Wunused-but-set-variable] 2912 | slpstop1 = 0, slpstop2 = 0; | ^~~~~~~~ salsap.c:2912:16: warning: variable ‘slpstop1’ set but not used [-Wunused-but-set-variable] 2912 | slpstop1 = 0, slpstop2 = 0; | ^~~~~~~~ salsap.c:2911:31: warning: variable ‘slpstart2’ set but not used [-Wunused-but-set-variable] 2911 | Int4 slpstart1 = 0, slpstart2 = 0, | ^~~~~~~~~ salsap.c:2911:16: warning: variable ‘slpstart1’ set but not used [-Wunused-but-set-variable] 2911 | Int4 slpstart1 = 0, slpstart2 = 0, | ^~~~~~~~~ salsap.c:2909:28: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2909 | Int4 start1 = 0, start2 = 0, | ^~~~~~ salsap.c:2909:16: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2909 | Int4 start1 = 0, start2 = 0, | ^~~~~~ In file included from ../include/sqnutils.h:51, from salsap.c:47: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salsap.c:3631:13: warning: ‘FindSeqAlignCallback’ defined but not used [-Wunused-function] 3631 | static void FindSeqAlignCallback (SeqEntryPtr sep, Pointer mydata, | ^~~~~~~~~~~~~~~~~~~~ salsap.c:2157:16: warning: ‘AreDenseSegSegmentsValid’ defined but not used [-Wunused-function] 2157 | static Boolean AreDenseSegSegmentsValid (DenseSegPtr dsp, Int4 start, Int4 num) | ^~~~~~~~~~~~~~~~~~~~~~~~ salsap.c: In function ‘CleanStrandsSeqAlign’: salsap.c:1610:15: warning: ‘lenp’ may be used uninitialized [-Wmaybe-uninitialized] 1610 | Int4Ptr lenp; | ^~~~ salsap.c:1611:15: warning: ‘startp’ may be used uninitialized [-Wmaybe-uninitialized] 1611 | Int4Ptr startp; | ^~~~~~ salsap.c:1662:29: warning: ‘numseg’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++) | ~~~~~~^~~~ salsap.c:1613:15: note: ‘numseg’ was declared here 1613 | Int4 numseg; | ^~~~~~ salsap.c:1662:29: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | for (j=0; j < numseg*dim && strandp!=NULL; j++, strandp++) | ~~~~~~^~~~ salsap.c:1614:15: note: ‘dim’ was declared here 1614 | Int2 dim; | ^~~ salsap.c: In function ‘LocalAlignToSeqAnnotDimn’: salsap.c:1735:13: warning: ‘the_lens’ may be used uninitialized [-Wmaybe-uninitialized] 1735 | while ( j < lens ) | ~~^~~~~~ salsap.c:1705:25: note: ‘the_lens’ was declared here 1705 | Int4 lenstmp, the_lens; | ^~~~~~~~ salsap.c: In function ‘multseqalign_from_pairseqalign’: salsap.c:4245:6: warning: ‘ok’ may be used uninitialized [-Wmaybe-uninitialized] 4245 | if (!ok) | ^ salsap.c:4209:20: note: ‘ok’ was declared here 4209 | Boolean ok; | ^~ salsap.c:4353:22: warning: ‘strandp’ may be used uninitialized [-Wmaybe-uninitialized] 4353 | strandtmp = *strandp; | ~~~~~~~~~~^~~~~~~~~~ salsap.c:4185:20: note: ‘strandp’ was declared here 4185 | Uint1Ptr strandp; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salstruc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salstruc.h:56, from salstruc.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salstruc.c: In function ‘prot_to_rputprot’: salstruc.c:734:18: warning: comparison between pointer and zero character constant [-Wpointer-compare] 734 | if (strptmp == '\0') break; | ^~ salstruc.c:734:10: note: did you mean to dereference the pointer? 734 | if (strptmp == '\0') break; | ^ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:1338:22: warning: variable ‘maxscroll’ set but not used [-Wunused-but-set-variable] 1338 | Int4 maxscroll; | ^~~~~~~~~ salstruc.c: In function ‘slpfeatcollfunc’: salstruc.c:1999:21: warning: the comparison will always evaluate as ‘false’ for the address of ‘features’ will never be NULL [-Waddress] 1999 | if(csop->features == NULL) | ^~ In file included from ../include/txalign.h:228, from ../include/salstruc.h:57: ../include/jzcoll.h:206:17: note: ‘features’ declared here 206 | Boolean features[FEATDEF_ANY]; /*for filtering unwanted features*/ | ^~~~~~~~ salstruc.c: In function ‘ShowAlignmentText’: salstruc.c:2203:29: warning: variable ‘itemtype’ set but not used [-Wunused-but-set-variable] 2203 | Uint2 entityID, itemtype; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from salstruc.c:40: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from salstruc.c:41: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salstruc.c: In function ‘prot_to_rputprot’: salstruc.c:707:11: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 707 | Int4 j, k; | ^ In function ‘update_fromalignnode’, inlined from ‘data_collect_arrange’ at salstruc.c:1363:13: salstruc.c:1064:46: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 1064 | adp->caret.entityID = entityID; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:1005:17: note: ‘entityID’ was declared here 1005 | Uint2 entityID; | ^~~~~~~~ In function ‘arrange_buffer’, inlined from ‘data_collect_arrange’ at salstruc.c:1433:6: salstruc.c:918:52: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 918 | if (OBJ_(tdp->feattype) == OBJ_BIOSEQ && (is_seqvisible(entityID, itemID, adp->seq_info)) ) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salstruc.c: In function ‘data_collect_arrange’: salstruc.c:872:19: note: ‘entityID’ was declared here 872 | Uint2 entityID; | ^~~~~~~~ salstruc.c: In function ‘ShowAlignmentText’: salstruc.c:2258:16: warning: ‘bspsip’ may be used uninitialized [-Wmaybe-uninitialized] 2258 | print_line (fout, tdp->label, bufstr, leftmargin, adp->columnpcell, bspsip, html_option, FALSE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salstruc.c:2194:19: note: ‘bspsip’ was declared here 2194 | SeqIdPtr bspsip; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from salutil.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salutil.c: In function ‘ReadBufferFromSap’: salutil.c:128:24: warning: variable ‘buffstart’ set but not used [-Wunused-but-set-variable] 128 | Int4 bufflen, buffstart; | ^~~~~~~~~ salutil.c:127:15: warning: variable ‘sumstart’ set but not used [-Wunused-but-set-variable] 127 | Int4 sumstart; | ^~~~~~~~ salutil.c: In function ‘IS_protSeqLoc’: salutil.c:594:11: warning: variable ‘seq’ set but not used [-Wunused-but-set-variable] 594 | CharPtr seq; | ^~~ salutil.c: In function ‘ReplaceSeqIdWithSeqId’: salutil.c:1236:20: warning: variable ‘oldscope’ set but not used [-Wunused-but-set-variable] 1236 | SeqEntryPtr oldscope; | ^~~~~~~~ salutil.c: In function ‘del_ssp_fromid’: salutil.c:1722:24: warning: variable ‘pressp’ set but not used [-Wunused-but-set-variable] 1722 | SelEdStructPtr ssp, pressp = NULL; | ^~~~~~ salutil.c: In function ‘checkCDSselect_forprotein’: salutil.c:2510:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2510 | if (feat != NULL) | ^ salutil.c: In function ‘NoMoreSegGapForOneAlignment’: salutil.c:3647:8: warning: implicit declaration of function ‘AlnMgr2IndexSingleChildSeqAlign’ [-Wimplicit-function-declaration] 3647 | AlnMgr2IndexSingleChildSeqAlign(salp); /* make sure it's dense-seg */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from salutil.c:53: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salutil.c: In function ‘sesp_to_slp’: salutil.c:1974:14: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 1974 | while (j>0) { | ~^~ salutil.c:1927:18: note: ‘j’ was declared here 1927 | Int2 j,k; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF udvseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udvseq.h:100, from udvseq.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvseq.c: In function ‘UDV_EncodeIdxFeat’: udvseq.c:448:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 448 | return *((Int4Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~ udvseq.c: In function ‘UDV_BigEncodeIdxFeat’: udvseq.c:473:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 473 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ udvseq.c: In function ‘UDV_EncodeIdxFeat’: udvseq.c:448:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 448 | return *((Int4Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~ udvseq.c:443:7: note: ‘index_g’ declared here 443 | Uint2 index_g[2]; | ^~~~~~~ udvseq.c: In function ‘UDV_BigEncodeIdxFeat’: udvseq.c:473:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 473 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ udvseq.c:466:7: note: ‘index_g’ declared here 466 | Uint2 index_g[4]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blocks.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/blocks.h:88, from blocks.c:93: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blocks.c: In function ‘IndexBlocks’: blocks.c:928:19: warning: operation on ‘segp_align->to’ may be undefined [-Wsequence-point] 928 | segp_align->to = segp_align->to = -1; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blocks.c: In function ‘IndexNewBlocks’: blocks.c:1084:19: warning: operation on ‘segp_align->to’ may be undefined [-Wsequence-point] 1084 | segp_align->to = segp_align->to = -1; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ blocks.c: In function ‘GetBlockOrientation’: blocks.c:2383:11: warning: ‘orient’ may be used uninitialized [-Wmaybe-uninitialized] 2383 | return orient; | ^~~~~~ blocks.c:2259:10: note: ‘orient’ was declared here 2259 | Int4 orient; | ^~~~~~ blocks.c: In function ‘SAMergeBlocks’: blocks.c:1572:28: warning: ‘tmp_head’ may be used uninitialized [-Wmaybe-uninitialized] 1572 | merged->segp_head = tmp_head; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ blocks.c:1318:16: note: ‘tmp_head’ was declared here 1318 | SegmentPtr tmp_head; | ^~~~~~~~ blocks.c:2071:27: warning: ‘tmp_curr’ may be used uninitialized [-Wmaybe-uninitialized] 2071 | tmp2->prev = tmp_curr; | ~~~~~~~~~~~^~~~~~~~~~ blocks.c:1317:16: note: ‘tmp_curr’ was declared here 1317 | SegmentPtr tmp_curr; | ^~~~~~~~ blocks.c:1709:27: warning: ‘prev’ may be used uninitialized [-Wmaybe-uninitialized] 1709 | tmp1->prev = prev; | ~~~~~~~~~~~^~~~~~ blocks.c:1311:16: note: ‘prev’ was declared here 1311 | SegmentPtr prev; | ^~~~ blocks.c:2162:30: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized] 2162 | tmp2->prev = tmp_curr; | ~~~~~~~~~~~^~~~~~~~~~ blocks.c:1320:16: note: ‘tmp2’ was declared here 1320 | SegmentPtr tmp2; | ^~~~ blocks.c: In function ‘SASplitBlock’: blocks.c:2796:25: warning: ‘segp2_prev’ may be used uninitialized [-Wmaybe-uninitialized] 2796 | segp2->prev = segp2_prev; | ~~~~~~~~~~~~^~~~~~~~~~~~ blocks.c:2765:16: note: ‘segp2_prev’ was declared here 2765 | SegmentPtr segp2_prev; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pgppop.c pgppop.c:58:2: warning: missing braces around initializer [-Wmissing-braces] 58 | { | ^ 59 | /* Red Grn Blue Color ColorID Old Hex New Hex */ 60 | 255, 255, 255, /* default 0 0xffffff - */ | { } 61 | 255, 00, 153, /* hotpink 1 0xff1493 0xff0099 */ | { } 62 | 255, 0, 255, /* magenta 2 0xff00ff - */ | { } 63 | 153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */ | { } 64 | 0, 0, 255, /* blue 4 0x0000ff - */ | { } 65 | 00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */ | { } 66 | 0, 255, 255, /* cyan 6 0x00ffff - */ | { } 67 | 0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */ | { } 68 | 0, 255, 0, /* green 8 0x00ff00 - */ | { } 69 | 255, 255, 0, /* yellow 9 0xffff00 - */ | { } 70 | 255, 204, 0, /* gold 10 0xffa500 0xffcc00 */ | { } 71 | 255, 102, 0, /* orange 11 0xff4500 0xff6600 */ | { } 72 | 255, 0, 0, /* red 12 0xff0000 - */ | { } 73 | 255, 153, 153, /* pink 13 0xff7256 0xff9999 */ | { } 74 | 255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */ | { } 75 | 255, 255, 255, /* white 15 0xffffff -*/ | { } 76 | 0, 0, 0, /* black 16 0x000000 - */ | { } 77 | 204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/ | { } 78 | 153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */ | { } 79 | 255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */ | { } 80 | 102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */ | { } 81 | 153, 102, 51, /* brown 21 0x8b5742 01x996633 */ | { } 82 | 255, 0, 0, /* perm colors 22: red 0xff0000 - */ | { } 83 | 0, 255, 0, /* perm colors 23: green 0x00ff00 - */ | { } 84 | 255, 0, 255, /* perm colors 24: magenta 0xff00ff - */ | { } 85 | 00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */ | { } 86 | 153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */ | { } 87 | 0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */ | { } 88 | 255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */ | { } 89 | 255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */ | { } 90 | 0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */ | { } 91 | 255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */ | { } 92 | 0, 0, 0 /* background colors 32: black 0x000000 - */ | { 93 | }; | } pgppop.c: In function ‘DDV_WWW_get_CDS_minus’: pgppop.c:329:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 329 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ pgppop.c:327:33: warning: variable ‘numivals2’ set but not used [-Wunused-but-set-variable] 327 | numivals2=0; | ^~~~~~~~~ pgppop.c: In function ‘DDV_WWW_get_CDS_plus’: pgppop.c:451:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 451 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ pgppop.c: In function ‘DDV_DisplayTopScale’: pgppop.c:1300:9: warning: unused variable ‘szBlank’ [-Wunused-variable] 1300 | Char szBlank[TABLE_LEFT_MARGIN+5]={""}; | ^~~~~~~ pgppop.c: In function ‘DDV_GetBLASTCompLine_1’: pgppop.c:1736:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1736 | if (matrix[s][q]>0){ | ^ pgppop.c:1736:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1736 | if (matrix[s][q]>0){ | ^ pgppop.c: In function ‘DDV_DisplayDefaultAlign’: pgppop.c:3169:25: warning: unused variable ‘sabp’ [-Wunused-variable] 3169 | SABlockPtr sabp=NULL;/*indexed SeqAlign*/ | ^~~~ pgppop.c: In function ‘DDV_ShowSeqAlign’: pgppop.c:3512:10: warning: unused variable ‘szPopSetAuth’ [-Wunused-variable] 3512 | Char szPopSetAuth[INFO_SIZE+1]={""}; | ^~~~~~~~~~~~ pgppop.c:3510:10: warning: unused variable ‘szPopSetName’ [-Wunused-variable] 3510 | Char szPopSetName[INFO_SIZE+1]={""};/*article title of the Pop-Set*/ | ^~~~~~~~~~~~ pgppop.c: In function ‘DDV_PrintPopSetSummary’: pgppop.c:3683:9: warning: variable ‘bPairwise’ set but not used [-Wunused-but-set-variable] 3683 | Boolean bPairwise=TRUE,bPrintTax,bPrintCom; | ^~~~~~~~~ In file included from ../include/sqnutils.h:51, from pgppop.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/ddvcreate.h:143, from pgppop.c:54: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ pgppop.c:2664:13: warning: ‘DDV_PrintFastaGappedSequence’ defined but not used [-Wunused-function] 2664 | static void DDV_PrintFastaGappedSequence(CharPtr szSequence,FILE *fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pgppop.c:2617:13: warning: ‘DDV_GetGappedSequence’ defined but not used [-Wunused-function] 2617 | static void DDV_GetGappedSequence(SegmentPtr segp,CharPtr szSequence, | ^~~~~~~~~~~~~~~~~~~~~ pgppop.c:1841:13: warning: ‘DDV_HideMaskedLetters’ defined but not used [-Wunused-function] 1841 | static void DDV_HideMaskedLetters(CharPtr szSeqMaster,ParaGPtr pgp,ValNodePtr mask) | ^~~~~~~~~~~~~~~~~~~~~ pgppop.c:314:13: warning: ‘DDV_WWW_get_CDS_minus’ defined but not used [-Wunused-function] 314 | static void DDV_WWW_get_CDS_minus(SeqMgrFeatContextPtr context,Int4 start, | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from pgppop.c:51: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ pgppop.c: In function ‘DDV_GetPubValues’: pgppop.c:2873:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2873 | sprintf(szBuf,"%d",year); | ^ In file included from /usr/include/stdio.h:980, from pgppop.c:41: In function ‘sprintf’, inlined from ‘DDV_GetPubValues’ at pgppop.c:2873:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 7 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pgppop.c: In function ‘DDV_PopDisplay2’: pgppop.c:1004:42: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1004 | vnp->next=NULL; | ^ pgppop.c:774:17: note: ‘vnp’ was declared here 774 | ValNodePtr vnp,vnp2;/*used to delete additional ParaG nodes, if needed; | ^~~ pgppop.c:997:36: warning: ‘pgp2’ may be used uninitialized [-Wmaybe-uninitialized] 997 | if (pgp2 && ((pgp2->StopLetter-pgp2->StartLetter+1)>=AbsLengthAli)) { | ^ pgppop.c:776:15: note: ‘pgp2’ was declared here 776 | ParaGPtr pgp1,pgp2;/*used to create new ParaGs*/ | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF samutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/samutil.h:230, from samutil.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ samutil.c: In function ‘SAM_AlignIdComp’: samutil.c:796:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 796 | if ((a == NULL) || (b == NULL)) | ^~ samutil.c:799:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 799 | choice = a->choice; | ^~~~~~ samutil.c: In function ‘SAM_AlignIdDup’: samutil.c:852:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 852 | if (oldid == NULL) | ^~ samutil.c:855:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 855 | newid = ValNodeNew(NULL); | ^~~~~ samutil.c: In function ‘DDE_FreeStack’: samutil.c:1556:11: warning: operation on ‘Index’ may be undefined [-Wsequence-point] 1556 | Index = ++Index % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Add’: samutil.c:1611:22: warning: operation on ‘pStack->StackMin’ may be undefined [-Wsequence-point] 1611 | pStack->StackMin = ++pStack->StackMin % DDE_STACK_SIZE; samutil.c:1622:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1622 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Prev’: samutil.c:1686:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1686 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_Next’: samutil.c:1717:22: warning: operation on ‘pStack->StackIndex’ may be undefined [-Wsequence-point] 1717 | pStack->StackIndex = ++pStack->StackIndex % DDE_STACK_SIZE; samutil.c: In function ‘DDE_ShowRow’: samutil.c:1984:26: warning: variable ‘NumRows’ set but not used [-Wunused-but-set-variable] 1984 | Int4 i, NumRows, HiRow, LowRow, tmp1, tmp2; | ^~~~~~~ samutil.c: In function ‘DDE_AddGapToEndOfAllRows’: samutil.c:3106:41: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 3106 | ValNodePtr ptxtList, last_vnp, vnp; | ^~~ samutil.c: In function ‘DDE_RightAddNode’: samutil.c:3707:33: warning: variable ‘new_vnp’ set but not used [-Wunused-but-set-variable] 3707 | ValNodePtr vnp, next_vnp, new_vnp; | ^~~~~~~ samutil.c: In function ‘DDE_LeftMergeAndAddNodeList’: samutil.c:3757:24: warning: variable ‘RetVal2’ set but not used [-Wunused-but-set-variable] 3757 | Boolean RetVal1, RetVal2, IsLeftAlignedGap, NodeDeleted; | ^~~~~~~ samutil.c: In function ‘DDE_RightMergeAndAddNodeList’: samutil.c:3813:38: warning: variable ‘RetVal2’ set but not used [-Wunused-but-set-variable] 3813 | Boolean RetVal=FALSE, RetVal1, RetVal2, HeadChanged; | ^~~~~~~ samutil.c: In function ‘DDE_ShiftRightBoundaryLeft1’: samutil.c:4592:41: warning: variable ‘Index’ set but not used [-Wunused-but-set-variable] 4592 | Int4 NumBlocks, i, NumRows, Index, BlockCount=0; | ^~~~~ samutil.c: In function ‘DDE_CreateArraysForDenseSeg’: samutil.c:5028:22: warning: variable ‘NumSegs’ set but not used [-Wunused-but-set-variable] 5028 | Int4 NumRows, NumSegs, i, StartIndex, StopIndex, ArrayIndex=0; | ^~~~~~~ samutil.c: In function ‘DDE_AddAGap’: samutil.c:2676:22: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 2676 | else if ((ptxtList == tail) && (!Before)) { | ~~~~~~~~~~^~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_RemoveGapFromEndOfAllRows’: samutil.c:3034:15: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3034 | last_msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c:3049:15: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3049 | last_msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_AddGapToEndOfAllRows’: samutil.c:3118:11: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3118 | vnp = DDE_AddAGap(pEditInfo, i, last_vnp, FALSE, TRUE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_GetLastVNP’: samutil.c:3143:9: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3143 | return(last_vnp); | ^ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_GetNumResidues’: samutil.c:3166:13: warning: ‘to’ may be used uninitialized [-Wmaybe-uninitialized] 3166 | return((to-from) + 1); | ~~~^~~~~~ samutil.c:3153:27: note: ‘to’ was declared here 3153 | Int4 from=-1, to; | ^~ samutil.c: In function ‘DDE_ShiftLeftList’: samutil.c:3923:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 3923 | msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_ShiftRowLeft1’: samutil.c:2325:13: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 2325 | last_msap = (MsaTxtDispPtr) last_vnp->data.ptrvalue; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_RemoveGap’: samutil.c:2854:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 2854 | msap = (MsaTxtDispPtr) vnp->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_ShiftRowRight1’: samutil.c:2356:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 2356 | msap = (MsaTxtDispPtr) DDE_GetLastVNP(ptxtList)->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ samutil.c: In function ‘DDE_LastColumnIsAligned’: samutil.c:4210:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 4210 | msap = (MsaTxtDispPtr) vnp->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ In function ‘DDE_LastColumnIsAligned’, inlined from ‘DDE_ShiftRightBoundaryLeft1’ at samutil.c:4599:7: samutil.c:4210:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 4210 | msap = (MsaTxtDispPtr) vnp->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c: In function ‘DDE_ShiftRightBoundaryLeft1’: samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ In function ‘DDE_LastColumnIsAligned’, inlined from ‘DDE_ShiftRightBoundaryRight1’ at samutil.c:4682:7: samutil.c:4210:8: warning: ‘last_vnp’ may be used uninitialized [-Wmaybe-uninitialized] 4210 | msap = (MsaTxtDispPtr) vnp->data.ptrvalue; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samutil.c: In function ‘DDE_ShiftRightBoundaryRight1’: samutil.c:3137:15: note: ‘last_vnp’ was declared here 3137 | ValNodePtr last_vnp; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvcolor.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvcolor.c:160: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvcolor.c: In function ‘DDV_GetColor’: ddvcolor.c:1422:10: warning: unused variable ‘retval’ [-Wunused-variable] 1422 | Int4 retval = 0; | ^~~~~~ In file included from ../include/samutil.h:234, from ddvcolor.c:165: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF viewmgr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/viewmgr.h:111, from viewmgr.c:165: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from viewmgr.c:167: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from viewmgr.c:168: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ viewmgr.c:683:13: warning: ‘ViewMgr_Swap’ defined but not used [-Wunused-function] 683 | static void ViewMgr_Swap(SeqAlign *salp1, SeqAlign *salp2) | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvcreate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ddvcreate.h:142, from ddvcreate.c:245: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvcreate.c:290:2: warning: missing braces around initializer [-Wmissing-braces] 290 | { | ^ 291 | /* Red Grn Blue Color ColorID Old Hex New Hex */ 292 | 255, 255, 255, /* default 0 0xffffff - */ | { } 293 | 255, 0, 153, /* hotpink 1 0xff1493 0xff0099 */ | { } 294 | 255, 0, 255, /* magenta 2 0xff00ff - */ | { } 295 | 153, 51, 255, /* purple 3 0x9b30ff 0x9933ff */ | { } 296 | 0, 0, 255, /* blue 4 0x0000ff - */ | { } 297 | 00, 153, 255, /* sky 5 0x1e90ff 0x0099ff */ | { } 298 | 0, 255, 255, /* cyan 6 0x00ffff - */ | { } 299 | 0, 255, 153, /* sea 7 0x00ff8f 0x00ff99 */ | { } 300 | 0, 192, 0, /* green 8 0x00ff00 - */ | { } 301 | 255, 255, 0, /* yellow 9 0xffff00 - */ | { } 302 | 255, 204, 0, /* gold 10 0xffa500 0xffcc00 */ | { } 303 | 255, 102, 0, /* orange 11 0xff4500 0xff6600 */ | { } 304 | 255, 0, 0, /* red 12 0xff0000 - */ | { } 305 | 255, 153, 153, /* pink 13 0xff7256 0xff9999 */ | { } 306 | 255, 204, 204, /* pinktint 14 0xffaeb9 0xffcccc */ | { } 307 | 255, 255, 255, /* white 15 0xffffff -*/ | { } 308 | 0, 0, 0, /* black 16 0x000000 - */ | { } 309 | 204, 204, 255, /* bluetint 17 0xb0e2ff - 0xccccff*/ | { } 310 | 153, 255, 153, /* greentint 18 0x9aff9a - 0x99ff99 */ | { } 311 | 255, 255, 153, /* yellowtint 19 0xffec8b - 0xffff99 */ | { } 312 | 102, 102, 102, /* gray 20 0x7d7d7d 0x666666 */ | { } 313 | 153, 102, 51, /* brown 21 0x8b5742 01x996633 */ | { } 314 | 255, 0, 0, /* perm colors 22: red 0xff0000 - */ | { } 315 | 0, 255, 0, /* perm colors 23: green 0x00ff00 - */ | { } 316 | 255, 0, 255, /* perm colors 24: magenta 0xff00ff - */ | { } 317 | 00, 153, 255, /* perm colors 25: sky 0x1e90ff 0x0099ff */ | { } 318 | 153, 51, 255, /* perm colors 26: purple 0x9b30ff 0x9933ff */ | { } 319 | 0, 255, 0, /* SS colors 27: helix, green 0x00ff00 - */ | { } 320 | 255, 204, 0, /* SS colors 28: strand, gold 0xffa500 0xffcc00 */ | { } 321 | 255, 102, 0, /* SS colors 29: turn, orange 0xff4500 0xff6600 */ | { } 322 | 0, 255, 255, /* SS colors 30: coil, cyan ox00ffff - */ | { } 323 | 255, 255, 0, /* highlight colors 31: yellow 0xffff00 - */ | { } 324 | 0, 0, 0 /* background colors 32: black 0x000000 - */ | { 325 | }; | } ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_1’: ddvcreate.c:493:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 493 | while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) | ^~~~ ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_2’: ddvcreate.c:529:21: warning: variable ‘more’ set but not used [-Wunused-but-set-variable] 529 | Boolean more; | ^~~~ ddvcreate.c: In function ‘DDV_CreateDisplayFromIndex_EX2’: ddvcreate.c:779:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 779 | while (more = AlnMgrGetNextAlnBit(mpplp->sap, amp)) | ^~~~ ddvcreate.c:690:21: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 690 | Boolean last; | ^~~~ ddvcreate.c:686:21: warning: variable ‘PopulateTo’ set but not used [-Wunused-but-set-variable] 686 | Int4 PopulateTo; | ^~~~~~~~~~ ddvcreate.c: In function ‘DDV_DisplayNewBLAST’: ddvcreate.c:1942:16: warning: variable ‘what’ set but not used [-Wunused-but-set-variable] 1942 | Uint1 what; | ^~~~ ddvcreate.c: In function ‘UDV_BigEncodeIdxFeat4’: ddvcreate.c:2878:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2878 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/ddvcreate.h:143: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ddvcreate.c:249: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:2362:16: warning: ‘DDV_DisplayBlastSAP’ defined but not used [-Wunused-function] 2362 | static Boolean DDV_DisplayBlastSAP(SeqAlignPtr sap, ValNodePtr mask, | ^~~~~~~~~~~~~~~~~~~ ddvcreate.c:525:16: warning: ‘DDV_CreateDisplayFromIndex_2’ defined but not used [-Wunused-function] 525 | static Boolean DDV_CreateDisplayFromIndex_2(SeqAlignPtr sap, MsaParaGPopListPtr mpplp, Int2 LineSize) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c: In function ‘UDV_BigEncodeIdxFeat4’: ddvcreate.c:2878:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 2878 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:2873:7: note: ‘index_g’ declared here 2873 | Uint4 index_g[2]; | ^~~~~~~ ddvcreate.c: In function ‘DDV_PopulateDisplayForDisc’: ddvcreate.c:1048:30: warning: ‘vnp_para’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | vnp_list[n-1]=vnp_para; | ~~~~~~~~~~~~~^~~~~~~~~ ddvcreate.c:845:31: note: ‘vnp_para’ was declared here 845 | ValNodePtr vnp,vnp2,vnp3,vnp_para,vnp_mtdp=NULL; | ^~~~~~~~ ddvcreate.c: In function ‘UABuildDescriptor2’: ddvcreate.c:1541:27: warning: ‘stopcopy’ may be used uninitialized [-Wmaybe-uninitialized] 1541 | *TotLength+=(stopcopy-startcopy);/*to be used for the display coord. system*/ | ^~ ddvcreate.c:1484:57: note: ‘stopcopy’ was declared here 1484 | Int4 length,r,cumulpop,StartLetter,startcopy,stopcopy,pop,UAnum; | ^~~~~~~~ ddvcreate.c: In function ‘DDV_DumpSAPInAFile’: ddvcreate.c:1798:9: warning: ‘matrix’ may be used uninitialized [-Wmaybe-uninitialized] 1798 | DDV_AffichageParaG(mpplp,0,0,mpplp->LengthAli-1,mpplp->LengthAli,0,option, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1799 | LineSize,hFile,byteSpp,matrix,gclr,NULL); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvcreate.c:1781:17: note: ‘matrix’ was declared here 1781 | Int4Ptr PNTR matrix ; | ^~~~~~ ddvcreate.c: In function ‘DDV_ReadSeqBin’: ddvcreate.c:2593:16: warning: ‘btr’ may be used uninitialized [-Wmaybe-uninitialized] 2593 | return btr; | ^~~ ddvcreate.c:2571:13: note: ‘btr’ was declared here 2571 | Uint1Ptr btr; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF jsavlt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/jsavlt.h:4, from jsavlt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF needleman.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/needleman.h:40, from needleman.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ needleman.c: In function ‘NeedlemanWunschQuadraticByLoc’: needleman.c:281:24: warning: variable ‘bestDbPos’ set but not used [-Wunused-but-set-variable] 281 | Int4 bestQueryPos, bestDbPos; /*position ending best score in | ^~~~~~~~~ needleman.c:281:10: warning: variable ‘bestQueryPos’ set but not used [-Wunused-but-set-variable] 281 | Int4 bestQueryPos, bestDbPos; /*position ending best score in | ^~~~~~~~~~~~ needleman.c: In function ‘FetchSequenceByLoc’: needleman.c:243:12: warning: ‘query’ may be used uninitialized [-Wmaybe-uninitialized] 243 | return query; | ^~~~~ needleman.c:202:13: note: ‘query’ was declared here 202 | Uint1 * query; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF txalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from ../include/txalign.h:228, from txalign.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ txalign.c: In function ‘addLinkoutForDefline’: txalign.c:188:13: warning: variable ‘hasLinkout’ set but not used [-Wunused-but-set-variable] 188 | Boolean hasLinkout=FALSE; | ^~~~~~~~~~ txalign.c: In function ‘addLinkoutForBioseq’: txalign.c:256:13: warning: variable ‘hasLinkout’ set but not used [-Wunused-but-set-variable] 256 | Boolean hasLinkout=FALSE; | ^~~~~~~~~~ txalign.c: In function ‘DrawTextToBuffer’: txalign.c:1254:123: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 1254 | snprintf(checkboxBuf, 200, "", sip->data.intvalue, query_number_glb); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld txalign.c: In function ‘load_align_sum_for_StdSeg’: txalign.c:2230:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2230 | if (bsp = BioseqLockById(SeqLocId(ssp->loc->next))) { | ^~~ txalign.c: In function ‘ShowAlignNodeText2Ex’: txalign.c:3030:13: warning: variable ‘is_end’ set but not used [-Wunused-but-set-variable] 3030 | Boolean is_end, strip_semicolon=TRUE; | ^~~~~~ txalign.c: In function ‘Tx_PrintDefLine’: txalign.c:4079:14: warning: unused variable ‘seqid_length’ [-Wunused-variable] 4079 | Int4 seqid_length = 0, total_length = 0; | ^~~~~~~~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4494:39: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 4494 | } else if (bestid != NULL && !(options & TXALIGN_NO_DUMPGNL) || (options & TXALIGN_NO_ENTREZ)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ txalign.c:4498:33: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 4498 | if (bsp = BioseqLockById(bestid)) { | ^~~ txalign.c:4200:10: warning: unused variable ‘ColumnDistance’ [-Wunused-variable] 4200 | Int2 ColumnDistance=2, extraSpace=0, extraSpace2=0, strLen=0, maxEvalWidth=5, maxNWidth=2; | ^~~~~~~~~~~~~~ txalign.c:4192:43: warning: unused variable ‘sip_list’ [-Wunused-variable] 4192 | SeqIdPtr bestid, gi_list, subject_id, sip_list=NULL, last_id; | ^~~~~~~~ txalign.c:4188:17: warning: variable ‘ptr_start’ set but not used [-Wunused-but-set-variable] 4188 | Char *ptr, *ptr_start, *eval_buff_ptr, *bit_score_buff_ptr; | ^~~~~~~~~ txalign.c: In function ‘FormatScoreFromSeqAlignEx’: txalign.c:4817:25: warning: unused variable ‘t_adj’ [-Wunused-variable] 4817 | Int4 m_adj = 0, t_adj = 0; | ^~~~~ txalign.c:4816:29: warning: unused variable ‘last_t_to’ [-Wunused-variable] 4816 | Int4 last_m_to = 0, last_t_to = 0; | ^~~~~~~~~ txalign.c: In function ‘FSFPrintOneDefline’: txalign.c:4925:14: warning: variable ‘seqid_len’ set but not used [-Wunused-but-set-variable] 4925 | Int4 gi, seqid_len = 0; | ^~~~~~~~~ txalign.c: In function ‘FormatScoreFunc’: txalign.c:5142:13: warning: variable ‘allocated’ set but not used [-Wunused-but-set-variable] 5142 | Boolean allocated, first; | ^~~~~~~~~ txalign.c: In function ‘OOFShowSingleAlignment’: txalign.c:5808:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 5808 | else if(matrix[line1[line_index]][line2[line_index]] > 0) | ~~~~~^~~~~~~~~~~~ txalign.c:5808:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 5808 | else if(matrix[line1[line_index]][line2[line_index]] > 0) | ~~~~~^~~~~~~~~~~~ txalign.c:5575:13: warning: variable ‘lines’ set but not used [-Wunused-but-set-variable] 5575 | Int4 i, lines, k, shift_info = 0; | ^~~~~ txalign.c: In function ‘OOFDisplayTraceBack1’: txalign.c:6063:33: warning: unused variable ‘st’ [-Wunused-variable] 6063 | tmp[10] = " ", *st; | ^~ txalign.c:6063:9: warning: unused variable ‘tmp’ [-Wunused-variable] 6063 | tmp[10] = " ", *st; | ^~~ txalign.c: In function ‘OOFDisplayTraceBack2’: txalign.c:6137:33: warning: unused variable ‘st’ [-Wunused-variable] 6137 | tmp[10] = " ", *st; | ^~ txalign.c: In function ‘FDGetTaxNamesFromBioseq’: txalign.c:6239:21: warning: variable ‘bdsp’ set but not used [-Wunused-but-set-variable] 6239 | BlastDefLinePtr bdsp; | ^~~~ txalign.c: At top level: txalign.c:310:19: warning: ‘ProcessTextInsertion’ declared ‘static’ but never defined [-Wunused-function] 310 | static ValNodePtr ProcessTextInsertion PROTO((AlignNodePtr anp, Int4 m_left, Int4 m_right, BioseqPtr bsp, Int4 line_len, Int1 frame)); | ^~~~~~~~~~~~~~~~~~~~ txalign.c:2915:1: warning: ‘get_seq_id’ defined but not used [-Wunused-function] 2915 | get_seq_id(SeqAlignPtr sap, Int2 index) | ^~~~~~~~~~ txalign.c:1820:16: warning: ‘has_hit_in_region’ defined but not used [-Wunused-function] 1820 | static Boolean has_hit_in_region(Uint1Ptr all_frame) | ^~~~~~~~~~~~~~~~~ txalign.c:112:16: warning: ‘getNameInitials’ defined but not used [-Wunused-function] 112 | static CharPtr getNameInitials(CharPtr name){ | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘snprintf’, inlined from ‘DrawTextToBuffer’ at txalign.c:1288:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: warning: ‘HTML_buffer’ may be used uninitialized [-Wmaybe-uninitialized] 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ txalign.c: In function ‘DrawTextToBuffer’: txalign.c:1094:17: note: ‘HTML_buffer’ was declared here 1094 | CharPtr HTML_buffer; | ^~~~~~~~~~~ txalign.c: In function ‘OOFShowSingleAlignment.isra.0’: txalign.c:5719:12: warning: ‘dna_line_start’ may be used uninitialized [-Wmaybe-uninitialized] 5719 | if (dna_line_start == 0) | ^ txalign.c:5571:32: note: ‘dna_line_start’ was declared here 5571 | Int4 dna_index, pro_index, dna_line_start, pro_line_start; | ^~~~~~~~~~~~~~ txalign.c:5722:11: warning: ‘pro_line_start’ may be used uninitialized [-Wmaybe-uninitialized] 5722 | if(pro_line_start == 0) | ^ txalign.c:5571:48: note: ‘pro_line_start’ was declared here 5571 | Int4 dna_index, pro_index, dna_line_start, pro_line_start; | ^~~~~~~~~~~~~~ In function ‘load_align_sum_for_DenseDiag’, inlined from ‘find_score_in_align’ at txalign.c:2404:21: txalign.c:1941:14: warning: ‘m_spp’ may be used uninitialized [-Wmaybe-uninitialized] 1941 | if(m_spp == NULL || t_spp == NULL) { | ^ txalign.c: In function ‘find_score_in_align’: txalign.c:1876:16: note: ‘m_spp’ was declared here 1876 | SeqPortPtr m_spp, t_spp; | ^~~~~ In function ‘load_align_sum_for_DenseDiag’, inlined from ‘find_score_in_align’ at txalign.c:2404:21: txalign.c:1941:31: warning: ‘t_spp’ may be used uninitialized [-Wmaybe-uninitialized] 1941 | if(m_spp == NULL || t_spp == NULL) { | ^ txalign.c: In function ‘find_score_in_align’: txalign.c:1876:23: note: ‘t_spp’ was declared here 1876 | SeqPortPtr m_spp, t_spp; | ^~~~~ In function ‘load_align_sum_for_DenseSeg’, inlined from ‘find_score_in_align’ at txalign.c:2413:13: txalign.c:2080:35: warning: ‘smtp’ may be used uninitialized [-Wmaybe-uninitialized] 2080 | stdaa_res = SeqMapTableConvert(smtp, t_res); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ txalign.c: In function ‘find_score_in_align’: txalign.c:1980:20: note: ‘smtp’ was declared here 1980 | SeqMapTablePtr smtp; | ^~~~ In file included from ../include/ncbi.h:58: In function ‘translate_faked_cds’, inlined from ‘ShowAlignNodeText2Ex.isra.0’ at txalign.c:3457:46: txalign.c:1753:63: warning: ‘m_len’ may be used uninitialized [-Wmaybe-uninitialized] 1753 | n = MAX(0, (master_len-1 - m_stop)/3 -1); | ~~~~~~~~~~^~ txalign.c: In function ‘ShowAlignNodeText2Ex.isra.0’: txalign.c:3025:10: note: ‘m_len’ was declared here 3025 | Int4 m_len; /*length of the master sequence*/ | ^~~~~ txalign.c: In function ‘ShowTextAlignFromAnnot3’: txalign.c:949:12: warning: ‘retval’ may be used uninitialized [-Wmaybe-uninitialized] 949 | return retval; | ^~~~~~ txalign.c:726:13: note: ‘retval’ was declared here 726 | Boolean retval, matrix_loaded=FALSE; | ^~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4647:50: warning: ‘%s’ directive writing up to 2048 bytes into a region of size 2038 [-Wformat-overflow=] 4647 | sprintf(buffer1, "%s", id_buffer, bit_score_buff_ptr); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintDefLinesFromSeqAlignWithPath’ at txalign.c:4647:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 2074 bytes into a destination of size 2049 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ txalign.c: In function ‘PrintDefLinesFromSeqAlignWithPath’: txalign.c:4645:51: warning: ‘%s’ directive writing up to 2048 bytes into a region of size 2037 [-Wformat-overflow=] 4645 | sprintf(buffer1, " %s", id_buffer, bit_score_buff_ptr); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘PrintDefLinesFromSeqAlignWithPath’ at txalign.c:4645:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 2074 bytes into a destination of size 2049 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF fdlobj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from fdlobj.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ fdlobj.c: In function ‘BlastDefLineSetAsnRead’: fdlobj.c:69:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 69 | AsnReadFunc func; | ^~~~ fdlobj.c: In function ‘BlastDefLineAsnRead’: fdlobj.c:202:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 202 | AsnReadFunc func; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF alignmgr2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/alignmgr2.h:110, from alignmgr2.c:242: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ alignmgr2.c: In function ‘AlnMgr2IndexSingleDenseSegSA’: alignmgr2.c:885:13: warning: statement with no effect [-Wunused-value] 885 | for (j; jnumseg && next == -1; j++) | ^~~ alignmgr2.c: In function ‘AlnMgr2CopySeg’: alignmgr2.c:2984:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2984 | if (ldelta = ABS(s->beg - beg)) { | ^~~~~~ alignmgr2.c: In function ‘AlnMgr2AddInNewPairwiseSA’: alignmgr2.c:3221:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3221 | while (a = AlnMgr2GetNextSeqPiece(a)) { | ^ alignmgr2.c:3223:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3223 | while (b = AlnMgr2GetNextLimitedSeqPiece(b, a)) { | ^ alignmgr2.c:3233:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3233 | while (A = AlnMgr2GetNextSeqPiece(A)) { | ^ alignmgr2.c:3237:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3237 | while (B = AlnMgr2GetNextLimitedSeqPiece(B, A)) {}; | ^ alignmgr2.c: In function ‘AlnMgr2SetUnaln’: alignmgr2.c:5410:22: warning: variable ‘dsp’ set but not used [-Wunused-but-set-variable] 5410 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2PrintSeqAlign’: alignmgr2.c:5623:17: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 5623 | while (more = AlnMgr2GetNextAlnBit(sap, amp)) | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNextAlnBit’: alignmgr2.c:5719:21: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 5719 | Boolean found; | ^~~~~ alignmgr2.c: In function ‘AlnMgr2GetUnalignedInfo’: alignmgr2.c:6085:22: warning: variable ‘saip’ set but not used [-Wunused-but-set-variable] 6085 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetInterruptInfo’: alignmgr2.c:6331:7: warning: statement with no effect [-Wunused-value] 6331 | for (i; isegnum; i++) | ^~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLength’: alignmgr2.c:6774:20: warning: comparison between pointer and zero character constant [-Wpointer-compare] 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ^~ alignmgr2.c:6774:8: note: did you mean to dereference the pointer? 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ^ alignmgr2.c: In function ‘AlnMgr2ComputeScoreForSeqAlign’: alignmgr2.c:8341:17: warning: variable ‘numseqs’ set but not used [-Wunused-but-set-variable] 8341 | Int4 numseqs; | ^~~~~~~ alignmgr2.c:8339:17: warning: variable ‘mismatch’ set but not used [-Wunused-but-set-variable] 8339 | Int4 mismatch; | ^~~~~~~~ alignmgr2.c:8338:17: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 8338 | Int4 len; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ alignmgr2.c:3557:13: warning: ‘AlnMgr2AddInNewSA’ defined but not used [-Wunused-function] 3557 | static void AlnMgr2AddInNewSA(SeqAlignPtr parent, SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~ alignmgr2.c:2368:18: warning: ‘AlnMgr2GetEdgeList’ defined but not used [-Wunused-function] 2368 | static AMEdgePtr AlnMgr2GetEdgeList(Int4 vertexnum, AMEdgePtr edge_head, AMEdgePtr already_used) | ^~~~~~~~~~~~~~~~~~ alignmgr2.c:2140:13: warning: ‘AlnMgr2SortVerticesByNumEdges’ defined but not used [-Wunused-function] 2140 | static void AlnMgr2SortVerticesByNumEdges(AMVertexPtr PNTR vertexarray, Int4 numvertices) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:1061:13: warning: ‘AlnMgr2UnpackSeqAlignChain’ defined but not used [-Wunused-function] 1061 | static void AlnMgr2UnpackSeqAlignChain(SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘AlnMgr2UnpackSeqAlign’, inlined from ‘AlnMgr2IndexLite’ at alignmgr2.c:1169:9: alignmgr2.c:1001:33: warning: ‘sap_segs_prev’ may be used uninitialized [-Wmaybe-uninitialized] 1001 | sap_segs_prev->next = (SeqAlignPtr)(sap_segs->segs); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2IndexLite’: alignmgr2.c:968:17: note: ‘sap_segs_prev’ was declared here 968 | SeqAlignPtr sap_segs_prev; | ^~~~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2GetUnalignedInfo’: alignmgr2.c:6106:26: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6106 | if (dsp->starts[dsp->dim*i+row-1] != -1) | ~~~^~~~~ alignmgr2.c:6082:21: note: ‘dsp’ was declared here 6082 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2GetMaxUnalignedLength’: alignmgr2.c:7066:23: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7066 | for (row=0; rowdim && !found; row++) | ~~~^~~~~ alignmgr2.c:7042:21: note: ‘dsp’ was declared here 7042 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7068:23: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7068 | for (i=0; isrdp[row]->numunaln && !found; i++) | ~~~~^~~~~~ alignmgr2.c:7048:22: note: ‘saip’ was declared here 7048 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetInterruptInfo’: alignmgr2.c:6178:11: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6178 | if (dsp->numseg < interrupt->segnum) | ~~~^~~~~~~~ alignmgr2.c:6148:22: note: ‘dsp’ was declared here 6148 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6180:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6180 | if (saip->anchor > 0) | ~~~~^~~~~~~~ alignmgr2.c:6157:22: note: ‘saip’ was declared here 6157 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c:6353:16: warning: ‘iip’ may be used uninitialized [-Wmaybe-uninitialized] 6353 | iip->strand = strand; | ~~~~~~~~~~~~^~~~~~~~ alignmgr2.c:6150:22: note: ‘iip’ was declared here 6150 | AMInterrInfoPtr iip; | ^~~ In function ‘AlnMgr2GetNthSeqRangeInSASet’, inlined from ‘AlnMgr2GetNthSeqRangeInSA’ at alignmgr2.c:6470:10: alignmgr2.c:6595:14: warning: ‘from’ may be used uninitialized [-Wmaybe-uninitialized] 6595 | *start = from; | ~~~~~~~^~~~~~ alignmgr2.c: In function ‘AlnMgr2GetNthSeqRangeInSA’: alignmgr2.c:6567:22: note: ‘from’ declared here 6567 | Int4 from; | ^~~~ In function ‘AlnMgr2GetNthSeqRangeInSASet’, inlined from ‘AlnMgr2GetNthSeqRangeInSA’ at alignmgr2.c:6470:10: alignmgr2.c:6595:14: warning: ‘from’ may be used uninitialized [-Wmaybe-uninitialized] 6595 | *start = from; | ~~~~~~~^~~~~~ alignmgr2.c: In function ‘AlnMgr2GetNthSeqRangeInSA’: alignmgr2.c:6567:22: note: ‘from’ declared here 6567 | Int4 from; | ^~~~ alignmgr2.c:6486:76: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6486 | end = dsp->starts[srdp->sect[srdp->numsect-1]*(dsp->dim) + n-1] + dsp->lens[srdp->sect[srdp->numsect-1]] - 1; | ~~~^~~~~~ alignmgr2.c:6449:21: note: ‘dsp’ was declared here 6449 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6476:16: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6476 | if (n > saip->numrows || n <= 0) | ~~~~^~~~~~~~~ alignmgr2.c:6451:22: note: ‘saip’ was declared here 6451 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthRowSpanInSA’: alignmgr2.c:6558:41: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6558 | *stop = saip->aligncoords[i] + dsp->lens[srdp->sect[srdp->numsect-1]] - 1; | ~~~^~~~~~ alignmgr2.c:6510:21: note: ‘dsp’ was declared here 6510 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6533:16: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6533 | if (n > saip->numrows || n <= 0) | ~~~~^~~~~~~~~ alignmgr2.c:6512:22: note: ‘saip’ was declared here 6512 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLength’: alignmgr2.c:6786:22: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6786 | for (i=0; inumseg; i++) | ~~~^~~~~~~~ alignmgr2.c:6751:21: note: ‘dsp’ was declared here 6751 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6774:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6774 | if (saip->unaln == FALSE || fill_in == FALSE) | ~~~~^~~~~~~ alignmgr2.c:6755:22: note: ‘saip’ was declared here 6755 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c:6789:17: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 6789 | len += AlnMgr2GetMaxUnalignedLength(salp, i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:6756:21: note: ‘salp’ was declared here 6756 | SeqAlignPtr salp; | ^~~~ In file included from ../include/ncbi.h:59: alignmgr2.c: In function ‘AlnMgr2GetNextAlnBit’: alignmgr2.c:5787:35: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 5787 | trans = (Uint2Ptr)MemNew(dsp->numseg*sizeof(Uint2)); | ~~~^~~~~~~~ alignmgr2.c:5717:21: note: ‘dsp’ was declared here 5717 | DenseSegPtr dsp; | ^~~ alignmgr2.c:5759:27: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 5759 | if (amp->row_num > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:5727:22: note: ‘saip’ was declared here 5727 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2IsSAPDiscAli’: alignmgr2.c:6813:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6813 | if (saip->numunaln > 0) | ~~~~^~~~~~~~~~ alignmgr2.c:6799:22: note: ‘saip’ was declared here 6799 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNumAlnBlocks’: alignmgr2.c:6836:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6836 | if (saip->numunaln >= 0) | ~~~~^~~~~~~~~~ alignmgr2.c:6822:22: note: ‘saip’ was declared here 6822 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthBlockRange’: alignmgr2.c:6866:17: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6866 | if (n >= saip->numunaln) | ~~~~^~~~~~~~~~ alignmgr2.c:6848:22: note: ‘saip’ was declared here 6848 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNthUnalignedForNthRow’: alignmgr2.c:6927:57: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 6927 | if (i == -1 || saip->srdp[row-1]->unaligned[i] >= dsp->numseg-1) | ~~~^~~~~~~~ alignmgr2.c:6887:22: note: ‘dsp’ was declared here 6887 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6907:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6907 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:6889:22: note: ‘saip’ was declared here 6889 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2GetNextLengthBit’: alignmgr2.c:7021:25: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7021 | maxseg = dsp->numseg-1; | ~~~^~~~~~~~ alignmgr2.c:6954:22: note: ‘dsp’ was declared here 6954 | DenseSegPtr dsp; | ^~~ alignmgr2.c:6974:12: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 6974 | if (saip->numunaln == -1) /* the whole thing is just one big aligned segment */ | ~~~~^~~~~~~~~~ alignmgr2.c:6958:22: note: ‘saip’ was declared here 6958 | SAIndex2Ptr saip; | ^~~~ In function ‘binary_search_on_uint4_list’, inlined from ‘AlnMgr2GetNumSegsInRange’ at alignmgr2.c:7185:12: alignmgr2.c:6038:13: warning: ‘aligncoords’ may be used uninitialized [-Wmaybe-uninitialized] 6038 | if (list == NULL || listlen == 0) | ^ alignmgr2.c: In function ‘AlnMgr2GetNumSegsInRange’: alignmgr2.c:7150:21: note: ‘aligncoords’ was declared here 7150 | Uint4Ptr aligncoords; | ^~~~~~~~~~~ alignmgr2.c:7185:62: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7185 | start = binary_search_on_uint4_list(aligncoords, from, dsp->numseg); | ~~~^~~~~~~~ alignmgr2.c:7152:21: note: ‘dsp’ was declared here 7152 | DenseSegPtr dsp; | ^~~ alignmgr2.c: In function ‘AlnMgr2MapBioseqToSeqAlign’: alignmgr2.c:7649:51: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7649 | offset = pos - dsp->starts[(srdp->sect[L])*(dsp->dim)+row-1]; | ~~~~^~~~~~ alignmgr2.c:7590:21: note: ‘dsp’ was declared here 7590 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7619:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7619 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:7596:22: note: ‘saip’ was declared here 7596 | SAIndex2Ptr saip; | ^~~~ alignmgr2.c: In function ‘AlnMgr2MapSeqAlignToBioseq’: alignmgr2.c:7728:36: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 7728 | return (dsp->starts[sect*(dsp->dim)+row-1] + offset); | ~~~~^~~~~~ alignmgr2.c:7685:21: note: ‘dsp’ was declared here 7685 | DenseSegPtr dsp; | ^~~ alignmgr2.c:7712:18: warning: ‘saip’ may be used uninitialized [-Wmaybe-uninitialized] 7712 | if (row > saip->numrows) | ~~~~^~~~~~~~~ alignmgr2.c:7688:21: note: ‘saip’ was declared here 7688 | SAIndex2Ptr saip; | ^~~~ In function ‘AlnMgr2FindAnchor’, inlined from ‘AlnMgr2GetSubAlign’ at alignmgr2.c:8036:13: alignmgr2.c:7554:7: warning: ‘sap_real’ may be used uninitialized [-Wmaybe-uninitialized] 7554 | if (sap == NULL || sap->saip == NULL) | ^ alignmgr2.c: In function ‘AlnMgr2GetSubAlign’: alignmgr2.c:7999:21: note: ‘sap_real’ was declared here 7999 | SeqAlignPtr sap_real; | ^~~~~~~~ alignmgr2.c: In function ‘AlnMgr2FillInUnaligned’: alignmgr2.c:9869:12: warning: ‘offset’ may be used uninitialized [-Wmaybe-uninitialized] 9869 | curr = curr + 1 + offset; | ~~~~~^~~~~~~~~~~~~~~~~~~ alignmgr2.c:9754:17: note: ‘offset’ was declared here 9754 | Int4 offset; | ^~~~~~ alignmgr2.c: In function ‘AlnMgr2MapBioseqToSeqAlignStdSeg’: alignmgr2.c:10175:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10175 | stop1 = SeqLocStop(slp_longest); | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2MapSeqAlignToBioseqStdSeg’: alignmgr2.c:10209:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10209 | stop1 = SeqLocStop(slp_longest); | ^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ alignmgr2.c: In function ‘AlnMgr2GetAlnLengthStdSeg’: alignmgr2.c:10236:12: warning: ‘slp_longest’ may be used uninitialized [-Wmaybe-uninitialized] 10236 | return (SeqLocLen(slp_longest)); | ~^~~~~~~~~~~~~~~~~~~~~~~ alignmgr2.c:10131:15: note: ‘slp_longest’ was declared here 10131 | SeqLocPtr slp_longest; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF alnread.c In function ‘s_AddDeflineFromOrganismLine’, inlined from ‘s_ReadOrgNamesFromText’ at alnread.c:2949:9: alnread.c:2876:17: warning: ‘free’ called on pointer ‘clp_145->end’ with nonzero offset 1 [-Wfree-nonheap-object] 2876 | free (defline); | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF acerdapi.c acerdapi.c: In function ‘DoesSeqStringMatchBsp’: acerdapi.c:201:30: warning: variable ‘seq_len’ set but not used [-Wunused-but-set-variable] 201 | Int4 ctr, pos = 0, i, len, seq_len; | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from acerdapi.c:40: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF aceread.c aceread.c:3308:12: warning: ‘s_GetUngappedPosition’ defined but not used [-Wunused-function] 3308 | static int s_GetUngappedPosition (int gapped_pos, char *seq) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:276:13: warning: ‘AdjustGapInfoFor3Trim’ defined but not used [-Wunused-function] 276 | static void AdjustGapInfoFor3Trim (TGapInfoPtr gap_info, int new_len) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:247:13: warning: ‘AdjustGapInfoFor5Trim’ defined but not used [-Wunused-function] 247 | static void AdjustGapInfoFor5Trim (TGapInfoPtr gap_info, int trim) | ^~~~~~~~~~~~~~~~~~~~~ aceread.c:134:12: warning: ‘s_IsGapChar’ defined but not used [-Wunused-function] 134 | static int s_IsGapChar (char ch, char *gap_chars) | ^~~~~~~~~~~ aceread.c: In function ‘ReadListFree’: aceread.c:2148:11: warning: pointer ‘r_next_11’ used after ‘free’ [-Wuse-after-free] 2148 | r = r_next; | ~~^~~~~~~~ aceread.c:2147:9: note: call to ‘free’ here 2147 | free (r); | ^~~~~~~~ aceread.c: In function ‘s_ReadContig’: aceread.c:1477:12: warning: ‘linestring’ may be used uninitialized [-Wmaybe-uninitialized] 1477 | if (linestring != NULL) free (linestring); | ^ aceread.c:1384:16: note: ‘linestring’ was declared here 1384 | char *linestring; | ^~~~~~~~~~ rm -f libncbiobj.a ar cru libncbiobj.a objacces.o objalign.o objall.o objbibli.o objfeat.o objgen.o objloc.o objmedli.o objpub.o objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o objsub.o objprt.o objfdef.o objalignloc.o objtable.o objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o objvalid.o mimapi.o cddapi.o seqport.o sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o valid.o valapi.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o acerdapi.o aceread.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiobj.a ../lib ranlib ../lib/libncbiobj.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cdentrez.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from cdentrez.c:162: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdentrez.c:283:23: warning: ‘CdEntMlSumGet’ declared ‘static’ but never defined [-Wunused-function] 283 | static DocSumPtr NEAR CdEntMlSumGet PROTO((Int4 uid)); | ^~~~~~~~~~~~~ cdentrez.c:310:23: warning: ‘CdEntSeqSumGet’ declared ‘static’ but never defined [-Wunused-function] 310 | static DocSumPtr NEAR CdEntSeqSumGet PROTO((Int4 uid, DocType type)); | ^~~~~~~~~~~~~~ cdentrez.c:2935:23: warning: ‘MedSumAsnRead’ defined but not used [-Wunused-function] 2935 | static DocSumPtr NEAR MedSumAsnRead (AsnIoPtr aip, DocUid uid) | ^~~~~~~~~~~~~ cdentrez.c:1616:26: warning: ‘FreePostingList’ defined but not used [-Wunused-function] 1616 | static ByteStorePtr NEAR FreePostingList (ByteStorePtr lst) | ^~~~~~~~~~~~~~~ cdentrez.c:307:20: warning: ‘BIOSEQ_id_E’ defined but not used [-Wunused-variable] 307 | static AsnTypePtr BIOSEQ_id_E = NULL; | ^~~~~~~~~~~ cdentrez.c: In function ‘CdEntrezMergeTerm’: cdentrez.c:2637:12: warning: ‘termpage’ may be used uninitialized [-Wmaybe-uninitialized] 2637 | if (termpage >= 0) { | ^ cdentrez.c:2573:9: note: ‘termpage’ was declared here 2573 | Int4 termpage; | ^~~~~~~~ cdentrez.c:2672:17: warning: ‘special’ may be used uninitialized [-Wmaybe-uninitialized] 2672 | *spcl = special; | ~~~~~~^~~~~~~~~ cdentrez.c:2570:9: note: ‘special’ was declared here 2570 | Int4 special; | ^~~~~~~ cdentrez.c:2665:18: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 2665 | if (scanOk && total > 0) { | ~~~~~~~^~~~~~~~~~~~ cdentrez.c:2572:9: note: ‘total’ was declared here 2572 | Int4 total; | ^~~~~ In file included from ../include/ncbi.h:62: cdentrez.c: In function ‘CdEntTLAddTerm’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ In function ‘FindTermNode’, inlined from ‘CdEntTLAddTerm’ at cdentrez.c:617:14: cdentrez.c:1895:24: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized] 1895 | if (scanOk && total > 0) { | ~~~~~~~^~~~~~~~~~~~ cdentrez.c: In function ‘CdEntTLAddTerm’: cdentrez.c:1787:13: note: ‘total’ was declared here 1787 | Int4 total; | ^~~~~ cdentrez.c: In function ‘CdLinkUidList’: cdentrez.c:938:16: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 938 | return count; | ^~~~~ cdentrez.c:926:14: note: ‘count’ was declared here 926 | Int4 count; | ^~~~~ cdentrez.c: In function ‘CdTermListByTerm’: cdentrez.c:1023:24: warning: ‘first’ may be used uninitialized [-Wmaybe-uninitialized] 1023 | the_first_page = first; | ~~~~~~~~~~~~~~~^~~~~~~ cdentrez.c:1011:15: note: ‘first’ was declared here 1011 | Int4 first; | ^~~~~ cdentrez.c: In function ‘CdEntrezFindTerm’: cdentrez.c:1119:20: warning: ‘ctp’ may be used uninitialized [-Wmaybe-uninitialized] 1119 | if (ctp == NULL) | ^ cdentrez.c:1100:19: note: ‘ctp’ was declared here 1100 | CdTermPtr ctp; | ^~~ cdentrez.c: In function ‘CdEntMedlineEntryListGet’: cdentrez.c:2715:20: warning: ‘aip’ may be used uninitialized [-Wmaybe-uninitialized] 2715 | if (aip != NULL) | ^ cdentrez.c:2697:18: note: ‘aip’ was declared here 2697 | AsnIoPtr aip; | ^~~ cdentrez.c: In function ‘CdSeqSumAsnRead’: cdentrez.c:3424:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3424 | sprintf (cds, " cds%d", (int) proteins); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘CdSeqSumAsnRead’ at cdentrez.c:3424:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cdromlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objacces.h:64, from ../include/cdromlib.h:71, from cdromlib.c:73: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cdnewlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objacces.h:64, from ../include/cdromlib.h:71, from cdnewlib.c:208: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdnewlib.c:600:27: warning: missing braces around initializer [-Wmissing-braces] 600 | struct CdFInfo _finfo[] = { | ^ 601 | "", 0, 0, | { } 602 | "hca", MAGIC_hca, FORMAT_hca, | { } 603 | "sum", MAGIC_sum, FORMAT_sum, | { } 604 | "lnk", MAGIC_lnk, FORMAT_lnk, | { } 605 | "ofs", MAGIC_ofs, FORMAT_ofs, | { } 606 | "oix", MAGIC_oix, FORMAT_oix, | { } 607 | "trm", MAGIC_trm, FORMAT_trm, | { } 608 | "tix", MAGIC_tix, FORMAT_tix, | { } 609 | "pst", MAGIC_pst, FORMAT_pst, | { } 610 | "inf", MAGIC_inf, FORMAT_inf | { 611 | }; | } cdnewlib.c:614:27: warning: missing braces around initializer [-Wmissing-braces] 614 | struct CdDirInfo _dir[] = { | ^ cdnewlib.c: In function ‘cd3_CdDocAsnOpen’: cdnewlib.c:1342:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1342 | return (AsnIo*) CatastrophicFailure(1); | ^ cdnewlib.c:1327:23: warning: unused variable ‘fdir’ [-Wunused-variable] 1327 | char *fdir = NULL; | ^~~~ cdnewlib.c: In function ‘UidIndex_ReadPage’: cdnewlib.c:1937:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1937 | return (long*)CatastrophicFailure(1); | ^ cdnewlib.c:1945:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1945 | return (long*)CatastrophicFailure(1); | ^ cdnewlib.c: In function ‘CdDevice_Init’: cdnewlib.c:2739:13: warning: variable ‘cd_num’ set but not used [-Wunused-but-set-variable] 2739 | int cd_num; | ^~~~~~ cdnewlib.c: At top level: cdnewlib.c:3605:13: warning: ‘Cache_Purge’ defined but not used [-Wunused-function] 3605 | static void Cache_Purge (Cache *cache) | ^~~~~~~~~~~ cdnewlib.c:3592:14: warning: ‘Cache_Peek’ defined but not used [-Wunused-function] 3592 | static void* Cache_Peek (Cache *cache, long id) | ^~~~~~~~~~ cdnewlib.c:3569:12: warning: ‘Cache_Touch’ defined but not used [-Wunused-function] 3569 | static int Cache_Touch (Cache *cache, long id) | ^~~~~~~~~~~ cdnewlib.c:3506:12: warning: ‘Cache_Delete’ defined but not used [-Wunused-function] 3506 | static int Cache_Delete (Cache *cache, long id) | ^~~~~~~~~~~~ cdnewlib.c:638:18: warning: ‘_div’ defined but not used [-Wunused-variable] 638 | static DivInfo * _div; | ^~~~ cdnewlib.c:582:15: warning: ‘_empty_string’ defined but not used [-Wunused-variable] 582 | static char * _empty_string = ""; | ^~~~~~~~~~~~~ cdnewlib.c: In function ‘trmncmp’: cdnewlib.c:2375:12: warning: ‘c1’ may be used uninitialized [-Wmaybe-uninitialized] 2375 | if (c1 == '/') | ^ cdnewlib.c:2362:16: note: ‘c1’ was declared here 2362 | int i, c1, c2; | ^~ cdnewlib.c:2377:17: warning: ‘c2’ may be used uninitialized [-Wmaybe-uninitialized] 2377 | else if (c2 == '/') | ^ cdnewlib.c:2362:20: note: ‘c2’ was declared here 2362 | int i, c1, c2; | ^~ cdnewlib.c: In function ‘CdDevice_FileBuildPath.isra.0’: cdnewlib.c:2679:33: warning: ‘__strncat_chk’ specified bound 16 equals destination size [-Wstringop-truncation] 2679 | strncat(volname,cddev->volume->volume_name,sizeof volname); | ^ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘CdDevice_FileBuildPath.isra.0’ at cdnewlib.c:2679:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 16 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ cdnewlib.c: In function ‘UnixFileGets’: cdnewlib.c:1509:6: warning: ‘ch’ may be used uninitialized [-Wmaybe-uninitialized] 1509 | if (ch == '\0') { | ^ cdnewlib.c:1489:8: note: ‘ch’ was declared here 1489 | int ch; | ^~ cdnewlib.c: In function ‘CdDevice_Init’: cdnewlib.c:2751:17: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-truncation] 2751 | strncat(fpath,cddev->inf.root,sizeof fpath); | ^ cdnewlib.c:2769:41: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-truncation] 2769 | strncat(fpath,cddev->inf.root,sizeof fpath); | ^ In function ‘strncat’, inlined from ‘CdDevice_Init’ at cdnewlib.c:2751:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘CdDevice_Init’ at cdnewlib.c:2769:6: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 256 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ cdnewlib.c: In function ‘TrmIndex_Lookup’: cdnewlib.c:2166:19: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized] 2166 | for ( ; d <= 0 && mid >0; --mid) | ~~^~~~ cdnewlib.c:2136:31: note: ‘d’ was declared here 2136 | int lo, hi, mid, len, d; | ^ cdnewlib.c:2166:31: warning: ‘mid’ may be used uninitialized [-Wmaybe-uninitialized] 2166 | for ( ; d <= 0 && mid >0; --mid) | ~~~~^~ cdnewlib.c:2136:21: note: ‘mid’ was declared here 2136 | int lo, hi, mid, len, d; | ^~~ cdnewlib.c:2168:41: warning: ‘term’ may be used uninitialized [-Wmaybe-uninitialized] 2168 | if (d==0 && len == (int)strlen(term)) | ^~~~~~~~~~~~ cdnewlib.c:2137:15: note: ‘term’ was declared here 2137 | char *term; | ^~~~ cdnewlib.c: In function ‘UidIndex_Lookup’: cdnewlib.c:1986:27: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 1986 | page_num = (uid < *p && mid >0) ? mid-1 : mid; | ^~ cdnewlib.c:1956:22: note: ‘p’ was declared here 1956 | long *page, *p; | ^ cdnewlib.c:1986:30: warning: ‘mid’ may be used uninitialized [-Wmaybe-uninitialized] 1986 | page_num = (uid < *p && mid >0) ? mid-1 : mid; | ~~~~~~~~~~^~~~~~~~~~ cdnewlib.c:1953:21: note: ‘mid’ was declared here 1953 | int lo, hi, mid; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF casn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from casn.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cdconfig.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cdconfig.c:75: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:58: cdconfig.c: In function ‘ChangeMedia’: ../include/ncbistd.h:247:15: warning: statement with no effect [-Wunused-value] 247 | #define FALSE ((Nlm_Boolean)0) | ^ ../include/ncbifile.h:144:76: note: in expansion of macro ‘FALSE’ 144 | #define EjectCd(sVolume, deviceName, rawDeviceName, mountPoint, mountCmd) FALSE | ^~~~~ cdconfig.c:941:29: note: in expansion of macro ‘EjectCd’ 941 | EjectCd(toBeEjected->entrez_info->volume_label, | ^~~~~~~ ../include/ncbistd.h:247:15: warning: statement with no effect [-Wunused-value] 247 | #define FALSE ((Nlm_Boolean)0) | ^ ../include/ncbifile.h:145:76: note: in expansion of macro ‘FALSE’ 145 | #define MountCd(sVolume, deviceName, mountPoint, mountCmd) FALSE | ^~~~~ cdconfig.c:960:17: note: in expansion of macro ‘MountCd’ 960 | MountCd(newMedia->entrez_info->volume_label, cdm->device_name, | ^~~~~~~ cdconfig.c: At top level: cdconfig.c:191:17: warning: ‘UnMarkLRUineligible’ declared ‘static’ but never defined [-Wunused-function] 191 | static void UnMarkLRUineligible PROTO((void)); | ^~~~~~~~~~~~~~~~~~~ cdconfig.c: In function ‘EntrezInfoMerge’: cdconfig.c:1174:46: warning: ‘InfoWithMaxTypes’ may be used uninitialized [-Wmaybe-uninitialized] 1174 | if (mediaCount <= 1 && ! InfoWithMaxTypes->no_compression) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ cdconfig.c:1140:19: note: ‘InfoWithMaxTypes’ was declared here 1140 | EntrezInfoPtr InfoWithMaxTypes; | ^~~~~~~~~~~~~~~~ cdconfig.c:1248:40: warning: ‘besttype’ may be used uninitialized [-Wmaybe-uninitialized] 1248 | new->types[i].minuid = besttype->minuid; | ~~~~~~~~^~~~~~~~ cdconfig.c:1141:23: note: ‘besttype’ was declared here 1141 | EntrezTypeDataPtr besttype; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/cdrom.h:9, from objentr.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objentr.c: In function ‘CdRomAsnLoad’: objentr.c:170:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 170 | if (loaded) | ^~ objentr.c:172:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 172 | loaded = TRUE; | ^~~~~~ objentr.c: In function ‘DocSumAsnRead’: objentr.c:970:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 970 | AsnReadFunc func; | ^~~~ objentr.c:969:12: warning: unused variable ‘isError’ [-Wunused-variable] 969 | Boolean isError = FALSE; | ^~~~~~~ objentr.c: At top level: objentr.c:806:23: warning: ‘EntrezDivInfo_Destruct’ defined but not used [-Wunused-function] 806 | static EntrezDivInfo* EntrezDivInfo_Destruct (EntrezDivInfo *div) | ^~~~~~~~~~~~~~~~~~~~~~ objentr.c:771:16: warning: ‘EntrezLinkInfo_AsnWrite’ defined but not used [-Wunused-function] 771 | static Boolean EntrezLinkInfo_AsnWrite (const EntrezLinkInfo *link, AsnIo *stream, AsnType *type) | ^~~~~~~~~~~~~~~~~~~~~~~ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:376:25: warning: ‘tinf’ may be used uninitialized [-Wmaybe-uninitialized] 376 | EntrezTypeInfo_AsnRead(tinf++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:238:25: note: ‘tinf’ was declared here 238 | EntrezTypeInfo *tinf; | ^~~~ objentr.c:378:25: warning: ‘fld’ may be used uninitialized [-Wmaybe-uninitialized] 378 | EntrezFieldInfo_AsnRead(fld++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:239:26: note: ‘fld’ was declared here 239 | EntrezFieldInfo *fld; | ^~~ objentr.c:380:25: warning: ‘link’ may be used uninitialized [-Wmaybe-uninitialized] 380 | EntrezLinkInfo_AsnRead(link++,stream,atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ objentr.c:240:25: note: ‘link’ was declared here 240 | EntrezLinkInfo *link; | ^~~~ In function ‘EntrezDivInfo_AsnRead’, inlined from ‘EntrezInfoAsnRead’ at objentr.c:392:4: objentr.c:818:12: warning: ‘div’ may be used uninitialized [-Wmaybe-uninitialized] 818 | if (div == NULL) | ^ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:241:24: note: ‘div’ was declared here 241 | EntrezDivInfo *div; | ^~~ In function ‘EntrezDivInfo_AsnRead’, inlined from ‘EntrezInfoAsnRead’ at objentr.c:392:4: objentr.c:856:44: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 856 | div->docs[i++] = val.intvalue; | ~^~ objentr.c: In function ‘EntrezInfoAsnRead’: objentr.c:824:21: note: ‘i’ was declared here 824 | int i; | ^ rm -f libncbicdr.a ar cru libncbicdr.a cdentrez.o cdromlib.o cdnewlib.o casn.o cdconfig.o objentr.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicdr.a ../lib ranlib ../lib/libncbicdr.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibbutns.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibbutns.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibbutns.c: In function ‘Nlm_CheckCallback’: vibbutns.c:354:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 354 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_RadioCallback’: vibbutns.c:373:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 373 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_SetButtonStatus’: vibbutns.c:694:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 694 | Nlm_Int2 val; | ^~~ vibbutns.c: In function ‘Nlm_NewButton.constprop.0’: vibbutns.c:1159:3: warning: ‘call’ may be used uninitialized [-Wmaybe-uninitialized] 1159 | XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vibbutns.c:1021:20: note: ‘call’ was declared here 1021 | String call; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibextra.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibextra.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibextra.c: In function ‘Nlm_RGB2HSL.constprop.0’: vibextra.c:1216:7: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | i = (min + 1); if ( i > 2 ) i=0; | ~~^~~~~~~~~~~ vibextra.c:1191:15: note: ‘min’ was declared here 1191 | int i, min; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibfiles.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibfiles.c: In function ‘Nlm_WriteCard’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ In function ‘Nlm_CardToStr’, inlined from ‘Nlm_WriteCard’ at vibfiles.c:350:3: vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3, inlined from ‘Nlm_WriteCard’ at vibfiles.c:350:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_WriteInt’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ In function ‘Nlm_IntToStr’, inlined from ‘Nlm_WriteInt’ at vibfiles.c:375:3: vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3, inlined from ‘Nlm_WriteInt’ at vibfiles.c:375:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_WriteLong’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ In function ‘Nlm_LongToStr’, inlined from ‘Nlm_WriteLong’ at vibfiles.c:400:3: vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3, inlined from ‘Nlm_WriteLong’ at vibfiles.c:400:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_CardToStr’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_IntToStr’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_LongToStr’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibforms.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibforms.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibgroup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibgroup.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF viblists.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from viblists.c:164: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ viblists.c: In function ‘Nlm_SetListPosition’: viblists.c:1121:15: warning: variable ‘is_realized’ set but not used [-Wunused-but-set-variable] 1121 | Nlm_Boolean is_realized; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibmenus.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmenus.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmenus.c: In function ‘Nlm_IsMenuItemChecked’: vibmenus.c:563:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 563 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CheckMenuItem’: vibmenus.c:591:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 591 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableMenuItem’: vibmenus.c:2006:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2006 | Nlm_Int2 itm; | ^~~ vibmenus.c:2005:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2005 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoice’: vibmenus.c:2072:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2072 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceGroup’: vibmenus.c:2122:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2122 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceItem’: vibmenus.c:2166:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2166 | Nlm_Int2 itm; | ^~~ vibmenus.c:2164:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2164 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableMenuItem’: vibmenus.c:2329:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2329 | Nlm_Int2 itm; | ^~~ vibmenus.c:2328:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2328 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoice’: vibmenus.c:2395:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2395 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoiceItem’: vibmenus.c:2489:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2489 | Nlm_Int2 itm; | ^~~ vibmenus.c:2487:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2487 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_RemoveSubMenu’: vibmenus.c:2627:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2627 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CountMenuItems’: vibmenus.c:3056:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3056 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetMenuItem’: vibmenus.c:3239:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3239 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetPopListTitle’: vibmenus.c:3349:18: warning: variable ‘m’ set but not used [-Wunused-but-set-variable] 3349 | Nlm_MenU m; | ^ vibmenus.c: In function ‘Nlm_AppendItems’: vibmenus.c:3978:17: warning: unused variable ‘accel’ [-Wunused-variable] 3978 | Nlm_Char accel; | ^~~~~ vibmenus.c: In function ‘Nlm_NewPopupList’: vibmenus.c:4969:19: warning: unused variable ‘lbl’ [-Wunused-variable] 4969 | Widget lbl; | ^~~ vibmenus.c:4967:19: warning: unused variable ‘color’ [-Wunused-variable] 4967 | Pixel color; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibprmpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibprmpt.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibsbars.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibsbars.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibslate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibslate.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibslate.c: In function ‘Nlm_EnableSlate’: vibslate.c:1199:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1199 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_DisableSlate’: vibslate.c:1254:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1254 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SelectSlate’: vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=] 1515 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=] 1517 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SelectPanel’: vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=] 1544 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=] 1546 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2026:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2026 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SlateClickCallback’: vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=] 2157 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=] 2159 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateInputCallback’: vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=] 2313 | XtVaGetValues(w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=] 2315 | XtVaGetValues(w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=] 2359 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=] 2361 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_ResetPanel’: vibslate.c:1389:6: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1389 | if (rst != NULL) { | ^ vibslate.c:1378:20: note: ‘pdata.reset’ was declared here 1378 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_RemoveSlate’: vibslate.c:1449:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.click’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.drag’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.hold’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.release’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.draw’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.reset’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_ResetSlate’: vibslate.c:1346:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.click’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.drag’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.hold’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.release’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.draw’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.reset’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.click’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.drag’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.hold’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.release’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.draw’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.reset’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2222:12: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2222 | if (drw != NULL && Nlm_GetVisible ((Nlm_GraphiC) p)) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:560:18: note: ‘pdata.draw’ was declared here 560 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2048:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.click’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.release’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.drag’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.hold’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.reset’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.draw’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2053:12: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2053 | if (clk != NULL && Nlm_GetEnabled ((Nlm_GraphiC) p) | ^ vibslate.c:524:18: note: ‘pdata.click’ was declared here 524 | Nlm_PanelData pdata; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibtexts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibtexts.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibtexts.c: In function ‘Nlm_TextCallback’: vibtexts.c:2982:24: warning: unused variable ‘cbs’ [-Wunused-variable] 2982 | XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data; | ^~~ vibtexts.c: In function ‘Nlm_LoseFocusCallback’: vibtexts.c:2999:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 2999 | XmAnyCallbackStruct *cbs; | ^~~ vibtexts.c: In function ‘Nlm_TabCallback’: vibtexts.c:3109:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3109 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenReturnCallback’: vibtexts.c:3122:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3122 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenActivateCallback’: vibtexts.c:3135:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 3135 | XmAnyCallbackStruct *cbs; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from vibutils.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibutils.c: In function ‘Nlm_VibMessageHook’: vibutils.c:776:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 776 | percent = (Nlm_Int4)Nlm_GetAppProperty( "VibrantMessageWidthMax" ); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibwndws.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibwndws.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibwndws.c: In function ‘Nlm_SetColorMap’: vibwndws.c:1060:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 1060 | int defaultdepth; | ^~~~~~~~~~~~ vibwndws.c: In function ‘Nlm_SetWindowTitle’: vibwndws.c:1567:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1567 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_GetWindowTitle’: vibwndws.c:1610:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1610 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_NewWindow’: vibwndws.c:2155:19: warning: variable ‘screen_num’ set but not used [-Wunused-but-set-variable] 2155 | int screen_num; | ^~~~~~~~~~ vibwndws.c: In function ‘Nlm_HideWindow’: vibwndws.c:2526:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2526 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowNormal’: vibwndws.c:2969:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2969 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowModal’: vibwndws.c:3014:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3014 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowDocument’: vibwndws.c:3060:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3060 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_VibMainPrelude’: vibwndws.c:6800:13: warning: unused variable ‘retval’ [-Wunused-variable] 6800 | Nlm_Int2 retval; | ^~~~~~ vibwndws.c: In function ‘Nlm_RemoveDyingWindows’: vibwndws.c:6922:20: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 6922 | Nlm_WindowTool wptr; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmain.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmain.c:121:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 121 | main (int argc, char *argv[]) | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbidraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidraw.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidraw.c: In function ‘Nlm_SelectFont.part.0’: ncbidraw.c:2879:8: warning: ‘fdata.print’ may be used uninitialized [-Wmaybe-uninitialized] 2879 | if (fdata.print != NULL && Nlm_nowPrinting) { | ^ ncbidraw.c:2875:17: note: ‘fdata.print’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ ncbidraw.c:2899:10: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 2899 | if (fdata.handle != NULL) { | ^ ncbidraw.c:2875:17: note: ‘fdata.handle’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ ncbidraw.c: In function ‘Nlm_EraseRect.part.0’: ncbidraw.c:4463:26: warning: ‘rtool.x’ may be used uninitialized [-Wmaybe-uninitialized] 4463 | rtool.x - Nlm_XOffset, rtool.y - Nlm_YOffset, | ~~~~~^~ ncbidraw.c:4430:16: note: ‘rtool.x’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4463:49: warning: ‘rtool.y’ may be used uninitialized [-Wmaybe-uninitialized] 4463 | rtool.x - Nlm_XOffset, rtool.y - Nlm_YOffset, | ~~~~~^~ ncbidraw.c:4430:16: note: ‘rtool.y’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4464:26: warning: ‘rtool.width’ may be used uninitialized [-Wmaybe-uninitialized] 4464 | rtool.width+1, rtool.height+1); | ~~~~~^~~~~~ ncbidraw.c:4430:16: note: ‘rtool.width’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4464:41: warning: ‘rtool.height’ may be used uninitialized [-Wmaybe-uninitialized] 4464 | rtool.width+1, rtool.height+1); | ~~~~~^~~~~~~ ncbidraw.c:4430:16: note: ‘rtool.height’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c: In function ‘s_DoQuadrant’: ncbidraw.c:5618:10: warning: ‘rr.right’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5618:22: warning: ‘rr.left’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5619:10: warning: ‘rr.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5619:22: warning: ‘rr.top’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c: In function ‘Nlm_CleanUpDrawingTools’: ncbidraw.c:7540:6: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 7540 | if (fdata.handle != NULL) { | ^ ncbidraw.c:7533:17: note: ‘fdata.handle’ was declared here 7533 | Nlm_FontData fdata; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF drawing.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from drawing.c:128: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mapping.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from mapping.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapping.c: In function ‘Nlm_MapRectToWorldBox’: mapping.c:139:8: warning: variable ‘curScale’ set but not used [-Wunused-but-set-variable] 139 | Int4 curScale; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF picture.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from picture.c:100: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF viewer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from viewer.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:12: warning: ‘port.left’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:24: warning: ‘port.right’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:12: warning: ‘port.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:26: warning: ‘port.top’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF document.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from document.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ document.c: In function ‘Nlm_PrintDocument’: document.c:4419:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4419 | system (cmmd); | ^~~~~~~~~~~~~ document.c:4423:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4423 | system (cmmd); | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF table.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from table.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ table.c: In function ‘TableClick’: table.c:1020:14: warning: ‘colRec.click’ may be used uninitialized [-Wmaybe-uninitialized] 1020 | if (actn != NULL) { | ^ table.c:987:14: note: ‘colRec.click’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~^~~~~ table.c:987:14: note: ‘colRec.pos’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:987:14: note: ‘colRec.width’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c: In function ‘SetTableBlockGray.part.0’: table.c:917:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~^~~~~ table.c:887:14: note: ‘colRec.pos’ was declared here 887 | ColRec colRec; | ^~~~~~ table.c:917:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:887:14: note: ‘colRec.width’ was declared here 887 | ColRec colRec; | ^~~~~~ table.c: In function ‘SetTableBlockHilight.part.0’: table.c:843:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~^~~~~ table.c:813:14: note: ‘colRec.pos’ was declared here 813 | ColRec colRec; | ^~~~~~ table.c:843:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:813:14: note: ‘colRec.width’ was declared here 813 | ColRec colRec; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF palette.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from palette.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF diagnost.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from diagnost.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF image.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from image.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ image.c: In function ‘ShiftXMask’: image.c:840:26: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 840 | if(!((mask >> hi + low) & (unsigned long)1)) break; | ~~~^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pictur3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/pictur3d.h:49, from ../include/ppict3d.h:49, from pictur3d.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pictur3d.c: In function ‘Nlm_DeleteFromSeg’: pictur3d.c:114:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 114 | else seg->first = b->next; | ^~~~ pictur3d.c:115:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 115 | if ( seg->last == b ) seg->last = bprev; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prim3d1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d1.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prim3d2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d2.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prim3d3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d3.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prim3d4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d4.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prim3d5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d5.c:66: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF viewer3d.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vibmouse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibmouse.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF netscape.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from netscape.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netscape.c: In function ‘NS_Obtain_lock’: netscape.c:236:10: warning: variable ‘waited’ set but not used [-Wunused-but-set-variable] 236 | Bool waited = False; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF imagelst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/imagelst.h:52, from imagelst.c:61: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF treeview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from treeview.c:91: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ treeview.c: In function ‘getNodeLength’: treeview.c:177:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 177 | length= (Int4)tree_getNode(cursor, TREE_NODE_FMT_DISTANCE, &size); | ^ treeview.c: In function ‘getIconId’: treeview.c:187:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 187 | a= (Int4) tree_getNode(cursor, TREE_NODE_FMT_ICON, &size); | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF shim3d.c shim3d.c: In function ‘Nlm_AddHalfWorm3D’: shim3d.c:3470:46: warning: unused variable ‘tmp’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:40: warning: unused variable ‘pCz’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:34: warning: unused variable ‘pCy’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:28: warning: unused variable ‘pCx’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:22: warning: unused variable ‘pNz’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:16: warning: unused variable ‘pNy’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3470:10: warning: unused variable ‘pNx’ [-Wunused-variable] 3470 | *pNx, *pNy, *pNz, *pCx, *pCy, *pCz, *tmp, *fblock = NULL; | ^~~ shim3d.c:3469:47: warning: unused variable ‘Cz’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:42: warning: unused variable ‘Cy’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:37: warning: unused variable ‘Cx’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:32: warning: unused variable ‘Nz’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:27: warning: unused variable ‘Ny’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3469:15: warning: unused variable ‘Nx’ [-Wunused-variable] 3469 | GLdouble *Nx = NULL, *Ny, *Nz, *Cx, *Cy, *Cz, | ^~ shim3d.c:3468:21: warning: unused variable ‘pi’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~ shim3d.c:3468:15: warning: unused variable ‘sinj’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~~~ shim3d.c:3468:9: warning: unused variable ‘cosj’ [-Wunused-variable] 3468 | cosj, sinj, pi = 3.14159265358979323846; | ^~~~ shim3d.c:3467:33: warning: unused variable ‘prevlen’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~~~~~~ shim3d.c:3467:29: warning: unused variable ‘Vz’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:25: warning: unused variable ‘Vy’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:21: warning: unused variable ‘Vx’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:17: warning: unused variable ‘Hz’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:13: warning: unused variable ‘Hy’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3467:9: warning: unused variable ‘Hx’ [-Wunused-variable] 3467 | Hx, Hy, Hz, Vx, Vy, Vz, prevlen, | ^~ shim3d.c:3466:21: warning: unused variable ‘dQtz’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3466:15: warning: unused variable ‘dQty’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3466:9: warning: unused variable ‘dQtx’ [-Wunused-variable] 3466 | dQtx, dQty, dQtz, /*ddQtx, ddQty, ddQtz,*/ | ^~~~ shim3d.c:3464:14: warning: unused variable ‘len’ [-Wunused-variable] 3464 | GLdouble len, R1x, R1y, R1z, R2x, R2y, R2z, MG[4][3], | ^~~ shim3d.c:3463:26: warning: unused variable ‘offset’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^~~~~~ shim3d.c:3463:23: warning: unused variable ‘m’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ shim3d.c:3463:20: warning: unused variable ‘k’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ shim3d.c:3463:17: warning: unused variable ‘j’ [-Wunused-variable] 3463 | Nlm_Int4 i, j, k, m, offset; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF odlbox.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from odlbox.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ odlbox.c: In function ‘LB_onVScroll’: odlbox.c:424:33: warning: variable ‘IsGoUp’ set but not used [-Wunused-but-set-variable] 424 | Boolean IsGoUp=FALSE; | ^~~~~~ rm -f libvibrant.a ar cru libvibrant.a vibbutns.o vibextra.o vibfiles.o vibforms.o vibgroup.o viblists.o vibmenus.o vibprmpt.o vibsbars.o vibslate.o vibtexts.o vibutils.o vibwndws.o vibmain.o ncbidraw.o drawing.o mapping.o picture.o viewer.o document.o table.o palette.o diagnost.o image.o pictur3d.o prim3d1.o prim3d2.o prim3d3.o prim3d4.o prim3d5.o viewer3d.o vibmouse.o netscape.o imagelst.o treeview.o shim3d.o odlbox.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibrant.a ../lib ranlib ../lib/libvibrant.a mv vibbutns.o vibbutns.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibbutns.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibbutns.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibbutns.c: In function ‘Nlm_CheckCallback’: vibbutns.c:354:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 354 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_RadioCallback’: vibbutns.c:373:20: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 373 | Nlm_ControlTool c; | ^ vibbutns.c: In function ‘Nlm_SetButtonStatus’: vibbutns.c:694:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 694 | Nlm_Int2 val; | ^~~ vibbutns.c: In function ‘Nlm_NewButton.constprop.0’: vibbutns.c:1159:3: warning: ‘call’ may be used uninitialized [-Wmaybe-uninitialized] 1159 | XtAddCallback (c, call, Nlm_ButtonCallback, (XtPointer) b); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vibbutns.c:1021:20: note: ‘call’ was declared here 1021 | String call; | ^~~~ mv vibbutns.o vibbutns.glo mv vibbutns.tmp vibbutns.o mv vibextra.o vibextra.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibextra.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibextra.c:87: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibextra.c: In function ‘Nlm_RGB2HSL.constprop.0’: vibextra.c:1216:7: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 1216 | i = (min + 1); if ( i > 2 ) i=0; | ~~^~~~~~~~~~~ vibextra.c:1191:15: note: ‘min’ was declared here 1191 | int i, min; | ^~~ mv vibextra.o vibextra.glo mv vibextra.tmp vibextra.o mv vibfiles.o vibfiles.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibfiles.c:54: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibfiles.c: In function ‘Nlm_WriteCard’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ In function ‘Nlm_CardToStr’, inlined from ‘Nlm_WriteCard’ at vibfiles.c:350:3: vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3, inlined from ‘Nlm_WriteCard’ at vibfiles.c:350:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_WriteInt’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ In function ‘Nlm_IntToStr’, inlined from ‘Nlm_WriteInt’ at vibfiles.c:375:3: vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3, inlined from ‘Nlm_WriteInt’ at vibfiles.c:375:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_WriteLong’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ In function ‘Nlm_LongToStr’, inlined from ‘Nlm_WriteLong’ at vibfiles.c:400:3: vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3, inlined from ‘Nlm_WriteLong’ at vibfiles.c:400:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_CardToStr’: vibfiles.c:715:19: warning: ‘%*u’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~ vibfiles.c:715:18: note: directive argument in the range [0, 65535] 715 | sprintf (temp, "%*u", length, (int)cardval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_CardToStr’ at vibfiles.c:715:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_IntToStr’: vibfiles.c:725:19: warning: ‘%*d’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 725 | sprintf (temp, "%*d", length, intval); | ^~~ vibfiles.c:725:18: note: directive argument in the range [-32768, 32767] 725 | sprintf (temp, "%*d", length, intval); | ^~~~~ In function ‘sprintf’, inlined from ‘Nlm_IntToStr’ at vibfiles.c:725:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ vibfiles.c: In function ‘Nlm_LongToStr’: vibfiles.c:735:19: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 80 [-Wformat-overflow=] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~ vibfiles.c:735:18: note: directive argument in the range [-2147483648, 2147483647] 735 | sprintf (temp, "%*ld", length, (long)longval); | ^~~~~~ In function ‘sprintf’, inlined from ‘Nlm_LongToStr’ at vibfiles.c:735:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mv vibfiles.o vibfiles.glo mv vibfiles.tmp vibfiles.o mv vibforms.o vibforms.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibforms.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibforms.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibforms.o vibforms.glo mv vibforms.tmp vibforms.o mv vibgroup.o vibgroup.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibgroup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibgroup.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibgroup.o vibgroup.glo mv vibgroup.tmp vibgroup.o mv viblists.o viblists.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viblists.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from viblists.c:164: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ viblists.c: In function ‘Nlm_SetListPosition’: viblists.c:1121:15: warning: variable ‘is_realized’ set but not used [-Wunused-but-set-variable] 1121 | Nlm_Boolean is_realized; | ^~~~~~~~~~~ mv viblists.o viblists.glo mv viblists.tmp viblists.o mv vibmenus.o vibmenus.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmenus.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmenus.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmenus.c: In function ‘Nlm_IsMenuItemChecked’: vibmenus.c:563:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 563 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CheckMenuItem’: vibmenus.c:591:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 591 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableMenuItem’: vibmenus.c:2006:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2006 | Nlm_Int2 itm; | ^~~ vibmenus.c:2005:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2005 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoice’: vibmenus.c:2072:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2072 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceGroup’: vibmenus.c:2122:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2122 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_EnableChoiceItem’: vibmenus.c:2166:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2166 | Nlm_Int2 itm; | ^~~ vibmenus.c:2164:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2164 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableMenuItem’: vibmenus.c:2329:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2329 | Nlm_Int2 itm; | ^~~ vibmenus.c:2328:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2328 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoice’: vibmenus.c:2395:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2395 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_DisableChoiceItem’: vibmenus.c:2489:17: warning: variable ‘itm’ set but not used [-Wunused-but-set-variable] 2489 | Nlm_Int2 itm; | ^~~ vibmenus.c:2487:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2487 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_RemoveSubMenu’: vibmenus.c:2627:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2627 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_CountMenuItems’: vibmenus.c:3056:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3056 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetMenuItem’: vibmenus.c:3239:17: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 3239 | Nlm_MenuTool h; | ^ vibmenus.c: In function ‘Nlm_GetPopListTitle’: vibmenus.c:3349:18: warning: variable ‘m’ set but not used [-Wunused-but-set-variable] 3349 | Nlm_MenU m; | ^ vibmenus.c: In function ‘Nlm_AppendItems’: vibmenus.c:3978:17: warning: unused variable ‘accel’ [-Wunused-variable] 3978 | Nlm_Char accel; | ^~~~~ vibmenus.c: In function ‘Nlm_NewPopupList’: vibmenus.c:4969:19: warning: unused variable ‘lbl’ [-Wunused-variable] 4969 | Widget lbl; | ^~~ vibmenus.c:4967:19: warning: unused variable ‘color’ [-Wunused-variable] 4967 | Pixel color; | ^~~~~ mv vibmenus.o vibmenus.glo mv vibmenus.tmp vibmenus.o mv vibprmpt.o vibprmpt.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibprmpt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibprmpt.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibprmpt.o vibprmpt.glo mv vibprmpt.tmp vibprmpt.o mv vibsbars.o vibsbars.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibsbars.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibsbars.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibsbars.o vibsbars.glo mv vibsbars.tmp vibsbars.o mv vibslate.o vibslate.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibslate.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibslate.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibslate.c: In function ‘Nlm_EnableSlate’: vibslate.c:1199:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1199 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_DisableSlate’: vibslate.c:1254:18: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 1254 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SelectSlate’: vibslate.c:1515:5: warning: missing sentinel in function call [-Wformat=] 1515 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1517:5: warning: missing sentinel in function call [-Wformat=] 1517 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SelectPanel’: vibslate.c:1544:3: warning: missing sentinel in function call [-Wformat=] 1544 | XtVaGetValues (h, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:1546:3: warning: missing sentinel in function call [-Wformat=] 1546 | XtVaGetValues (h, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2026:20: warning: variable ‘h’ set but not used [-Wunused-but-set-variable] 2026 | Nlm_SlateTool h; | ^ vibslate.c: In function ‘Nlm_SlateClickCallback’: vibslate.c:2157:3: warning: missing sentinel in function call [-Wformat=] 2157 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2159:3: warning: missing sentinel in function call [-Wformat=] 2159 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateInputCallback’: vibslate.c:2313:7: warning: missing sentinel in function call [-Wformat=] 2313 | XtVaGetValues(w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2315:7: warning: missing sentinel in function call [-Wformat=] 2315 | XtVaGetValues(w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2359:3: warning: missing sentinel in function call [-Wformat=] 2359 | XtVaGetValues (w, XmNbackground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c:2361:3: warning: missing sentinel in function call [-Wformat=] 2361 | XtVaGetValues (w, XmNforeground, &color, 0); | ^~~~~~~~~~~~~ vibslate.c: In function ‘Nlm_Set3DColorMap’: vibslate.c:2686:17: warning: unused variable ‘testvisual’ [-Wunused-variable] 2686 | Boolean testvisual; | ^~~~~~~~~~ vibslate.c:2685:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 2685 | int defaultdepth; | ^~~~~~~~~~~~ vibslate.c: In function ‘Nlm_ResetPanel’: vibslate.c:1389:6: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1389 | if (rst != NULL) { | ^ vibslate.c:1378:20: note: ‘pdata.reset’ was declared here 1378 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_RemoveSlate’: vibslate.c:1449:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.click’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.drag’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.hold’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1449:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1449 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1403:20: note: ‘pdata.release’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.draw’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1450:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1450 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1403:20: note: ‘pdata.reset’ was declared here 1403 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_ResetSlate’: vibslate.c:1346:6: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.click’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:27: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.drag’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:49: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.hold’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1346:71: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 1346 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:1303:20: note: ‘pdata.release’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:29: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.draw’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:1347:51: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 1347 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:1303:20: note: ‘pdata.reset’ was declared here 1303 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.click’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.drag’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.hold’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2215:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2215 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.release’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.draw’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2216:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2216 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:2202:20: note: ‘pdata.reset’ was declared here 2202 | Nlm_PanelData pdata; | ^~~~~ In function ‘Nlm_DrawSlate’, inlined from ‘Nlm_SlateDrawCallback’ at vibslate.c:2393:3: vibslate.c:2222:12: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2222 | if (drw != NULL && Nlm_GetVisible ((Nlm_GraphiC) p)) { | ^ vibslate.c: In function ‘Nlm_SlateDrawCallback’: vibslate.c:560:18: note: ‘pdata.draw’ was declared here 560 | Nlm_PanelData pdata; | ^~~~~ vibslate.c: In function ‘Nlm_SlateClick’: vibslate.c:2048:10: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.click’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:75: warning: ‘pdata.release’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.release’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:31: warning: ‘pdata.drag’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.drag’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2048:53: warning: ‘pdata.hold’ may be used uninitialized [-Wmaybe-uninitialized] 2048 | if (pdata.click != NULL || pdata.drag != NULL || pdata.hold != NULL || | ^ vibslate.c:2031:20: note: ‘pdata.hold’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:55: warning: ‘pdata.reset’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.reset’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2049:33: warning: ‘pdata.draw’ may be used uninitialized [-Wmaybe-uninitialized] 2049 | pdata.release != NULL || pdata.draw != NULL || pdata.reset != NULL) { | ^ vibslate.c:2031:20: note: ‘pdata.draw’ was declared here 2031 | Nlm_PanelData pdata; | ^~~~~ vibslate.c:2053:12: warning: ‘pdata.click’ may be used uninitialized [-Wmaybe-uninitialized] 2053 | if (clk != NULL && Nlm_GetEnabled ((Nlm_GraphiC) p) | ^ vibslate.c:524:18: note: ‘pdata.click’ was declared here 524 | Nlm_PanelData pdata; | ^~~~~ mv vibslate.o vibslate.glo mv vibslate.tmp vibslate.o mv vibtexts.o vibtexts.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibtexts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibtexts.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibtexts.c: In function ‘Nlm_TextCallback’: vibtexts.c:2982:24: warning: unused variable ‘cbs’ [-Wunused-variable] 2982 | XmAnyCallbackStruct *cbs = (XmAnyCallbackStruct *)call_data; | ^~~ vibtexts.c: In function ‘Nlm_LoseFocusCallback’: vibtexts.c:2999:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 2999 | XmAnyCallbackStruct *cbs; | ^~~ vibtexts.c: In function ‘Nlm_TabCallback’: vibtexts.c:3109:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3109 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenReturnCallback’: vibtexts.c:3122:15: warning: variable ‘event’ set but not used [-Wunused-but-set-variable] 3122 | XKeyEvent *event; | ^~~~~ vibtexts.c: In function ‘Nlm_HiddenActivateCallback’: vibtexts.c:3135:25: warning: variable ‘cbs’ set but not used [-Wunused-but-set-variable] 3135 | XmAnyCallbackStruct *cbs; | ^~~ mv vibtexts.o vibtexts.glo mv vibtexts.tmp vibtexts.o mv vibutils.o vibutils.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from vibutils.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibutils.c: In function ‘Nlm_VibMessageHook’: vibutils.c:776:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 776 | percent = (Nlm_Int4)Nlm_GetAppProperty( "VibrantMessageWidthMax" ); | ^ mv vibutils.o vibutils.glo mv vibutils.tmp vibutils.o mv vibwndws.o vibwndws.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibwndws.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibwndws.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibwndws.c: In function ‘Nlm_SetColorMap’: vibwndws.c:1060:13: warning: variable ‘defaultdepth’ set but not used [-Wunused-but-set-variable] 1060 | int defaultdepth; | ^~~~~~~~~~~~ vibwndws.c: In function ‘Nlm_SetWindowTitle’: vibwndws.c:1567:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1567 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_GetWindowTitle’: vibwndws.c:1610:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 1610 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_NewWindow’: vibwndws.c:2155:19: warning: variable ‘screen_num’ set but not used [-Wunused-but-set-variable] 2155 | int screen_num; | ^~~~~~~~~~ vibwndws.c: In function ‘Nlm_HideWindow’: vibwndws.c:2526:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2526 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowNormal’: vibwndws.c:2969:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 2969 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowModal’: vibwndws.c:3014:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3014 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_ShowDocument’: vibwndws.c:3060:19: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 3060 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: In function ‘Nlm_VibMainPrelude’: vibwndws.c:6800:13: warning: unused variable ‘retval’ [-Wunused-variable] 6800 | Nlm_Int2 retval; | ^~~~~~ vibwndws.c: In function ‘Nlm_RemoveDyingWindows’: vibwndws.c:6922:20: warning: variable ‘wptr’ set but not used [-Wunused-but-set-variable] 6922 | Nlm_WindowTool wptr; | ^~~~ vibwndws.c: At top level: vibwndws.c:1318:16: warning: ‘Nlm_StandardColormap’ defined but not used [-Wunused-function] 1318 | static Boolean Nlm_StandardColormap(Colormap *cMap, | ^~~~~~~~~~~~~~~~~~~~ mv vibwndws.o vibwndws.glo mv vibwndws.tmp vibwndws.o mv vibmain.o vibmain.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from vibmain.c:40: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vibmain.c:121:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 121 | main (int argc, char *argv[]) | ^~~~ mv vibmain.o vibmain.glo mv vibmain.tmp vibmain.o mv ncbidraw.o ncbidraw.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL ncbidraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidraw.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidraw.c: In function ‘Nlm_SelectFont.part.0’: ncbidraw.c:2879:8: warning: ‘fdata.print’ may be used uninitialized [-Wmaybe-uninitialized] 2879 | if (fdata.print != NULL && Nlm_nowPrinting) { | ^ ncbidraw.c:2875:17: note: ‘fdata.print’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ ncbidraw.c:2899:10: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 2899 | if (fdata.handle != NULL) { | ^ ncbidraw.c:2875:17: note: ‘fdata.handle’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ ncbidraw.c: In function ‘Nlm_EraseRect.part.0’: ncbidraw.c:4463:26: warning: ‘rtool.x’ may be used uninitialized [-Wmaybe-uninitialized] 4463 | rtool.x - Nlm_XOffset, rtool.y - Nlm_YOffset, | ~~~~~^~ ncbidraw.c:4430:16: note: ‘rtool.x’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4463:49: warning: ‘rtool.y’ may be used uninitialized [-Wmaybe-uninitialized] 4463 | rtool.x - Nlm_XOffset, rtool.y - Nlm_YOffset, | ~~~~~^~ ncbidraw.c:4430:16: note: ‘rtool.y’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4464:26: warning: ‘rtool.width’ may be used uninitialized [-Wmaybe-uninitialized] 4464 | rtool.width+1, rtool.height+1); | ~~~~~^~~~~~ ncbidraw.c:4430:16: note: ‘rtool.width’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c:4464:41: warning: ‘rtool.height’ may be used uninitialized [-Wmaybe-uninitialized] 4464 | rtool.width+1, rtool.height+1); | ~~~~~^~~~~~~ ncbidraw.c:4430:16: note: ‘rtool.height’ was declared here 4430 | Nlm_RectTool rtool; | ^~~~~ ncbidraw.c: In function ‘s_DoQuadrant’: ncbidraw.c:5618:10: warning: ‘rr.right’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5618:22: warning: ‘rr.left’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5619:10: warning: ‘rr.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c:5619:22: warning: ‘rr.top’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~ ncbidraw.c:5614:12: note: ‘rr’ declared here 5614 | Nlm_RecT rr; | ^~ ncbidraw.c: In function ‘Nlm_CleanUpDrawingTools’: ncbidraw.c:7540:6: warning: ‘fdata.handle’ may be used uninitialized [-Wmaybe-uninitialized] 7540 | if (fdata.handle != NULL) { | ^ ncbidraw.c:7533:17: note: ‘fdata.handle’ was declared here 7533 | Nlm_FontData fdata; | ^~~~~ mv ncbidraw.o ncbidraw.glo mv ncbidraw.tmp ncbidraw.o mv drawing.o drawing.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL drawing.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from drawing.c:128: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv drawing.o drawing.glo mv drawing.tmp drawing.o mv mapping.o mapping.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL mapping.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from mapping.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapping.c: In function ‘Nlm_MapRectToWorldBox’: mapping.c:139:8: warning: variable ‘curScale’ set but not used [-Wunused-but-set-variable] 139 | Int4 curScale; | ^~~~~~~~ mv mapping.o mapping.glo mv mapping.tmp mapping.o mv picture.o picture.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL picture.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbidraw.h:47, from picture.c:100: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv picture.o picture.glo mv picture.tmp picture.o mv viewer.o viewer.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from viewer.c:120: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:12: warning: ‘port.left’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:582:24: warning: ‘port.right’ may be used uninitialized [-Wmaybe-uninitialized] 582 | if (box->left > box->right) { | ~~~^~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:12: warning: ‘port.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ In function ‘s_NormalizeBoxUpsideDown’, inlined from ‘CalculateScaling.part.0’ at viewer.c:730:3: viewer.c:587:26: warning: ‘port.top’ may be used uninitialized [-Wmaybe-uninitialized] 587 | if (box->bottom > box->top) { | ~~~^~~~~ viewer.c: In function ‘CalculateScaling.part.0’: viewer.c:615:14: note: ‘port’ declared here 615 | BoxInfo port; | ^~~~ mv viewer.o viewer.glo mv viewer.tmp viewer.o mv document.o document.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL document.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from document.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ document.c: In function ‘Nlm_PrintDocument’: document.c:4419:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4419 | system (cmmd); | ^~~~~~~~~~~~~ document.c:4423:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4423 | system (cmmd); | ^~~~~~~~~~~~~ mv document.o document.glo mv document.tmp document.o mv table.o table.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL table.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from table.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ table.c: In function ‘TableClick’: table.c:1020:14: warning: ‘colRec.click’ may be used uninitialized [-Wmaybe-uninitialized] 1020 | if (actn != NULL) { | ^ table.c:987:14: note: ‘colRec.click’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~^~~~~ table.c:987:14: note: ‘colRec.pos’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c:1017:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 1017 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:987:14: note: ‘colRec.width’ was declared here 987 | ColRec colRec; | ^~~~~~ table.c: In function ‘SetTableBlockGray.part.0’: table.c:917:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~^~~~~ table.c:887:14: note: ‘colRec.pos’ was declared here 887 | ColRec colRec; | ^~~~~~ table.c:917:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 917 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:887:14: note: ‘colRec.width’ was declared here 887 | ColRec colRec; | ^~~~~~ table.c: In function ‘SetTableBlockHilight.part.0’: table.c:843:20: warning: ‘colRec.pos’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~^~~~~ table.c:813:14: note: ‘colRec.pos’ was declared here 813 | ColRec colRec; | ^~~~~~ table.c:843:34: warning: ‘colRec.width’ may be used uninitialized [-Wmaybe-uninitialized] 843 | r.right = r.left + colRec.width; | ~~~~~~^~~~~~ table.c:813:14: note: ‘colRec.width’ was declared here 813 | ColRec colRec; | ^~~~~~ mv table.o table.glo mv table.tmp table.o mv palette.o palette.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL palette.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/panels.h:68, from palette.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv palette.o palette.glo mv palette.tmp palette.o mv diagnost.o diagnost.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL diagnost.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from diagnost.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv diagnost.o diagnost.glo mv diagnost.tmp diagnost.o mv image.o image.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL image.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from image.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ image.c: In function ‘ShiftXMask’: image.c:840:26: warning: suggest parentheses around ‘+’ inside ‘>>’ [-Wparentheses] 840 | if(!((mask >> hi + low) & (unsigned long)1)) break; | ~~~^~~~~ mv image.o image.glo mv image.tmp image.o mv pictur3d.o pictur3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL pictur3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/pictur3d.h:49, from ../include/ppict3d.h:49, from pictur3d.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pictur3d.c: In function ‘Nlm_DeleteFromSeg’: pictur3d.c:114:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 114 | else seg->first = b->next; | ^~~~ pictur3d.c:115:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 115 | if ( seg->last == b ) seg->last = bprev; | ^~ mv pictur3d.o pictur3d.glo mv pictur3d.tmp pictur3d.o mv prim3d1.o prim3d1.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d1.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d1.o prim3d1.glo mv prim3d1.tmp prim3d1.o mv prim3d2.o prim3d2.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d2.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d2.o prim3d2.glo mv prim3d2.tmp prim3d2.o mv prim3d3.o prim3d3.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d3.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d3.o prim3d3.glo mv prim3d3.tmp prim3d3.o mv prim3d4.o prim3d4.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d4.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d4.o prim3d4.glo mv prim3d4.tmp prim3d4.o mv prim3d5.o prim3d5.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL prim3d5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from prim3d5.c:66: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv prim3d5.o prim3d5.glo mv prim3d5.tmp prim3d5.o mv viewer3d.o viewer3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL viewer3d.c mv viewer3d.o viewer3d.glo mv viewer3d.tmp viewer3d.o mv vibmouse.o vibmouse.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL vibmouse.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vibmouse.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv vibmouse.o vibmouse.glo mv vibmouse.tmp vibmouse.o mv netscape.o netscape.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL netscape.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from netscape.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netscape.c: In function ‘NS_Obtain_lock’: netscape.c:236:10: warning: variable ‘waited’ set but not used [-Wunused-but-set-variable] 236 | Bool waited = False; | ^~~~~~ mv netscape.o netscape.glo mv netscape.tmp netscape.o mv imagelst.o imagelst.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL imagelst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/imagelst.h:52, from imagelst.c:61: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv imagelst.o imagelst.glo mv imagelst.tmp imagelst.o mv treeview.o treeview.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL treeview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/treemgr.h:67, from treeview.c:91: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ treeview.c: In function ‘getNodeLength’: treeview.c:177:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 177 | length= (Int4)tree_getNode(cursor, TREE_NODE_FMT_DISTANCE, &size); | ^ treeview.c: In function ‘getIconId’: treeview.c:187:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 187 | a= (Int4) tree_getNode(cursor, TREE_NODE_FMT_ICON, &size); | ^ mv treeview.o treeview.glo mv treeview.tmp treeview.o mv shim3d.o shim3d.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL shim3d.c shim3d.c: In function ‘OGL_AddCylinder3D’: shim3d.c:918:14: warning: unused variable ‘iCount’ [-Wunused-variable] 918 | Nlm_Int4 iCount; | ^~~~~~ shim3d.c: In function ‘OGL_AddText3D’: shim3d.c:1210:22: warning: unused variable ‘i’ [-Wunused-variable] 1210 | Nlm_Int4 Length, i; | ^ shim3d.c: In function ‘OGL_Zoom_DragMA’: shim3d.c:1770:16: warning: unused variable ‘OGL_Data’ [-Wunused-variable] 1770 | TOGL_Data *OGL_Data = MAToOGL(ma); | ^~~~~~~~ shim3d.c: In function ‘write_row_callback’: shim3d.c:2923:48: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 2923 | (((float) row) / (-nRows)) * ((end - start) / 15) | ~~~~~^~~~~~~~ shim3d.c:2911:15: note: ‘start’ was declared here 2911 | float start, end; | ^~~~~ shim3d.c:2923:48: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 2923 | (((float) row) / (-nRows)) * ((end - start) / 15) | ~~~~~^~~~~~~~ shim3d.c:2911:22: note: ‘end’ was declared here 2911 | float start, end; | ^~~ shim3d.c: In function ‘Nlm_FindAvailableFonts’: shim3d.c:2234:9: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 2234 | strncpy(fnd_fam,list[i]+1,256); | ^ shim3d.c: In function ‘SetOGLFont’: shim3d.c:2369:21: warning: ‘list’ may be used uninitialized [-Wmaybe-uninitialized] 2369 | pos = list[ii]; | ~~~~^~~~~~~~~~ shim3d.c:2334:28: note: ‘list’ was declared here 2334 | char query[256], **list, *pos; | ^~~~ shim3d.c:2376:37: warning: ‘mindiff’ may be used uninitialized [-Wmaybe-uninitialized] 2376 | if (ii == 0 || diff < mindiff) { | ~~~~~^~~~~~~~~ shim3d.c:2335:41: note: ‘mindiff’ was declared here 2335 | int nFound, ii, ib, size, diff, mindiff, closest; | ^~~~~~~ shim3d.c:2381:64: warning: ‘closest’ may be used uninitialized [-Wmaybe-uninitialized] 2381 | fontInfo = XLoadQueryFont(Nlm_currentXDisplay, list[closest]); | ^ shim3d.c:2335:50: note: ‘closest’ was declared here 2335 | int nFound, ii, ib, size, diff, mindiff, closest; | ^~~~~~~ shim3d.c: In function ‘Nlm_AddHalfWorm3D’: shim3d.c:3463:26: warning: ‘offset’ may be used uninitialized [-Wmaybe-uninitialized] 3463 | Nlm_Int4 i, j, k, m, offset; | ^~~~~~ mv shim3d.o shim3d.glo mv shim3d.tmp shim3d.o mv odlbox.o odlbox.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL odlbox.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from odlbox.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ odlbox.c: In function ‘LB_onVScroll’: odlbox.c:424:33: warning: variable ‘IsGoUp’ set but not used [-Wunused-but-set-variable] 424 | Boolean IsGoUp=FALSE; | ^~~~~~ mv odlbox.o odlbox.glo mv odlbox.tmp odlbox.o rm -f libvibrantOGL.a ar cru libvibrantOGL.a vibbutns.glo vibextra.glo vibfiles.glo vibforms.glo vibgroup.glo viblists.glo vibmenus.glo vibprmpt.glo vibsbars.glo vibslate.glo vibtexts.glo vibutils.glo vibwndws.glo vibmain.glo ncbidraw.glo drawing.glo mapping.glo picture.glo viewer.glo document.glo table.glo palette.glo diagnost.glo image.glo pictur3d.glo prim3d1.glo prim3d2.glo prim3d3.glo prim3d4.glo prim3d5.glo viewer3d.glo vibmouse.glo netscape.glo imagelst.glo treeview.glo shim3d.glo odlbox.glo ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibrantOGL.a ../lib ranlib ../lib/libvibrantOGL.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF accentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from accentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ accentr.c: In function ‘EntrezBiostrucGet’: accentr.c:2113:17: warning: unused variable ‘retval’ [-Wunused-variable] 2113 | BiostrucPtr retval = NULL; | ^~~~~~ accentr.c: In function ‘EntrezGIForSeqIdFunc’: accentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ accentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ accentr.c: In function ‘EntrezMedlineEntryGet’: accentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at accentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ accentr.c: In function ‘EntrezSeqEntryGet’: accentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at accentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF accutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from ../include/accutils.h:119, from accutils.c:149: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/ncbi.h:62: accutils.c: In function ‘EntrezFieldToString’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ output may be truncated copying 5 bytes from a string of length 6 [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ rm -f libncbiacc.a ar cru libncbiacc.a accentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiacc.a ../lib ranlib ../lib/libncbiacc.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF drawseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from drawseq.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ drawseq.c: In function ‘AddFlatNodeSymbol’: drawseq.c:811:14: warning: unused variable ‘symbol_height’ [-Wunused-variable] 811 | Int4 symbol_height = 8; | ^~~~~~~~~~~~~ drawseq.c: In function ‘AddAlignBlocks’: drawseq.c:970:14: warning: variable ‘c_num’ set but not used [-Wunused-but-set-variable] 970 | Int2 c_num; | ^~~~~ drawseq.c: In function ‘AddAlignFeature’: drawseq.c:1369:15: warning: unused variable ‘ptype’ [-Wunused-variable] 1369 | Uint1 ptype = 0; | ^~~~~ drawseq.c: In function ‘AddAlignmentMismatch’: drawseq.c:1523:14: warning: variable ‘i_right’ set but not used [-Wunused-but-set-variable] 1523 | Int4 i_right; | ^~~~~~~ drawseq.c: In function ‘DrawRestrictionMap’: drawseq.c:1811:17: warning: unused variable ‘retval’ [-Wunused-variable] 1811 | Boolean retval = FALSE; | ^~~~~~ drawseq.c:1802:22: warning: variable ‘center’ set but not used [-Wunused-but-set-variable] 1802 | Int4 x1, x2, center; | ^~~~~~ drawseq.c: In function ‘DrawFeatures’: drawseq.c:2563:14: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 2563 | Int2 entityID; | ^~~~~~~~ drawseq.c: In function ‘DrawOneSeqLoc’: drawseq.c:3020:17: warning: variable ‘show_seq_label’ set but not used [-Wunused-but-set-variable] 3020 | Boolean show_seq_label = TRUE; /*show the label of a sequence*/ | ^~~~~~~~~~~~~~ drawseq.c:3009:17: warning: variable ‘ends’ set but not used [-Wunused-but-set-variable] 3009 | Boolean ends; | ^~~~ drawseq.c: In function ‘Label_GData’: drawseq.c:3439:17: warning: variable ‘success’ set but not used [-Wunused-but-set-variable] 3439 | Boolean success = FALSE; | ^~~~~~~ drawseq.c: In function ‘DrawEquivAlign’: drawseq.c:3594:15: warning: unused variable ‘my_gray_color’ [-Wunused-variable] 3594 | Uint1 my_gray_color[]={63, 63, 63}; | ^~~~~~~~~~~~~ drawseq.c: In function ‘load_align_label_rectangle’: drawseq.c:4352:17: warning: variable ‘found_it’ set but not used [-Wunused-but-set-variable] 4352 | Boolean found_it; | ^~~~~~~~ drawseq.c: In function ‘PicForAlignNode’: drawseq.c:4558:25: warning: variable ‘min_scale’ set but not used [-Wunused-but-set-variable] 4558 | Int4 max_width, min_scale; | ^~~~~~~~~ drawseq.c: At top level: drawseq.c:3525:22: warning: ‘get_ith_arp’ defined but not used [-Wunused-function] 3525 | static AlignRangePtr get_ith_arp(AlignRangePtr arp, Int2 i) | ^~~~~~~~~~~ drawseq.c:3511:18: warning: ‘get_map_pos’ defined but not used [-Wunused-function] 3511 | static MapPosPtr get_map_pos(MapLayoutPtr mlp, SeqIdPtr sip) | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dotmatrx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dotmatrx.h:47, from dotmatrx.c:32: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF fea2seg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from fea2seg.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF fstyle.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from fstyle.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF smdlg1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg1.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF smdlg2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg2.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ smdlg2.c: In function ‘Nlm_CreateDlgGroup’: smdlg2.c:631:12: warning: variable ‘toAlign’ set but not used [-Wunused-but-set-variable] 631 | Handle toAlign[3]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF smdlg3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smdlg3.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF smtools.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from smtools.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ smtools.c: In function ‘Nlm_CtreateToolsSM’: smtools.c:534:30: warning: ‘%s’ directive writing up to 227 bytes into a region of size 32 [-Wformat-overflow=] 534 | sprintf ( fullFontName, "%s %d", fontNames[i].name, fontNames[i].size ); | ^~ smtools.c:534:29: note: directive argument in the range [-32768, 32767] 534 | sprintf ( fullFontName, "%s %d", fontNames[i].name, fontNames[i].size ); | ^~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Nlm_CtreateToolsSM’ at smtools.c:534:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 3 and 235 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF styleman.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from styleman.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF stylemui.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from stylemui.c:48: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF glbpic.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from glbpic.c:22: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ glbpic.c: In function ‘label_linear_mark’: glbpic.c:1295:14: warning: unused variable ‘tick_len’ [-Wunused-variable] 1295 | Int4 tick_len = TICK_LEN; | ^~~~~~~~ glbpic.c: In function ‘add_alignment_to_global’: glbpic.c:1552:15: warning: variable ‘p_val’ set but not used [-Wunused-but-set-variable] 1552 | Uint1 p_val; | ^~~~~ glbpic.c: At top level: glbpic.c:1748:16: warning: ‘get_print_score’ defined but not used [-Wunused-function] 1748 | static Boolean get_print_score(FloatHi min_score, FloatHi max_score, CharPtr label, Uint1 status) | ^~~~~~~~~~~~~~~ glbpic.c:584:19: warning: ‘extract_align_range’ defined but not used [-Wunused-function] 584 | static ValNodePtr extract_align_range(ValNodePtr PNTR arp_list, Uint1 displayOrder) | ^~~~~~~~~~~~~~~~~~~ glbpic.c: In function ‘get_circle_label_align’: glbpic.c:2349:16: warning: ‘align’ may be used uninitialized [-Wmaybe-uninitialized] 2349 | return align; | ^~~~~ glbpic.c:2339:15: note: ‘align’ was declared here 2339 | Uint1 align; | ^~~~~ glbpic.c: In function ‘label_circle_mark.isra.0’: glbpic.c:2417:28: warning: ‘p_align’ may be used uninitialized [-Wmaybe-uninitialized] 2417 | Uint1 label_align, p_align, first_align; | ^~~~~~~ glbpic.c:2469:56: warning: ‘first_width’ may be used uninitialized [-Wmaybe-uninitialized] 2469 | t_width = (first_width + width)/2; | ~~~~~~~~~~~~~^~~~~~~~ glbpic.c:2412:25: note: ‘first_width’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~~~ glbpic.c:2470:35: warning: ‘first_align’ may be used uninitialized [-Wmaybe-uninitialized] 2470 | if(label_align != first_align) | ^ glbpic.c:2417:37: note: ‘first_align’ was declared here 2417 | Uint1 label_align, p_align, first_align; | ^~~~~~~~~~~ In file included from ../include/ncbi.h:58: glbpic.c:2488:74: warning: ‘first_top’ may be used uninitialized [-Wmaybe-uninitialized] 2488 | if(ABS(first_top - top )< (font_height+3)) glbpic.c:2412:14: note: ‘first_top’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~ glbpic.c:2483:75: warning: ‘first_left’ may be used uninitialized [-Wmaybe-uninitialized] 2483 | if(ABS(first_left - left) < (t_width +3)) glbpic.c:2412:38: note: ‘first_left’ was declared here 2412 | Int4 first_top, first_width, first_left; /*first marker*/ | ^~~~~~~~~~ In file included from ../include/glbpic.h:7, from glbpic.c:23: glbpic.c: In function ‘add_alignment_to_global’: ../include/picture.h:511:22: warning: ‘g_top’ may be used uninitialized [-Wmaybe-uninitialized] 511 | #define AddRectangle Nlm_AddRectangle glbpic.c:1560:14: note: ‘g_top’ was declared here 1560 | Int4 g_top, g_bottom; | ^~~~~ In function ‘Draw_Global_Linear’, inlined from ‘Draw_Global’ at glbpic.c:2840:4: glbpic.c:2177:40: warning: ‘seglen’ may be used uninitialized [-Wmaybe-uninitialized] 2177 | m_stop += seglen; | ~~~~~~~^~~~~~~~~ glbpic.c: In function ‘Draw_Global’: glbpic.c:1943:8: note: ‘seglen’ was declared here 1943 | Int4 seglen; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF layout.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/maputil.h:113, from ../include/jzcoll.h:123, from ../include/layout.h:3, from layout.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ layout.c: In function ‘LayoutNodeFlat’: layout.c:326:31: warning: variable ‘prev’ set but not used [-Wunused-but-set-variable] 326 | ValNodePtr vnp, next, prev; | ^~~~ layout.c: In function ‘layout_uncompressed_group’: layout.c:1244:27: warning: variable ‘group_stop’ set but not used [-Wunused-but-set-variable] 1244 | Int2 group_start, group_stop; | ^~~~~~~~~~ layout.c: In function ‘LayoutFeatNode’: layout.c:1365:24: warning: variable ‘y_next’ set but not used [-Wunused-but-set-variable] 1365 | Int4 cur_line, y_next; | ^~~~~~ layout.c:1364:24: warning: variable ‘labelstyle’ set but not used [-Wunused-but-set-variable] 1364 | Int4 segstyle, labelstyle; | ^~~~~~~~~~ layout.c:1363:17: warning: variable ‘show_trunc’ set but not used [-Wunused-but-set-variable] 1363 | Boolean show_trunc = FALSE; | ^~~~~~~~~~ layout.c:1350:17: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 1350 | Int2 i, k; | ^ layout.c: In function ‘LayoutAlignNode’: layout.c:2208:14: warning: unused variable ‘num’ [-Wunused-variable] 2208 | Int4 num = 0; | ^~~ layout.c: At top level: layout.c:1779:16: warning: ‘modify_master_line’ defined but not used [-Wunused-function] 1779 | static Boolean modify_master_line(ValNodePtr vnp, Int4Ptr m_left, Int4Ptr m_right, Int4 maxScale, Uint1 label_align) | ^~~~~~~~~~~~~~~~~~ In function ‘link_to_group’, inlined from ‘make_prev_group’ at layout.c:761:4, inlined from ‘GroupFeatNode’ at layout.c:810:2: layout.c:635:22: warning: ‘prev’ may be used uninitialized [-Wmaybe-uninitialized] 635 | next = prev->next; | ~~~~~^~~~~~~~~~~~ layout.c: In function ‘GroupFeatNode’: layout.c:594:42: note: ‘prev’ was declared here 594 | ValNodePtr my_node = NULL, curr, prev, next; | ^~~~ layout.c: In function ‘LayoutFeatNode’: layout.c:1435:35: warning: ‘p_left’ may be used uninitialized [-Wmaybe-uninitialized] 1435 | if(left < p_left) | ^ layout.c:1351:27: note: ‘p_left’ was declared here 1351 | Int4 left, right, p_left, p_right; | ^~~~~~ layout.c:1447:35: warning: ‘p_right’ may be used uninitialized [-Wmaybe-uninitialized] 1447 | if(right > p_right) | ^ layout.c:1351:35: note: ‘p_right’ was declared here 1351 | Int4 left, right, p_left, p_right; | ^~~~~~~ layout.c:1461:29: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 1461 | fnp->bottom = height; | ~~~~~~~~~~~~^~~~~~~~ layout.c:1348:14: note: ‘height’ was declared here 1348 | Int4 height; | ^~~~~~ layout.c: In function ‘LayoutAlignNode’: layout.c:2352:16: warning: ‘next_line’ may be used uninitialized [-Wmaybe-uninitialized] 2352 | return next_line; | ^~~~~~~~~ layout.c:2215:24: note: ‘next_line’ was declared here 2215 | Int4 cur_line, next_line; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF saldist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/saldist.h:48, from saldist.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ saldist.c: In function ‘AAcode’: saldist.c:1003:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1003 | if (car=='A') return(1); if (car=='B') return(2); | ^~ saldist.c:1003:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1003 | if (car=='A') return(1); if (car=='B') return(2); | ^~ saldist.c:1004:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1004 | if (car=='C') return(3); if (car=='D') return(4); | ^~ saldist.c:1004:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1004 | if (car=='C') return(3); if (car=='D') return(4); | ^~ saldist.c:1005:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1005 | if (car=='E') return(5); if (car=='F') return(6); | ^~ saldist.c:1005:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1005 | if (car=='E') return(5); if (car=='F') return(6); | ^~ saldist.c:1006:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1006 | if (car=='G') return(7); if (car=='H') return(8); | ^~ saldist.c:1006:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1006 | if (car=='G') return(7); if (car=='H') return(8); | ^~ saldist.c:1007:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1007 | if (car=='I') return(9); if (car=='K') return(10); | ^~ saldist.c:1007:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1007 | if (car=='I') return(9); if (car=='K') return(10); | ^~ saldist.c:1008:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1008 | if (car=='L') return(11); if (car=='M') return(12); | ^~ saldist.c:1008:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1008 | if (car=='L') return(11); if (car=='M') return(12); | ^~ saldist.c:1009:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1009 | if (car=='N') return(13); if (car=='P') return(14); | ^~ saldist.c:1009:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1009 | if (car=='N') return(13); if (car=='P') return(14); | ^~ saldist.c:1010:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1010 | if (car=='Q') return(15); if (car=='R') return(16); | ^~ saldist.c:1010:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1010 | if (car=='Q') return(15); if (car=='R') return(16); | ^~ saldist.c:1011:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1011 | if (car=='S') return(17); if (car=='T') return(18); | ^~ saldist.c:1011:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1011 | if (car=='S') return(17); if (car=='T') return(18); | ^~ saldist.c:1012:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1012 | if (car=='V') return(19); if (car=='W') return(20); | ^~ saldist.c:1012:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1012 | if (car=='V') return(19); if (car=='W') return(20); | ^~ saldist.c:1013:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1013 | if (car=='X') return(21); if (car=='Y') return(22); | ^~ saldist.c:1013:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1013 | if (car=='X') return(21); if (car=='Y') return(22); | ^~ saldist.c:1014:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1014 | if (car=='Z') return(23); if (car=='U') return(24); | ^~ saldist.c:1014:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1014 | if (car=='Z') return(23); if (car=='U') return(24); | ^~ saldist.c: In function ‘copy_string’: saldist.c:1289:12: warning: value computed is not used [-Wunused-value] 1289 | *from++; | ^~~~~~~ saldist.c:1302:11: warning: value computed is not used [-Wunused-value] 1302 | *from++; | ^~~~~~~ saldist.c: In function ‘nss_ref_complength’: saldist.c:1479:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1479 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1455:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1455 | c1, c2; | ^~ saldist.c:1455:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1455 | c1, c2; | ^~ saldist.c: In function ‘nss_pw_complength’: saldist.c:1572:18: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1572 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1547:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1547 | c1, c2; | ^~ saldist.c:1547:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1547 | c1, c2; | ^~ saldist.c: In function ‘nss_gp_complength’: saldist.c:1675:21: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1675 | if (s1[0] != '-' && s1[1] != '-' && s1[2] != '-' && s2[0] != '-' && s2[1] != '-' && s2[2] != '-') | ^ saldist.c:1640:16: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 1640 | c1, c2; | ^~ saldist.c:1640:12: warning: variable ‘c1’ set but not used [-Wunused-but-set-variable] 1640 | c1, c2; | ^~ saldist.c: In function ‘SortbySimProc’: saldist.c:2139:31: warning: variable ‘newsalpd’ set but not used [-Wunused-but-set-variable] 2139 | SeqAlignPtr newsalp, newsalpd; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from saldist.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ saldist.c:1853:22: warning: ‘scangp_calcul’ defined but not used [-Wunused-function] 1853 | static Int4Ptr PNTR scangp_calcul (EditAlignDataPtr adp, Int2 seq1, Int2 seq2, Int4 from, Int4 to, Int2 group, Int2 choice, Int2 win_width) | ^~~~~~~~~~~~~ saldist.c:1080:24: warning: ‘FloatLomatrix’ defined but not used [-Wunused-function] 1080 | static FloatLoPtr PNTR FloatLomatrix (Int2 nrows, Int2 ncol) | ^~~~~~~~~~~~~ saldist.c:999:13: warning: ‘AAcode’ defined but not used [-Wunused-function] 999 | static Int2 AAcode(Char car) | ^~~~~~ saldist.c:928:16: warning: ‘new_matrice’ defined but not used [-Wunused-function] 928 | static Boolean new_matrice (Int2 simmatrix, CharPtr path) | ^~~~~~~~~~~ saldist.c:910:14: warning: ‘matrixlst’ defined but not used [-Wunused-variable] 910 | static Char *matrixlst [] = {"", "idmat", | ^~~~~~~~~ saldist.c: In function ‘writematrixhalf.constprop.0’: saldist.c:1225:18: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1225 | vnp=vnp->next; | ~~~^~~~~~~~~~ saldist.c:1174:19: note: ‘vnp’ was declared here 1174 | ValNodePtr vnp, | ^~~ In function ‘writematrix’, inlined from ‘PwDistProc’ at saldist.c:2019:9: saldist.c:1151:18: warning: ‘vnp’ may be used uninitialized [-Wmaybe-uninitialized] 1151 | vnp=vnp->next; | ~~~^~~~~~~~~~ saldist.c: In function ‘PwDistProc’: saldist.c:1104:19: note: ‘vnp’ was declared here 1104 | ValNodePtr vnp, | ^~~ In function ‘SortbyLenProc’, inlined from ‘SortbyLenItem’ at saldist.c:2323:3: saldist.c:2191:14: warning: ‘mink’ may be used uninitialized [-Wmaybe-uninitialized] 2191 | sortlst [mink] = j + 1; | ^ saldist.c: In function ‘SortbyLenItem’: saldist.c:2172:28: note: ‘mink’ was declared here 2172 | Int2 j, k, mink; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF saled.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from saled.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ saled.c: In function ‘ReadAlignmentForSeqEntry’: saled.c:3310:21: warning: unused variable ‘dirty’ [-Wunused-variable] 3310 | dirty = FALSE; | ^~~~~ saled.c:3306:21: warning: unused variable ‘salp’ [-Wunused-variable] 3306 | SeqAlignPtr salp=NULL, | ^~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from saled.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from saled.c:55: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salfiles.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from ../include/salfiles.h:48, from salfiles.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salfiles.c: In function ‘NewFastaRead’: salfiles.c:315:30: warning: variable ‘lastsegsip’ set but not used [-Wunused-but-set-variable] 315 | SeqIdPtr segsip=NULL, lastsegsip=NULL; | ^~~~~~~~~~ salfiles.c: In function ‘ReadAlignmentToStrings’: salfiles.c:664:16: warning: unused variable ‘nseq’ [-Wunused-variable] 664 | Int2 nseq = 0; | ^~~~ salfiles.c: In function ‘MacawRead’: salfiles.c:1257:15: warning: unused variable ‘vnp’ [-Wunused-variable] 1257 | vnp = NULL; | ^~~ salfiles.c: In function ‘ReadLocalAlign’: salfiles.c:1444:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1444 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1444:22: note: did you mean to dereference the pointer? 1444 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1446:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1446 | if (tmp!='\0') | ^~ salfiles.c:1446:19: note: did you mean to dereference the pointer? 1446 | if (tmp!='\0') | ^ salfiles.c:1455:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1455 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1455:22: note: did you mean to dereference the pointer? 1455 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1457:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1457 | if (tmp!='\0') | ^~ salfiles.c:1457:19: note: did you mean to dereference the pointer? 1457 | if (tmp!='\0') | ^ salfiles.c:1536:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1536 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1536:22: note: did you mean to dereference the pointer? 1536 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1538:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1538 | if (tmp!='\0') | ^~ salfiles.c:1538:19: note: did you mean to dereference the pointer? 1538 | if (tmp!='\0') | ^ salfiles.c:1547:25: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1547 | while (tmp!='\0' && !isdigit (*tmp)) | ^~ salfiles.c:1547:22: note: did you mean to dereference the pointer? 1547 | while (tmp!='\0' && !isdigit (*tmp)) | ^ salfiles.c:1549:22: warning: comparison between pointer and zero character constant [-Wpointer-compare] 1549 | if (tmp!='\0') | ^~ salfiles.c:1549:19: note: did you mean to dereference the pointer? 1549 | if (tmp!='\0') | ^ salfiles.c:1370:14: warning: variable ‘tmp1’ set but not used [-Wunused-but-set-variable] 1370 | tmp1; | ^~~~ salfiles.c: In function ‘ImportFromFile’: salfiles.c:2072:20: warning: unused variable ‘sep’ [-Wunused-variable] 2072 | SeqEntryPtr sep = NULL; | ^~~ salfiles.c:2071:20: warning: unused variable ‘sap’ [-Wunused-variable] 2071 | SeqAnnotPtr sap = NULL; | ^~~ salfiles.c: In function ‘FindSeqEntryForSeqIdCallback’: salfiles.c:2672:12: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2672 | if (SeqIdForSameBioseq(cip->sip, sip)) | ^~ salfiles.c:2674:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2674 | cip->bsp = bsp; | ^~~ salfiles.c: In function ‘sesp_to_pept’: salfiles.c:2713:18: warning: unused variable ‘bufferPtr’ [-Wunused-variable] 2713 | bufferPtr = NULL; | ^~~~~~~~~ salfiles.c: In function ‘SaveFeatProc’: salfiles.c:3387:22: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 3387 | Int2 handled; | ^~~~~~~ salfiles.c: In function ‘CCReadAnythingLoop’: salfiles.c:3685:16: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 3685 | Uint2 entityID; | ^~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salfiles.c:48: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ salfiles.c:501:19: warning: ‘get_lens_fromseqalign’ defined but not used [-Wunused-function] 501 | static ValNodePtr get_lens_fromseqalign (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~~ salfiles.c: In function ‘NewFastaRead.constprop.0’: salfiles.c:460:6: warning: ‘sip’ may be used uninitialized [-Wmaybe-uninitialized] 460 | if (sip!=NULL) | ^ salfiles.c:312:17: note: ‘sip’ was declared here 312 | SeqIdPtr sip; | ^~~ In function ‘ReadAlignmentToStrings’, inlined from ‘GapFastaRead’ at salfiles.c:811:12: salfiles.c:724:15: warning: ‘startp’ may be used uninitialized [-Wmaybe-uninitialized] 724 | if (!startp) { | ^ salfiles.c: In function ‘GapFastaRead’: salfiles.c:660:16: note: ‘startp’ was declared here 660 | Boolean startp; | ^~~~~~ In function ‘ReadAlignmentToStrings’, inlined from ‘GapFastaRead’ at salfiles.c:811:12: salfiles.c:747:25: warning: ‘seqstr’ may be used uninitialized [-Wmaybe-uninitialized] 747 | seqstr [lgseq] = strp[j]; | ^ salfiles.c: In function ‘GapFastaRead’: salfiles.c:654:16: note: ‘seqstr’ was declared here 654 | seqstr; | ^~~~~~ In file included from ../include/sequtil.h:43, from ../include/gather.h:169, from ../include/saledit.h:52: In function ‘align_this’, inlined from ‘CCDownloadProc’ at salfiles.c:2364:9: ../include/objsset.h:230:26: warning: ‘new_sep’ may be used uninitialized [-Wmaybe-uninitialized] 230 | #define IS_Bioseq(a) ((a)->choice == 1) | ~~~^~~~~~~~ salfiles.c: In function ‘CCDownloadProc’: salfiles.c:2286:15: note: ‘new_sep’ was declared here 2286 | SeqEntryPtr new_sep; | ^~~~~~~ In function ‘MacawRead’, inlined from ‘ReadLocalAlignment’ at salfiles.c:2045:19: salfiles.c:1278:6: warning: ‘seqvnp’ may be used uninitialized [-Wmaybe-uninitialized] 1278 | if (seqvnp == NULL) | ^ salfiles.c: In function ‘ReadLocalAlignment’: salfiles.c:1113:19: note: ‘seqvnp’ was declared here 1113 | ValNodePtr vnp, seqvnp; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/saledit.h:48, from salpanel.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salpanel.c: In function ‘go_to_next_to_draw’: salpanel.c:331:17: warning: statement with no effect [-Wunused-value] 331 | offsettmp; | ^~~~~~~~~ salpanel.c: In function ‘next_to_draw’: salpanel.c:471:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 471 | if ( curstr != NULL ) | ^ salpanel.c: In function ‘AssociatePropagatedSubloc’: salpanel.c:3131:16: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 3131 | ValNodePtr vnp; | ^~~ salpanel.c: In function ‘FeaturePropagateForm’: salpanel.c:4674:15: warning: variable ‘ppt’ set but not used [-Wunused-but-set-variable] 4674 | PrompT ppt; | ^~~ salpanel.c:4669:15: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 4669 | ButtoN b; | ^ salpanel.c: In function ‘OkToContinueWithFeatureApply’: salpanel.c:6103:14: warning: unused variable ‘num_missing’ [-Wunused-variable] 6103 | Int4 num_missing = 0, seq_num, start_num; | ^~~~~~~~~~~ salpanel.c: In function ‘DoApplyFeatureToAlignment’: salpanel.c:6219:31: warning: unused variable ‘found_null’ [-Wunused-variable] 6219 | Boolean found_null = FALSE; | ^~~~~~~~~~ salpanel.c: In function ‘ApplyFeatureToAlignment’: salpanel.c:6421:31: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 6421 | ButtoN b; | ^ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salpanel.c:45: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salpanel.c:52: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salpanel.c:5059:13: warning: ‘BatchApplyFeatureDetailsMessage’ defined but not used [-Wunused-function] 5059 | static void BatchApplyFeatureDetailsMessage (DialoG d, Int2 mssg) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpanel.c:224:13: warning: ‘get_client_rectxy’ defined but not used [-Wunused-function] 224 | static void get_client_rectxy (PaneL p, RectPtr prc, Int2 x, Int2 y) | ^~~~~~~~~~~~~~~~~ salpanel.c:113:14: warning: ‘leftOvalFillSym’ defined but not used [-Wunused-variable] 113 | static Uint1 leftOvalFillSym [] = { | ^~~~~~~~~~~~~~~ salpanel.c:110:14: warning: ‘rightOvalFillSym’ defined but not used [-Wunused-variable] 110 | static Uint1 rightOvalFillSym [] = { | ^~~~~~~~~~~~~~~~ salpanel.c:107:14: warning: ‘leftOvalSym’ defined but not used [-Wunused-variable] 107 | static Uint1 leftOvalSym [] = { | ^~~~~~~~~~~ salpanel.c:104:14: warning: ‘rightOvalSym’ defined but not used [-Wunused-variable] 104 | static Uint1 rightOvalSym [] = { | ^~~~~~~~~~~~ salpanel.c:101:14: warning: ‘downTriFillSym’ defined but not used [-Wunused-variable] 101 | static Uint1 downTriFillSym [] = { | ^~~~~~~~~~~~~~ salpanel.c:98:14: warning: ‘upTriFillSym’ defined but not used [-Wunused-variable] 98 | static Uint1 upTriFillSym [] = { | ^~~~~~~~~~~~ salpanel.c:89:14: warning: ‘ovalFillSym’ defined but not used [-Wunused-variable] 89 | static Uint1 ovalFillSym [] = { | ^~~~~~~~~~~ salpanel.c:86:14: warning: ‘diamondFillSym’ defined but not used [-Wunused-variable] 86 | static Uint1 diamondFillSym [] = { | ^~~~~~~~~~~~~~ salpanel.c:80:14: warning: ‘downTriSym’ defined but not used [-Wunused-variable] 80 | static Uint1 downTriSym [] = { | ^~~~~~~~~~ salpanel.c:77:14: warning: ‘upTriSym’ defined but not used [-Wunused-variable] 77 | static Uint1 upTriSym [] = { | ^~~~~~~~ salpanel.c:68:14: warning: ‘ovalSym’ defined but not used [-Wunused-variable] 68 | static Uint1 ovalSym [] = { | ^~~~~~~ salpanel.c:65:14: warning: ‘diamondSym’ defined but not used [-Wunused-variable] 65 | static Uint1 diamondSym [] = { | ^~~~~~~~~~ In function ‘draw_line’, inlined from ‘draw_feat.isra.0’ at salpanel.c:2208:3: salpanel.c:1988:30: warning: ‘col1’ may be used uninitialized [-Wmaybe-uninitialized] 1988 | for (j=0, gap=gapline; jitemtype, FALSE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salpanel.c:2348:28: note: ‘draw_diff’ was declared here 2348 | Boolean is_master, draw_diff; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salparam.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from ../include/salparam.h:48, from salparam.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salparam.c: In function ‘mergelst’: salparam.c:1325:20: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 1325 | Boolean val; | ^~~ salparam.c: In function ‘unmergelst’: salparam.c:1340:20: warning: variable ‘dbdp’ set but not used [-Wunused-but-set-variable] 1340 | DialogBoxDataPtr dbdp; | ^~~~ salparam.c: In function ‘FormulaDialog’: salparam.c:1398:36: warning: variable ‘b5’ set but not used [-Wunused-but-set-variable] 1398 | ButtoN b1, b2, b3, b4, b5; | ^~ salparam.c: In function ‘JK_NTPattern2Ex’: salparam.c:1596:19: warning: variable ‘debug_str’ set but not used [-Wunused-but-set-variable] 1596 | CharPtr debug_str; | ^~~~~~~~~ salparam.c: In function ‘get_string_fromtext’: salparam.c:1721:11: warning: the comparison will always evaluate as ‘false’ for the address of ‘str’ will never be NULL [-Waddress] 1721 | if (str == NULL) | ^~ salparam.c:1715:22: note: ‘str’ declared here 1715 | Char str [128]; | ^~~ salparam.c: In function ‘DotPlotBtn’: salparam.c:1936:22: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1936 | Int2 status; | ^~~~~~ salparam.c: In function ‘DotPlotDialog’: salparam.c:1973:20: warning: variable ‘bt1’ set but not used [-Wunused-but-set-variable] 1973 | ButtoN bt1, bt2; | ^~~ salparam.c: In function ‘DotPlotItem’: salparam.c:2004:22: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 2004 | Int2 status; | ^~~~~~ salparam.c: In function ‘SelectSeqFunc’: salparam.c:2308:20: warning: variable ‘str’ set but not used [-Wunused-but-set-variable] 2308 | CharPtr str; | ^~~ salparam.c: In function ‘HighlightSelectionFunc’: salparam.c:2344:22: warning: variable ‘wdp’ set but not used [-Wunused-but-set-variable] 2344 | SeqEditViewFormPtr wdp; | ^~~ salparam.c: In function ‘PropagateFeatureProc’: salparam.c:2623:25: warning: variable ‘iID’ set but not used [-Wunused-but-set-variable] 2623 | Uint2 eID, iID, | ^~~ salparam.c:2614:20: warning: variable ‘salp’ set but not used [-Wunused-but-set-variable] 2614 | SeqAlignPtr salp; | ^~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2959:22: warning: the comparison will always evaluate as ‘true’ for the address of ‘label’ will never be NULL [-Waddress] 2959 | if (feat->label != NULL) | ^~ ../include/salsa.h:171:20: note: ‘label’ declared here 171 | Char label[101]; | ^~~~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salparam.c:49: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from salparam.c:58: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salparam.c: In function ‘FileInProc’: salparam.c:782:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 782 | fscanf(fp, "%d %ld", &n, &lens); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ salparam.c: In function ‘DotPlotBtn’: salparam.c:1950:9: warning: ‘sep’ may be used uninitialized [-Wmaybe-uninitialized] 1950 | if (sep != NULL && IS_Bioseq (sep)) { | ^ salparam.c:1931:22: note: ‘sep’ was declared here 1931 | SeqEntryPtr sep; | ^~~ salparam.c: In function ‘SalsaExportDialog’: salparam.c:2258:19: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size 10 [-Wformat-overflow=] 2258 | sprintf (str2, "%ld", (long) adp->int4value); | ^~~ salparam.c:2258:18: note: directive argument in the range [-2147483648, 2147483647] 2258 | sprintf (str2, "%ld", (long) adp->int4value); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SalsaExportDialog’ at salparam.c:2258:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘SalsaExportDialog’: salparam.c:2261:19: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size 10 [-Wformat-overflow=] 2261 | sprintf (str2, "%ld", (long) adp->int4value2); | ^~~ salparam.c:2261:18: note: directive argument in the range [-2147483648, 2147483647] 2261 | sprintf (str2, "%ld", (long) adp->int4value2); | ^~~~~ In function ‘sprintf’, inlined from ‘SalsaExportDialog’ at salparam.c:2261:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2964:32: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 9 and 19 [-Wformat-overflow=] 2964 | sprintf (str2, " (%ld..%ld)", (long)start, (long)stop); | ^~~ salparam.c:2964:24: note: directive argument in the range [-2147483647, 2147483647] 2964 | sprintf (str2, " (%ld..%ld)", (long)start, (long)stop); | ^~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PropagateFeatDialog’ at salparam.c:2964:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 28 bytes into a destination of size 24 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ salparam.c: In function ‘PropagateFeatDialog’: salparam.c:2962:32: warning: ‘%ld’ directive writing between 1 and 11 bytes into a region of size between 9 and 19 [-Wformat-overflow=] 2962 | sprintf (str2, " (%ld..%ld) minus strand", (long)start, (long)stop); | ^~~ salparam.c:2962:24: note: directive argument in the range [-2147483647, 2147483647] 2962 | sprintf (str2, " (%ld..%ld) minus strand", (long)start, (long)stop); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘PropagateFeatDialog’ at salparam.c:2962:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 21 and 41 bytes into a destination of size 24 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salsa.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salsa.h:48, from salsa.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salsa.c: In function ‘UndoProc’: salsa.c:1799:20: warning: the comparison will always evaluate as ‘true’ for the address of ‘tmpfile’ will never be NULL [-Waddress] 1799 | if (adp->tmpfile != NULL && adp->tmpfile[0] != '\0') | ^~ ../include/salsa.h:364:19: note: ‘tmpfile’ declared here 364 | Char tmpfile [PATH_MAX]; /* path + filename */ | ^~~~~~~ salsa.c: In function ‘SelectSubsProc’: salsa.c:2140:23: warning: variable ‘svpp’ set but not used [-Wunused-but-set-variable] 2140 | SeqEditViewProcsPtr svpp=NULL; | ^~~~ salsa.c: In function ‘SetSeqInfo’: salsa.c:3195:17: warning: unused variable ‘vnp’ [-Wunused-variable] 3195 | ValNodePtr vnp = NULL; | ^~~ salsa.c: In function ‘SetupAlignDataSap’: salsa.c:3410:16: warning: variable ‘entityID_sap’ set but not used [-Wunused-but-set-variable] 3410 | Uint2 entityID_sap; | ^~~~~~~~~~~~ salsa.c: In function ‘get_bestpos_formerge’: salsa.c:4304:17: warning: variable ‘insert_after’ set but not used [-Wunused-but-set-variable] 4304 | insert_after=FALSE; | ^~~~~~~~~~~~ salsa.c:4303:17: warning: variable ‘insert_before’ set but not used [-Wunused-but-set-variable] 4303 | Boolean insert_before=FALSE, | ^~~~~~~~~~~~~ salsa.c: In function ‘CreateSeqAlignViewForm’: salsa.c:4689:22: warning: variable ‘mergebtn’ set but not used [-Wunused-but-set-variable] 4689 | ButtoN mergebtn; | ^~~~~~~~ salsa.c: In function ‘AlgEditFunc’: salsa.c:4976:23: warning: unused variable ‘wdp’ [-Wunused-variable] 4976 | SeqEditViewFormPtr wdp = NULL; | ^~~ salsa.c:4974:23: warning: unused variable ‘w’ [-Wunused-variable] 4974 | WindoW w = NULL; | ^ salsa.c: In function ‘OldAlignmentEditor’: salsa.c:5106:16: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 5106 | Int2 rval; | ^~~~ salsa.c: In function ‘LaunchAnnotAlignEditor’: salsa.c:5293:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5293 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignEditor’: salsa.c:5310:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5310 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignViewer’: salsa.c:5327:20: warning: variable ‘handled’ set but not used [-Wunused-but-set-variable] 5327 | Int2 handled; | ^~~~~~~ salsa.c: In function ‘LaunchAlignEditorFromDesktop’: salsa.c:5342:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 5342 | OMProcControlPtr ompcp; | ^~~~~ salsa.c: In function ‘LaunchAlignEditorFromDesktop2’: salsa.c:5359:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 5359 | OMProcControlPtr ompcp; | ^~~~~ salsa.c: In function ‘InsertSeqProc’: salsa.c:5538:17: warning: variable ‘cnclbt’ set but not used [-Wunused-but-set-variable] 5538 | ButtoN insbt, cnclbt; | ^~~~~~ salsa.c:5536:10: warning: variable ‘insprt’ set but not used [-Wunused-but-set-variable] 5536 | PrompT insprt; | ^~~~~~ salsa.c: In function ‘SeqAlignBestHit’: salsa.c:5605:22: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 5605 | Int4 last; | ^~~~ salsa.c: In function ‘SeqAlignStartUpdate’: salsa.c:5791:22: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 5791 | Int2 index, k, j; | ^ salsa.c:5790:15: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5790 | start; | ^~~~~ salsa.c:5789:15: warning: variable ‘len_sum’ set but not used [-Wunused-but-set-variable] 5789 | Int4 len_sum, | ^~~~~~~ salsa.c:5786:15: warning: variable ‘lenp’ set but not used [-Wunused-but-set-variable] 5786 | Int4Ptr lenp, | ^~~~ salsa.c:5785:15: warning: variable ‘pre’ set but not used [-Wunused-but-set-variable] 5785 | SeqIdPtr pre, sip, next; | ^~~ salsa.c: In function ‘CCNormalizeSeqAlignId’: salsa.c:6746:23: warning: unused variable ‘gi’ [-Wunused-variable] 6746 | Int4 gi = 0; | ^~ salsa.c:6745:17: warning: unused variable ‘missing_fmt’ [-Wunused-variable] 6745 | CharPtr missing_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\n"; | ^~~~~~~~~~~ salsa.c:6744:17: warning: unused variable ‘missing_cont_fmt’ [-Wunused-variable] 6744 | CharPtr missing_cont_fmt = "The alignment contains %s that can not be found in GenBank.\nPlease check the accession number.\nContinue anyway?\n"; | ^~~~~~~~~~~~~~~~ salsa.c: In function ‘ValidateSeqAlignandACCEx’: salsa.c:7106:16: warning: variable ‘ans’ set but not used [-Wunused-but-set-variable] 7106 | MsgAnswer ans; | ^~~ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/salpanel.h:53, from salsa.c:48: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salsa.c:68: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salsa.c:87:13: warning: ‘InsertSequenceDlg’ declared ‘static’ but never defined [-Wunused-function] 87 | static void InsertSequenceDlg (ButtoN b); | ^~~~~~~~~~~~~~~~~ salsa.c:5973:13: warning: ‘SWPrintFarpointerAln’ defined but not used [-Wunused-function] 5973 | static void SWPrintFarpointerAln(SeqAlignPtr sap, FILE *fp) | ^~~~~~~~~~~~~~~~~~~~ salsa.c:2360:13: warning: ‘MakeCdRgnrProc’ defined but not used [-Wunused-function] 2360 | static void MakeCdRgnrProc (IteM i) { | ^~~~~~~~~~~~~~ salsa.c:2356:13: warning: ‘MakeCdRgnProc’ defined but not used [-Wunused-function] 2356 | static void MakeCdRgnProc (IteM i) { | ^~~~~~~~~~~~~ salsa.c:1760:13: warning: ‘AcceptCloseWindowButton’ defined but not used [-Wunused-function] 1760 | static void AcceptCloseWindowButton (ButtoN b) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from salsa.c:52: ../include/salprop.h:50:16: warning: ‘GBFeat’ defined but not used [-Wunused-variable] 50 | static CharPtr GBFeat[number_GBFeat] = { | ^~~~~~ In file included from ../include/ncbi.h:65: salsa.c: In function ‘ExportFASTAForUnselectedUpdates’: ../include/ncbifile.h:113:19: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized] 113 | #define FileClose Nlm_FileClose salsa.c:6350:23: note: ‘fp’ was declared here 6350 | FILE *fp; | ^~ salsa.c: In function ‘ExportBadAlignments’: ../include/ncbifile.h:113:19: warning: ‘fp’ may be used uninitialized [-Wmaybe-uninitialized] 113 | #define FileClose Nlm_FileClose salsa.c:6318:23: note: ‘fp’ was declared here 6318 | FILE *fp; | ^~ salsa.c: In function ‘SeqAlignBestHit.constprop.0’: salsa.c:5748:24: warning: ‘beg’ may be used uninitialized [-Wmaybe-uninitialized] 5748 | *nonly = -(beg+end); | ~~~~^~~~~ salsa.c:5598:22: note: ‘beg’ was declared here 5598 | Int4 beg; | ^~~ salsa.c:5748:24: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 5748 | *nonly = -(beg+end); | ~~~~^~~~~ salsa.c:5600:22: note: ‘end’ was declared here 5600 | Int4 end; | ^~~ salsa.c:5745:10: warning: ‘nctr’ may be used uninitialized [-Wmaybe-uninitialized] 5745 | if (nctr > 0) | ^ salsa.c:5608:22: note: ‘nctr’ was declared here 5608 | Int4 nctr; | ^~~~ salsa.c: In function ‘SkipThisWindowProc’: salsa.c:4590:6: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 4590 | if (salp) | ^ salsa.c:4574:22: note: ‘salp’ was declared here 4574 | SeqAlignPtr salp; | ^~~~ salsa.c: In function ‘DeleteProc’: salsa.c:1945:14: warning: ‘sap’ may be used uninitialized [-Wmaybe-uninitialized] 1945 | newsalp = (SeqAlignPtr)sap->data; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ salsa.c:1921:22: note: ‘sap’ was declared here 1921 | SeqAnnotPtr sap; | ^~~ In function ‘update_length’, inlined from ‘BioseqEditMsgFunc’ at salsa.c:1165:14: salsa.c:912:32: warning: ‘anp’ may be used uninitialized [-Wmaybe-uninitialized] 912 | ssp = SelStructNew (anp->seq_entityID, anp->bsp_itemID, OBJ_BIOSEQ, from, to, anp->sip, Seq_strand_plus, FALSE); | ~~~^~~~~~~~~~~~~~ salsa.c: In function ‘BioseqEditMsgFunc’: salsa.c:890:20: note: ‘anp’ was declared here 890 | AlignNodePtr anp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqfltr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqfltr.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqfltr.c: In function ‘FilterSeq’: seqfltr.c:253:10: warning: ‘fptr’ may be used uninitialized [-Wmaybe-uninitialized] 253 | if (fptr == NULL) | ^ seqfltr.c:213:17: note: ‘fptr’ was declared here 213 | FloatHiPtr fptr; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqgraph.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqgraph.c: In function ‘EndPointDialogToEndPointValNode’: seqgraph.c:140:10: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 140 | return (Pointer) eplist; | ^~~~~~~~~~~~~~~~ seqgraph.c:133:22: note: ‘eplist’ was declared here 133 | ValNodePtr eplist; | ^~~~~~ seqgraph.c: In function ‘SeqLocGraphViewProc’: seqgraph.c:1136:17: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 1136 | while (eplist != NULL) | ^ seqgraph.c:1120:31: note: ‘eplist’ was declared here 1120 | ValNodePtr ephead, eplist; | ^~~~~~ seqgraph.c: In function ‘MarkPrims’: seqgraph.c:911:11: warning: ‘fval’ may be used uninitialized [-Wmaybe-uninitialized] 911 | val = fval/2; | ~~~~^~~~~~~~ seqgraph.c:841:14: note: ‘fval’ was declared here 841 | FloatHi fval; | ^~~~ seqgraph.c: In function ‘CutOffProc’: seqgraph.c:1018:17: warning: ‘eplist’ may be used uninitialized [-Wmaybe-uninitialized] 1018 | while (eplist != NULL) | ^ seqgraph.c:1005:23: note: ‘eplist’ was declared here 1005 | ValNodePtr eplist, ephead, epprev, epnext; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqgrphx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqgrphx.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqgrphx.c:301:13: warning: ‘CleanupGCFilterForm’ defined but not used [-Wunused-function] 301 | static void CleanupGCFilterForm (GraphiC g, VoidPtr data) | ^~~~~~~~~~~~~~~~~~~ seqgrphx.c:152:25: warning: ‘FilterMsgFunc’ defined but not used [-Wunused-function] 152 | static Int2 LIBCALLBACK FilterMsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~~~ seqgrphx.c:28:25: warning: ‘MatrixMsgFunc’ defined but not used [-Wunused-function] 28 | static Int2 LIBCALLBACK MatrixMsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqmtrx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqmtrx.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqmtrx.c:387:20: warning: ‘MatrixSearch’ defined but not used [-Wunused-function] 387 | static SeqGraphPtr MatrixSearch (BioseqPtr bsp, Int2 matrixtype) | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqpcc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from seqpcc.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqpcc.c: In function ‘PCCProc’: seqpcc.c:229:14: warning: ‘pbsp’ may be used uninitialized [-Wmaybe-uninitialized] 229 | if ((spp = SeqPortNew (pbsp, start, end, 0, Seq_code_iupacaa)) != NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpcc.c:196:16: note: ‘pbsp’ was declared here 196 | BioseqPtr pbsp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqanal.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from seqanal.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF aacomp.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from aacomp.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ aacomp.c:86:20: warning: ‘AACGraph’ defined but not used [-Wunused-function] 86 | static SeqGraphPtr AACGraph (SeqPortPtr spp, Int4 start, Int4 end, Int4 window, | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqscrl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from ../include/seqscrl.h:4, from seqscrl.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF valdlg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vibforms.h:46, from valdlg.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ valdlg.c: In function ‘ClickRulesDoc’: valdlg.c:373:22: warning: unused variable ‘scroll_pos’ [-Wunused-variable] 373 | Int2 scroll_pos = 0; | ^~~~~~~~~~ valdlg.c:372:22: warning: unused variable ‘sb_vert’ [-Wunused-variable] 372 | BaR sb_vert = NULL; | ^~~~~~~ valdlg.c: In function ‘UpdateRuleList’: valdlg.c:479:26: warning: unused variable ‘last_cr’ [-Wunused-variable] 479 | CommentRulePtr new_cr, last_cr = NULL; | ^~~~~~~ valdlg.c: In function ‘SaveRuleChanges’: valdlg.c:540:23: warning: variable ‘dlg’ set but not used [-Wunused-but-set-variable] 540 | CommentSetDlgPtr dlg; | ^~~ valdlg.c: In function ‘LaunchCommentRulesEditor’: valdlg.c:553:23: warning: unused variable ‘m’ [-Wunused-variable] 553 | MenU m; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vsm.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vsmpriv.h:48, from vsm.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsm.c: In function ‘VSMDrawAbout’: vsm.c:1436:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1436 | if (vsmp->title != NULL) | ^~ vsm.c:1438:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1438 | if (vsmp->aboutinfo != NULL) | ^~ vsm.c: In function ‘VSMAboutProc’: vsm.c:1466:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 1466 | PaneL p; | ^ vsm.c: In function ‘VSeqMgrCreateMainWindow’: vsm.c:1569:19: warning: variable ‘omp’ set but not used [-Wunused-but-set-variable] 1569 | ObjMgrPtr omp; | ^~~ vsm.c: In function ‘VSeqMgrPopulateMain’: vsm.c:1710:20: warning: variable ‘atp’ set but not used [-Wunused-but-set-variable] 1710 | AsnTypePtr atp; | ^~~ vsm.c: In function ‘VSMGatherPictProc’: vsm.c:2193:22: warning: variable ‘bssp’ set but not used [-Wunused-but-set-variable] 2193 | BioseqSetPtr bssp; | ^~~~ vsm.c:2188:37: warning: variable ‘bottom’ set but not used [-Wunused-but-set-variable] 2188 | Int4 top, lineheight, left, bottom, width, maxwidth; | ^~~~~~ vsm.c: In function ‘VSMAddPictureToEntity’: vsm.c:2821:17: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 2821 | Pointer ptr; | ^~~ vsm.c:2820:20: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2820 | ValNodePtr vnp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vsmfile.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/vsmpriv.h:48, from vsmfile.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsmfile.c: In function ‘VSMGenericBinAsnOpen’: vsmfile.c:259:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 259 | ButtoN b; | ^ vsmfile.c: In function ‘VSMGenericFastaSave’: vsmfile.c:395:11: warning: variable ‘code’ set but not used [-Wunused-but-set-variable] 395 | Uint1 code; | ^~~~ vsmfile.c: In function ‘VSMFastaProtSaveWithProduct’: vsmfile.c:527:11: warning: variable ‘code’ set but not used [-Wunused-but-set-variable] 527 | Uint1 code; | ^~~~ vsmfile.c: In function ‘VSMSaveSetsAsFiles’: vsmfile.c:1368:20: warning: variable ‘ompcp’ set but not used [-Wunused-but-set-variable] 1368 | OMProcControlPtr ompcp; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vsmutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from vsmutil.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vsmutil.c: In function ‘GetDocPosForError’: vsmutil.c:1743:18: warning: variable ‘val’ set but not used [-Wunused-but-set-variable] 1743 | Int2 val; | ^~~ vsmutil.c: At top level: vsmutil.c:1628:16: warning: ‘MakeFieldReports’ defined but not used [-Wunused-function] 1628 | static Boolean MakeFieldReports (ValNodePtr report_list, ValNodePtr field_list, FILE *fp) | ^~~~~~~~~~~~~~~~ vsmutil.c:387:20: warning: ‘GetSeqDescGivenIDs’ defined but not used [-Wunused-function] 387 | static SeqDescrPtr GetSeqDescGivenIDs (Uint2 entityID, Uint4 itemID, Uint2 itemtype) | ^~~~~~~~~~~~~~~~~~ vsmutil.c: In function ‘ContinueProc’: vsmutil.c:2256:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2256 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2255:26: note: within this loop 2255 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘RevalidateProc’: vsmutil.c:2223:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2223 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2222:26: note: within this loop 2222 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘SetVerbosityAndRepopulate’: vsmutil.c:2297:23: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2297 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2296:26: note: within this loop 2296 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘ClearValidateWindow’: vsmutil.c:613:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 613 | vep->counts [sev] = 0; | ~~~~~~~~~~~~~~~~~~^~~ vsmutil.c:612:32: note: within this loop 612 | for (sev = SEV_NONE; sev <= SEV_MAX; sev++) { | ~~~~^~~~~~~~~~ vsmutil.c: In function ‘CreateValidateWindowExExEx’: vsmutil.c:2620:27: warning: iteration 6 invokes undefined behavior [-Waggressive-loop-optimizations] 2620 | vep->counts [i] = 0; | ~~~~~~~~~~~~~~~~^~~ vsmutil.c:2619:30: note: within this loop 2619 | for (i = SEV_NONE; i <= SEV_MAX; i++) { | ~~^~~~~~~~~~ vsmutil.c: In function ‘ContinueProc’: vsmutil.c:2256:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2256 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘RevalidateProc’: vsmutil.c:2223:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2223 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘SetVerbosityAndRepopulate’: vsmutil.c:2297:19: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2297 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘ClearValidateWindow’: vsmutil.c:613:21: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 613 | vep->counts [sev] = 0; | ~~~~~~~~~~~~^~~~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘CreateValidateWindowExExEx’: vsmutil.c:2620:23: warning: array subscript 6 is above array bounds of ‘Nlm_Int4[6]’ [-Warray-bounds=] 2620 | vep->counts [i] = 0; | ~~~~~~~~~~~~^~~ vsmutil.c:107:18: note: while referencing ‘counts’ 107 | Int4 counts [6]; | ^~~~~~ vsmutil.c: In function ‘ShowValidateDoc’: vsmutil.c:2758:61: warning: ‘ REJECT: ’ directive writing 14 bytes into a region of size between 13 and 43 [-Wformat-overflow=] 2758 | sprintf (str, "INFO: %ld WARNING: %ld ERROR: %ld REJECT: %ld", | ^~~~~~~~~~~~~~ vsmutil.c:2758:17: note: directive argument in the range [-2147483648, 2147483647] 2758 | sprintf (str, "INFO: %ld WARNING: %ld ERROR: %ld REJECT: %ld", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ShowValidateDoc’ at vsmutil.c:2758:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 53 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF udvgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvgraph.c:177: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvgraph.c: In function ‘UDV_click_item’: udvgraph.c:877:9: warning: unused variable ‘IsTransNeeded’ [-Wunused-variable] 877 | Boolean IsTransNeeded=FALSE; | ^~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_SendBSPSelectMsg’: udvgraph.c:1230:13: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 1230 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ udvgraph.c:1226:30: warning: variable ‘bsp_coord_old’ set but not used [-Wunused-but-set-variable] 1226 | Int4 first_bsp_coord, bsp_coord_old,old_pos; | ^~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_draw_helixDNA’: udvgraph.c:1827:15: warning: variable ‘cyChar_2’ set but not used [-Wunused-but-set-variable] 1827 | Int2 cxChar_2,cyChar_2; | ^~~~~~~~ udvgraph.c: In function ‘draw_logo’: udvgraph.c:1940:38: warning: variable ‘cyGlobal’ set but not used [-Wunused-but-set-variable] 1940 | Int2 pos,cxChar=7,cyChar=13,cxGlobal,cyGlobal; | ^~~~~~~~ udvgraph.c: In function ‘UDV_draw_CDS_minus’: udvgraph.c:2337:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 2337 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ udvgraph.c:2332:33: warning: variable ‘numivals2’ set but not used [-Wunused-but-set-variable] 2332 | numivals2=0, | ^~~~~~~~~ udvgraph.c: In function ‘UDV_draw_CDS_plus’: udvgraph.c:2461:9: warning: variable ‘bGiForProductOk’ set but not used [-Wunused-but-set-variable] 2461 | Boolean bGiForProductOk=FALSE; | ^~~~~~~~~~~~~~~ udvgraph.c: In function ‘UDV_draw_panel’: udvgraph.c:4111:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4111 | if(vdp->vgp->MasterViewer == SAMVIEWDDV) | ^~ udvgraph.c:4113:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4113 | Row = ViewMgr_GetRow(svpp, vdp->userkey); | ^~~ udvgraph.c:4041:21: warning: unused variable ‘vnp_seqinfo’ [-Wunused-variable] 4041 | ValNodePtr vnp_seqinfo=NULL; | ^~~~~~~~~~~ udvgraph.c:4035:68: warning: variable ‘nLinesDraw’ set but not used [-Wunused-but-set-variable] 4035 | Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw; | ^~~~~~~~~~ udvgraph.c:4035:60: warning: variable ‘nTotRow’ set but not used [-Wunused-but-set-variable] 4035 | Int4 decal_haut,from_row,to_row,nTotRow,nLinesDraw; | ^~~~~~~ udvgraph.c: At top level: udvgraph.c:3921:14: warning: ‘UDV_calc_decalRC’ defined but not used [-Wunused-function] 3921 | static Int4 UDV_calc_decalRC(ValNodePtr ParaG,Int4 ScrollPos, | ^~~~~~~~~~~~~~~~ udvgraph.c:3433:14: warning: ‘UDV_Draw_features_label’ defined but not used [-Wunused-function] 3433 | static void UDV_Draw_features_label(UnDViewerGraphDataPtr GrData, | ^~~~~~~~~~~~~~~~~~~~~~~ udvgraph.c:1298:13: warning: ‘UDV_AutoSelectAllSeq’ defined but not used [-Wunused-function] 1298 | static void UDV_AutoSelectAllSeq(ViewerDialogDataPtr vdp,Boolean bSelect) | ^~~~~~~~~~~~~~~~~~~~ udvgraph.c:971:17: warning: ‘UDV_draw_horz_cursor’ defined but not used [-Wunused-function] 971 | static void UDV_draw_horz_cursor(UnDViewerGraphDataPtr GrData, | ^~~~~~~~~~~~~~~~~~~~ udvgraph.c:948:13: warning: ‘UDV_draw_vert_cursor’ defined but not used [-Wunused-function] 948 | static void UDV_draw_vert_cursor(RecT rcClip,PoinT pos) | ^~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from udvgraph.c:180: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ udvgraph.c: In function ‘UDV_GetCurrentDispRange’: udvgraph.c:638:22: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 638 | *from_bsp=pgp->StartLetter; | ~~~^~~~~~~~~~~~~ udvgraph.c:610:12: note: ‘pgp’ was declared here 610 | ParaGPtr pgp; | ^~~ In file included from ../include/udviewer.h:225: udvgraph.c: In function ‘UDV_Draw_features’: udvgraph.c:3182:77: warning: ‘idx1’ may be used uninitialized [-Wmaybe-uninitialized] 3182 | start2=_max_(pgp->StartLetter,context->ivals[idx1]); | ^ udvgraph.c:2809:6: note: ‘idx1’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3189:66: warning: ‘idx2’ may be used uninitialized [-Wmaybe-uninitialized] 3189 | UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y, | ~~~~~~~~^~~~~~ udvgraph.c:2809:11: note: ‘idx2’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3189:86: warning: ‘idx3’ may be used uninitialized [-Wmaybe-uninitialized] 3189 | UDV_draw_thin_line((Int2)(start_x+idx2),(Int2)(stop_x+idx3),y, | ~~~~~~~^~~~~~ udvgraph.c:2809:16: note: ‘idx3’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3196:75: warning: ‘idx4’ may be used uninitialized [-Wmaybe-uninitialized] 3196 | stop2=_min_(pgp->StopLetter,context->ivals[idx4]); | ^ udvgraph.c:2809:21: note: ‘idx4’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3203:66: warning: ‘idx5’ may be used uninitialized [-Wmaybe-uninitialized] 3203 | UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y, | ~~~~~~~~^~~~~~ udvgraph.c:2809:26: note: ‘idx5’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ udvgraph.c:3203:86: warning: ‘idx6’ may be used uninitialized [-Wmaybe-uninitialized] 3203 | UDV_draw_thin_line((Int2)(start_x+idx5),(Int2)(stop_x+idx6),y, | ~~~~~~~^~~~~~ udvgraph.c:2809:31: note: ‘idx6’ was declared here 2809 | Int2 idx1,idx2,idx3,idx4,idx5,idx6,nLines=0; | ^~~~ ../include/udvdef.h:187:40: warning: ‘stop_x2’ may be used uninitialized [-Wmaybe-uninitialized] 187 | #define _max_(a,b) ((a)>=(b)?(a):(b)) | ~~~~~~~~~~~~~^~~~~ udvgraph.c:2803:21: note: ‘stop_x2’ was declared here 2803 | Int2 start_x,stop_x,stop_x2, /*id. but in pixels*/ | ^~~~~~~ udvgraph.c: In function ‘UDV_ClickProc’: udvgraph.c:1458:52: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 1458 | if (vmp && vmp->hFeatDlg){/*update Features List Dlg if needed; | ^ udvgraph.c:1382:25: note: ‘vmp’ was declared here 1382 | ViewerMainPtr vmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF udvopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvopen.c:101: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvopen.c: In function ‘UDV_FileOpen’: udvopen.c:875:38: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 875 | ButtoN b,b1,b2; | ^~ udvopen.c:875:33: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 875 | ButtoN b,b1,b2; | ^ udvopen.c: In function ‘UDV_CreateListBioseqDlg’: udvopen.c:1180:37: warning: the address of ‘szName’ will always evaluate as ‘true’ [-Waddress] 1180 | if (szName){ | ^~~~~~ udvopen.c: In function ‘UDV_FOpenCancelProc’: udvopen.c:792:23: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 792 | UDV_set_PullMenus(&vmp->MainMenu,TRUE); | ^~~~~~~~~~~~~~ udvopen.c:779:25: note: ‘vmp’ was declared here 779 | ViewerMainPtr vmp; | ^~~ udvopen.c: In function ‘UDV_analyze_SEP_for_open’: udvopen.c:327:21: warning: ‘dataptr’ may be used uninitialized [-Wmaybe-uninitialized] 327 | vmp->dataptr=dataptr; | ~~~~~~~~~~~~^~~~~~~~ udvopen.c:241:13: note: ‘dataptr’ was declared here 241 | Pointer dataptr; | ^~~~~~~ udvopen.c:242:22: warning: ‘entityID’ may be used uninitialized [-Wmaybe-uninitialized] 242 | Uint2 datatype,entityID,eID; | ^~~~~~~~ udvopen.c: In function ‘UDV_FOpenAcceptProc’: udvopen.c:855:23: warning: ‘vmp’ may be used uninitialized [-Wmaybe-uninitialized] 855 | UDV_set_PullMenus(&vmp->MainMenu,TRUE); | ^~~~~~~~~~~~~~ udvopen.c:811:25: note: ‘vmp’ was declared here 811 | ViewerMainPtr vmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF udvpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvpanel.c:197: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvpanel.c: In function ‘UDV_GotoBtnProc’: udvpanel.c:2080:22: warning: variable ‘old_ivalue’ set but not used [-Wunused-but-set-variable] 2080 | Int4 iValue,old_ivalue,line_num,from_bsp,to_bsp, | ^~~~~~~~~~ udvpanel.c:2079:15: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2079 | ValNodePtr vnp; | ^~~ udvpanel.c: In function ‘CreateMainControls’: udvpanel.c:2165:8: warning: variable ‘cxChar’ set but not used [-Wunused-but-set-variable] 2165 | Int2 cxChar,cyChar,Margins; | ^~~~~~ udvpanel.c: In function ‘UDV_SearchFeatForKey’: udvpanel.c:3478:36: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3478 | ButtoN b1,b2; | ^~ udvpanel.c: At top level: udvpanel.c:2773:28: warning: ‘FeaturesListBoxScan’ defined but not used [-Wunused-function] 2773 | static Boolean LIBCALLBACK FeaturesListBoxScan (SeqFeatPtr sfp, | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dotvibrant.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/dotviewer.h:15, from dotvibrant.c:84: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dotvibrant.c: In function ‘DOT_DisplayHits’: dotvibrant.c:564:18: warning: variable ‘ycomp’ set but not used [-Wunused-but-set-variable] 564 | Int4 ycomp, xcomp; | ^~~~~ dotvibrant.c: In function ‘DOT_VscrlProc’: dotvibrant.c:918:16: warning: variable ‘visLines’ set but not used [-Wunused-but-set-variable] 918 | Int2 visLines, vmargin, hmargin; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_HscrlProc’: dotvibrant.c:972:20: warning: variable ‘visLines’ set but not used [-Wunused-but-set-variable] 972 | Int2 dx, visLines, offset, hmargin, vmargin; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_VCrossHairs’: dotvibrant.c:1402:10: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1402 | Int4 cursor_size =15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_HCrossHairs’: dotvibrant.c:1427:9: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1427 | Int4 cursor_size = 15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MoveCrossHairs’: dotvibrant.c:1453:18: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 1453 | DOTSelDataPtr data; | ^~~~ dotvibrant.c:1452:10: warning: unused variable ‘cursor_size’ [-Wunused-variable] 1452 | Int4 cursor_size = 15; | ^~~~~~~~~~~ dotvibrant.c: In function ‘DOT_DrawXAxis’: dotvibrant.c:1532:38: warning: unused variable ‘title’ [-Wunused-variable] 1532 | Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/ | ^~~~~ dotvibrant.c: In function ‘DOT_DrawYAxis’: dotvibrant.c:1642:38: warning: unused variable ‘title’ [-Wunused-variable] 1642 | Char scale_buf[15] = {""}, title[50]={""}; /*scale value*/ | ^~~~~ dotvibrant.c:1641:55: warning: variable ‘Fh_4’ set but not used [-Wunused-but-set-variable] 1641 | Int4 pos, ylen, x, y, scale_pos, i, j, Fh_2,Fh_4; | ^~~~ dotvibrant.c: In function ‘DOT_SVDisplayDiags’: dotvibrant.c:1770:28: warning: variable ‘aln_diag’ set but not used [-Wunused-but-set-variable] 1770 | Int4 diag, aln_diag; | ^~~~~~~~ dotvibrant.c:1770:22: warning: variable ‘diag’ set but not used [-Wunused-but-set-variable] 1770 | Int4 diag, aln_diag; | ^~~~ dotvibrant.c:1766:22: warning: variable ‘width’ set but not used [-Wunused-but-set-variable] 1766 | Int4 width, height; | ^~~~~ dotvibrant.c:1765:31: warning: variable ‘p_HFrom’ set but not used [-Wunused-but-set-variable] 1765 | Int4 p_VFrom, p_HFrom; | ^~~~~~~ dotvibrant.c:1765:22: warning: variable ‘p_VFrom’ set but not used [-Wunused-but-set-variable] 1765 | Int4 p_VFrom, p_HFrom; | ^~~~~~~ dotvibrant.c:1762:28: warning: unused variable ‘cutoff’ [-Wunused-variable] 1762 | Int4 stop, cutoff=0, q_start, s_start, length; | ^~~~~~ dotvibrant.c:1760:34: warning: variable ‘seg3’ set but not used [-Wunused-but-set-variable] 1760 | SegmenT seg1, seg2, seg3, seg4; | ^~~~ dotvibrant.c: In function ‘DOT_FillNewSeqBufs’: dotvibrant.c:2197:19: warning: unused variable ‘alp’ [-Wunused-variable] 2197 | DOTAlignInfoPtr alp=NULL; | ^~~ dotvibrant.c: In function ‘DOT_InitCInfo’: dotvibrant.c:2258:14: warning: unused variable ‘colBuf’ [-Wunused-variable] 2258 | Char colBuf[12]={""}; | ^~~~~~ dotvibrant.c: In function ‘DOT_SVDisplaySequence’: dotvibrant.c:2379:16: warning: variable ‘matrix’ set but not used [-Wunused-but-set-variable] 2379 | Int4Ptr PNTR matrix; | ^~~~~~ dotvibrant.c:2367:14: warning: variable ‘vis_2’ set but not used [-Wunused-but-set-variable] 2367 | Int4 vis_2, buf_len; | ^~~~~ dotvibrant.c:2364:14: warning: unused variable ‘prot_threshold’ [-Wunused-variable] 2364 | Int4 prot_threshold=0, bloc_cntr; | ^~~~~~~~~~~~~~ dotvibrant.c:2350:24: warning: variable ‘mip2’ set but not used [-Wunused-but-set-variable] 2350 | DOTMainDataPtr mip1, mip2; | ^~~~ dotvibrant.c: In function ‘DOT_SVClickProc’: dotvibrant.c:2807:17: warning: unused variable ‘handled’ [-Wunused-variable] 2807 | Int2 handled=0; | ^~~~~~~ dotvibrant.c: In function ‘DOT_ResizeFeatWindow’: dotvibrant.c:3016:63: warning: variable ‘SubjectHeight’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~~~~~~~~~~~ dotvibrant.c:3016:51: warning: variable ‘QueryHeight’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~~~~~~~~~ dotvibrant.c:3016:37: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 3016 | Int2 height,width,vsbWidth,in,gap,hsbHeight,QueryHeight,SubjectHeight, halfw; | ^~~ dotvibrant.c: In function ‘DOT_ResizeSequenceWindow’: dotvibrant.c:3098:25: warning: variable ‘is_visible2’ set but not used [-Wunused-but-set-variable] 3098 | Boolean is_visible1, is_visible2; | ^~~~~~~~~~~ dotvibrant.c:3098:12: warning: variable ‘is_visible1’ set but not used [-Wunused-but-set-variable] 3098 | Boolean is_visible1, is_visible2; | ^~~~~~~~~~~ dotvibrant.c:3095:51: warning: variable ‘V1Height’ set but not used [-Wunused-but-set-variable] 3095 | Int2 height,width,gap,vsbWidth,in,hsbHeight,V1Height,V2Height, goHeight; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_HideFeatDlg’: dotvibrant.c:3745:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 3745 | ButtoN b; | ^ dotvibrant.c: In function ‘DOT_SVBuildDiagViewer’: dotvibrant.c:4031:18: warning: variable ‘mip’ set but not used [-Wunused-but-set-variable] 4031 | DOTMainDataPtr mip; | ^~~ dotvibrant.c:4029:28: warning: unused variable ‘str2’ [-Wunused-variable] 4029 | Char str1[41]={""}, str2[41]={""}; | ^~~~ dotvibrant.c:4029:13: warning: unused variable ‘str1’ [-Wunused-variable] 4029 | Char str1[41]={""}, str2[41]={""}; | ^~~~ dotvibrant.c:4022:18: warning: variable ‘pr2’ set but not used [-Wunused-but-set-variable] 4022 | PrompT pr1, pr2; | ^~~ dotvibrant.c:4022:13: warning: variable ‘pr1’ set but not used [-Wunused-but-set-variable] 4022 | PrompT pr1, pr2; | ^~~ dotvibrant.c: In function ‘DOT_UpdateDataRects’: dotvibrant.c:4166:19: warning: variable ‘dy’ set but not used [-Wunused-but-set-variable] 4166 | Int4 comp, dx, dy, xstart, ystart; | ^~ dotvibrant.c:4166:15: warning: variable ‘dx’ set but not used [-Wunused-but-set-variable] 4166 | Int4 comp, dx, dy, xstart, ystart; | ^~ dotvibrant.c: In function ‘DOT_MsgFunc’: dotvibrant.c:4215:17: warning: variable ‘vdp2’ set but not used [-Wunused-but-set-variable] 4215 | DOTVibDataPtr vdp2 = NULL; | ^~~~ dotvibrant.c: In function ‘DOT_ReleaseProc’: dotvibrant.c:4373:32: warning: unused variable ‘yaxis_incr’ [-Wunused-variable] 4373 | Boolean xaxis_incr=TRUE, yaxis_incr=TRUE; | ^~~~~~~~~~ dotvibrant.c:4373:15: warning: unused variable ‘xaxis_incr’ [-Wunused-variable] 4373 | Boolean xaxis_incr=TRUE, yaxis_incr=TRUE; | ^~~~~~~~~~ dotvibrant.c:4371:19: warning: variable ‘alp’ set but not used [-Wunused-but-set-variable] 4371 | DOTAlignInfoPtr alp=NULL; | ^~~ dotvibrant.c:4370:18: warning: variable ‘mip1’ set but not used [-Wunused-but-set-variable] 4370 | DOTMainDataPtr mip1=NULL; | ^~~~ dotvibrant.c: In function ‘DOT_StartDOTPLOT’: dotvibrant.c:4891:23: warning: variable ‘vdp’ set but not used [-Wunused-but-set-variable] 4891 | DOTVibDataPtr vdp; | ^~~ dotvibrant.c: In function ‘DOT_DoZoom’: dotvibrant.c:5106:18: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 5106 | DOTSelDataPtr data; | ^~~~ dotvibrant.c: In function ‘DOT_ZoomProc’: dotvibrant.c:5204:23: warning: variable ‘temport’ set but not used [-Wunused-but-set-variable] 5204 | WindoW temport, w; | ^~~~~~~ dotvibrant.c: In function ‘AlnMgr2GetNextLine’: dotvibrant.c:5315:3: warning: value computed is not used [-Wunused-value] 5315 | *n++; | ^~~~ dotvibrant.c: In function ‘DOT_GetAlign’: dotvibrant.c:5332:44: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 5332 | Int4 x1, y1, x2, y2, numlines=0, n=0, i=0; | ^ dotvibrant.c: In function ‘DOT_FillAlignInfoPointer’: dotvibrant.c:5565:16: warning: unused variable ‘i’ [-Wunused-variable] 5565 | Int4 i=0, n=0; | ^ dotvibrant.c: In function ‘DOT_Prob_FillAlignInfoPointer’: dotvibrant.c:5681:16: warning: unused variable ‘i’ [-Wunused-variable] 5681 | Int4 i=0, n=0; | ^ dotvibrant.c:5680:16: warning: unused variable ‘numsaps’ [-Wunused-variable] 5680 | Int4 numsaps = 0, numlines = 0; | ^~~~~~~ dotvibrant.c:5678:37: warning: unused variable ‘sap_tmp’ [-Wunused-variable] 5678 | SeqAlignPtr sap=NULL, salp=NULL, sap_tmp=NULL; | ^~~~~~~ dotvibrant.c: In function ‘DOT_DoBlast’: dotvibrant.c:5918:23: warning: unused variable ‘eval’ [-Wunused-variable] 5918 | Char eval[11]={""}; | ^~~~ dotvibrant.c:5917:23: warning: variable ‘is_local’ set but not used [-Wunused-but-set-variable] 5917 | Boolean is_local; | ^~~~~~~~ dotvibrant.c:5915:23: warning: unused variable ‘entityID’ [-Wunused-variable] 5915 | Uint2 entityID=0; | ^~~~~~~~ dotvibrant.c: In function ‘DOT_CreateWindowDetails’: dotvibrant.c:6214:27: warning: variable ‘pr2’ set but not used [-Wunused-but-set-variable] 6214 | PrompT pr1, pr2; | ^~~ dotvibrant.c:6214:22: warning: variable ‘pr1’ set but not used [-Wunused-but-set-variable] 6214 | PrompT pr1, pr2; | ^~~ dotvibrant.c:6207:21: warning: variable ‘g1’ set but not used [-Wunused-but-set-variable] 6207 | GrouP g, g1, g2; | ^~ dotvibrant.c: In function ‘DOT_ResizeMainWindow’: dotvibrant.c:6273:35: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 6273 | Int2 height, width, in , gap; | ^~~ dotvibrant.c: In function ‘DOT_OpenSeqAnnotFile’: dotvibrant.c:6451:16: warning: the comparison will always evaluate as ‘true’ for the address of ‘path’ will never be NULL [-Waddress] 6451 | if (path != NULL) | ^~ dotvibrant.c:6439:13: note: ‘path’ declared here 6439 | Char path [PATH_MAX]; | ^~~~ dotvibrant.c: In function ‘DOT_FindAlignment’: dotvibrant.c:6662:29: warning: unused variable ‘rb_fixed’ [-Wunused-variable] 6662 | Boolean lt_fixed=FALSE, rb_fixed=FALSE; | ^~~~~~~~ dotvibrant.c:6662:13: warning: unused variable ‘lt_fixed’ [-Wunused-variable] 6662 | Boolean lt_fixed=FALSE, rb_fixed=FALSE; | ^~~~~~~~ dotvibrant.c:6661:17: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 6661 | DOTSelDataPtr data; | ^~~~ dotvibrant.c: In function ‘SCP_CompareOrderOrganizeBioseqs’: dotvibrant.c:6792:25: warning: variable ‘itemID’ set but not used [-Wunused-but-set-variable] 6792 | Uint4 itemID=0; | ^~~~~~ dotvibrant.c: In function ‘SCP_OrganizeAlnsInSet’: dotvibrant.c:6873:21: warning: variable ‘indextype’ set but not used [-Wunused-but-set-variable] 6873 | Int4 indextype; | ^~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from ../include/dotviewer.h:32: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dotvibrant.c:6642:16: warning: ‘DOT_DeselectPrim’ defined but not used [-Wunused-function] 6642 | static Boolean DOT_DeselectPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata) | ^~~~~~~~~~~~~~~~ dotvibrant.c:6346:13: warning: ‘DOT_NewAnalysis’ defined but not used [-Wunused-function] 6346 | static void DOT_NewAnalysis (ButtoN b) | ^~~~~~~~~~~~~~~ dotvibrant.c:5894:16: warning: ‘DOT_get_eval’ defined but not used [-Wunused-function] 5894 | static FloatHi DOT_get_eval(Int4 exp) | ^~~~~~~~~~~~ dotvibrant.c:5325:16: warning: ‘DOT_GetAlign’ defined but not used [-Wunused-function] 5325 | static Boolean DOT_GetAlign (DOTAlignInfoPtr alp) | ^~~~~~~~~~~~ dotvibrant.c:5281:16: warning: ‘AlnMgr2GetNextLine’ defined but not used [-Wunused-function] 5281 | static Boolean AlnMgr2GetNextLine(SeqAlignPtr sap, AlnMsg2Ptr amp1, AlnMsg2Ptr amp2, Int4Ptr x1, Int4Ptr y1, Int4Ptr x2, Int4Ptr y2, Int4Ptr n) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:4767:13: warning: ‘DOT_FeatAnalysisProc’ defined but not used [-Wunused-function] 4767 | static void DOT_FeatAnalysisProc(ButtoN b) | ^~~~~~~~~~~~~~~~~~~~ dotvibrant.c:4749:13: warning: ‘DOT_GetInfoProc’ defined but not used [-Wunused-function] 4749 | static void DOT_GetInfoProc (IteM i) | ^~~~~~~~~~~~~~~ dotvibrant.c:4213:25: warning: ‘DOT_MsgFunc’ defined but not used [-Wunused-function] 4213 | static Int2 LIBCALLBACK DOT_MsgFunc (OMMsgStructPtr ommsp) | ^~~~~~~~~~~ dotvibrant.c:3688:13: warning: ‘DOT_HideAcceptProc’ defined but not used [-Wunused-function] 3688 | static void DOT_HideAcceptProc(ButtoN b) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:3318:13: warning: ‘DOT_AddFeatureToSegment’ defined but not used [-Wunused-function] 3318 | static void DOT_AddFeatureToSegment(SeqMgrFeatContextPtr context, | ^~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c:2954:13: warning: ‘DOT_SVChangeLabels’ defined but not used [-Wunused-function] 2954 | static void DOT_SVChangeLabels (GrouP g) | ^~~~~~~~~~~~~~~~~~ dotvibrant.c:2760:16: warning: ‘DOT_SVGetDiag’ defined but not used [-Wunused-function] 2760 | static Boolean DOT_SVGetDiag (Uint2 segID, Uint2 primID, VoidPtr userdata) | ^~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_GetNthSeqFromAlign’: dotvibrant.c:5064:6: warning: ‘spp’ may be used uninitialized [-Wmaybe-uninitialized] 5064 | if (spp == NULL) | ^ dotvibrant.c:5038:20: note: ‘spp’ was declared here 5038 | SeqPortPtr spp; | ^~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2503:6: warning: ‘s’ may be used uninitialized [-Wmaybe-uninitialized] 2503 | end=s+buf_len-1; | ~~~^~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2357:14: note: ‘s’ was declared here 2357 | Uint1Ptr s; | ^ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2545:18: warning: ‘is_na’ may be used uninitialized [-Wmaybe-uninitialized] 2545 | if (is_na) | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2361:27: note: ‘is_na’ was declared here 2361 | Boolean ambig=FALSE, is_na; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2503:16: warning: ‘buf_len’ may be used uninitialized [-Wmaybe-uninitialized] 2503 | end=s+buf_len-1; | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2367:21: note: ‘buf_len’ was declared here 2367 | Int4 vis_2, buf_len; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2570:26: warning: ‘hit_start’ may be used uninitialized [-Wmaybe-uninitialized] 2570 | if (hit_start<=i && i<=(hit_stop+bloc_size)) | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:14: note: ‘hit_start’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2504:21: warning: ‘hit_stop’ may be used uninitialized [-Wmaybe-uninitialized] 2504 | hit_stop+=hit_stop/10; | ~~~~~~~~^~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:25: note: ‘hit_stop’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘q_pos’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:35: note: ‘q_pos’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘s_pos’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2370:42: note: ‘s_pos’ was declared here 2370 | Int4 hit_start, hit_stop, q_pos, s_pos; | ^~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2583:37: warning: ‘residue_names’ may be used uninitialized [-Wmaybe-uninitialized] 2583 | sBuf[c]=*residue_names[(int)*s]; | ^ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2378:16: note: ‘residue_names’ was declared here 2378 | CharPtr PNTR residue_names; | ^~~~~~~~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘strand1’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2380:14: note: ‘strand1’ was declared here 2380 | Uint1 strand1, strand2; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2611:19: warning: ‘strand2’ may be used uninitialized [-Wmaybe-uninitialized] 2611 | DOT_DrawScale(sbSeg, strand1, strand2, rc, margin, res_cnt, bloc_cntr, Fh, q_pos, s_pos, chw_2, chw_4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2380:23: note: ‘strand2’ was declared here 2380 | Uint1 strand1, strand2; | ^~~~~~~ In function ‘DOT_SVDisplaySequence’, inlined from ‘DOT_SVPopulateSequenceViewer.part.0’ at dotvibrant.c:2695:7: dotvibrant.c:2547:23: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized] 2547 | if (*q > 3 || *s > 3) | ^~ dotvibrant.c: In function ‘DOT_SVPopulateSequenceViewer.part.0’: dotvibrant.c:2356:14: note: ‘q’ was declared here 2356 | Uint1Ptr q; | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘qname’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6208:23: note: ‘qname’ was declared here 6208 | Char PNTR qname, PNTR sname; | ^~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘sname’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6208:35: note: ‘sname’ was declared here 6208 | Char PNTR qname, PNTR sname; | ^~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘q_start’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:18: note: ‘q_start’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘q_stop’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:27: note: ‘q_stop’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘s_start’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:35: note: ‘s_start’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~~ In function ‘sprintf’, inlined from ‘DOT_CreateWindowDetails’ at dotvibrant.c:6248:3, inlined from ‘DOT_MakeMainViewer’ at dotvibrant.c:6607:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘s_stop’ may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dotvibrant.c: In function ‘DOT_MakeMainViewer’: dotvibrant.c:6209:44: note: ‘s_stop’ was declared here 6209 | Int4 q_start, q_stop, s_start, s_stop; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dlgutil1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from dlgutil1.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dlgutil1.c: In function ‘IsAuthList’: dlgutil1.c:2962:8: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 2962 | Int4 len; | ^~~ dlgutil1.c: In function ‘TestIntervalEditor’: dlgutil1.c:5324:20: warning: variable ‘fuzz_to’ set but not used [-Wunused-but-set-variable] 5324 | Int2 fuzz_to; | ^~~~~~~ dlgutil1.c:5323:20: warning: variable ‘fuzz_from’ set but not used [-Wunused-but-set-variable] 5323 | Int2 fuzz_from; | ^~~~~~~~~ dlgutil1.c:5322:41: warning: variable ‘fuzz_before’ set but not used [-Wunused-but-set-variable] 5322 | Boolean isInterval, isPoint, fuzz_before, fuzz_after; | ^~~~~~~~~~~ dlgutil1.c: In function ‘DbtagDialogToDbtagPtr’: dlgutil1.c:7254:16: warning: unused variable ‘val’ [-Wunused-variable] 7254 | long int val; | ^~~ dlgutil1.c:7250:16: warning: unused variable ‘ptr’ [-Wunused-variable] 7250 | CharPtr ptr; | ^~~ dlgutil1.c:7247:16: warning: unused variable ‘num_digits’ [-Wunused-variable] 7247 | Int2 num_digits; | ^~~~~~~~~~ dlgutil1.c:7246:16: warning: unused variable ‘notallzero’ [-Wunused-variable] 7246 | Boolean notallzero; | ^~~~~~~~~~ dlgutil1.c:7243:16: warning: unused variable ‘leadingzero’ [-Wunused-variable] 7243 | Boolean leadingzero; | ^~~~~~~~~~~ dlgutil1.c:7238:16: warning: unused variable ‘alldigits’ [-Wunused-variable] 7238 | Boolean alldigits; | ^~~~~~~~~ dlgutil1.c: In function ‘CreateStandardEditMenu’: dlgutil1.c:9427:8: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 9427 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from dlgutil1.c:55: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dlgutil1.c:8603:25: warning: ‘GetNthNameValuePair’ defined but not used [-Wunused-function] 8603 | static NameValuePairPtr GetNthNameValuePair (Int4 n, ValNodePtr list) | ^~~~~~~~~~~~~~~~~~~ dlgutil1.c:8051:16: warning: ‘ParseSpecimenVoucherOk’ defined but not used [-Wunused-function] 8051 | static Boolean ParseSpecimenVoucherOk (CharPtr str) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil1.c:1293:13: warning: ‘GbqualsToVisStringDialog’ defined but not used [-Wunused-function] 1293 | static void GbqualsToVisStringDialog (SeqFeatPtr sfp, DialoG d, CharPtr qual) | ^~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dlgutil2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from dlgutil2.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dlgutil2.c: In function ‘CitListToDialog’: dlgutil2.c:945:18: warning: the comparison will always evaluate as ‘false’ for the address of ‘last’ will never be NULL [-Waddress] 945 | if (last == NULL || StringCmp (cldp->label, last) != 0) { | ^~ dlgutil2.c:897:19: note: ‘last’ declared here 897 | Char last [128]; | ^~~~ dlgutil2.c: In function ‘CreateImportFields’: dlgutil2.c:1401:19: warning: variable ‘is_gap’ set but not used [-Wunused-but-set-variable] 1401 | Boolean is_gap = FALSE; | ^~~~~~ dlgutil2.c: In function ‘UpdateTableDisplayDialogScrollBars’: dlgutil2.c:3552:11: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] 3552 | Int4 x, y; | ^ dlgutil2.c:3552:8: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] 3552 | Int4 x, y; | ^ dlgutil2.c: In function ‘GetTableDisplayCell’: dlgutil2.c:3951:8: warning: variable ‘start_row’ set but not used [-Wunused-but-set-variable] 3951 | Int4 start_row, start_col; | ^~~~~~~~~ dlgutil2.c: In function ‘NewCreateInferenceDialog’: dlgutil2.c:7633:19: warning: variable ‘fnt’ set but not used [-Wunused-but-set-variable] 7633 | FonT fnt; | ^~~ dlgutil2.c: In function ‘ClickableListOnKey’: dlgutil2.c:10479:20: warning: variable ‘clp’ set but not used [-Wunused-but-set-variable] 10479 | ClickableListPtr clp; | ^~~ dlgutil2.c: In function ‘GetSelectedClickableListText’: dlgutil2.c:11151:36: warning: variable ‘char_offset’ set but not used [-Wunused-but-set-variable] 11151 | Int2 item, row, col, char_offset; | ^~~~~~~~~~~ dlgutil2.c: In function ‘AutomatchFeatures’: dlgutil2.c:14210:36: warning: variable ‘s3’ set but not used [-Wunused-but-set-variable] 14210 | SeqIntPtr s1, s2, s3; | ^~ dlgutil2.c: At top level: dlgutil2.c:12342:16: warning: ‘ParseMultiListQualOk’ defined but not used [-Wunused-function] 12342 | static Boolean ParseMultiListQualOk (CharPtr val) | ^~~~~~~~~~~~~~~~~~~~ dlgutil2.c:10336:13: warning: ‘ClickClickableListItem’ defined but not used [-Wunused-function] 10336 | static void ClickClickableListItem (DoC d, PoinT pt) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:10316:13: warning: ‘DrawClickableListItem’ defined but not used [-Wunused-function] 10316 | static void DrawClickableListItem (DoC d, RectPtr r, Int2 item, Int2 firstLine) | ^~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:8854:13: warning: ‘GetCategoryNumFromName’ defined but not used [-Wunused-function] 8854 | static Int4 GetCategoryNumFromName (CharPtr category) | ^~~~~~~~~~~~~~~~~~~~~~ dlgutil2.c:1676:16: warning: ‘GetNameForFeature’ defined but not used [-Wunused-function] 1676 | static CharPtr GetNameForFeature (SeqFeatPtr sfp) | ^~~~~~~~~~~~~~~~~ dlgutil2.c: In function ‘PopulateDayPopup’: dlgutil2.c:11438:24: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 11438 | sprintf (day, "%d", i); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PopulateDayPopup’ at dlgutil2.c:11438:7, inlined from ‘PopulateDayPopup’ at dlgutil2.c:11428:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF e2trmlst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from e2trmlst.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ e2trmlst.c: In function ‘ReadAFew’: e2trmlst.c:2230:61: warning: left-hand operand of comma expression has no effect [-Wunused-value] 2230 | for (row = 1, termPtr = e2TermListPtr->list; row <= *count, termPtr != NULL; row++, termPtr = termPtr->next) { | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF e2docsum.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from e2docsum.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ e2docsum.c: In function ‘FormatCdsSeq’: e2docsum.c:1523:22: warning: variable ‘gene’ set but not used [-Wunused-but-set-variable] 1523 | SeqFeatPtr gene = NULL; | ^~~~ e2docsum.c: In function ‘FetchSequence’: e2docsum.c:1591:16: warning: variable ‘currDbName’ set but not used [-Wunused-but-set-variable] 1591 | CharPtr currDbName; | ^~~~~~~~~~ e2docsum.c:1580:16: warning: variable ‘group_segs’ set but not used [-Wunused-but-set-variable] 1580 | Uint1 group_segs = 0; | ^~~~~~~~~~ e2docsum.c: In function ‘ReleaseDocSum’: e2docsum.c:3305:27: warning: the comparison will always evaluate as ‘true’ for the address of ‘launchPopups’ will never be NULL [-Waddress] 3305 | if (sfp->launchPopups != NULL) { | ^~ e2docsum.c:490:25: note: ‘launchPopups’ declared here 490 | PopuP launchPopups [MAX_DBS + 1]; | ^~~~~~~~~~~~ e2docsum.c: In function ‘SaveDocsumProject’: e2docsum.c:3606:16: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 3606 | SummFormPtr sfp; | ^~~ e2docsum.c: In function ‘RetrieveGeneration’: e2docsum.c:4135:19: warning: variable ‘e2ip’ set but not used [-Wunused-but-set-variable] 4135 | Entrez2InfoPtr e2ip; | ^~~~ e2docsum.c: In function ‘SetupMenus’: e2docsum.c:4849:16: warning: variable ‘c’ set but not used [-Wunused-but-set-variable] 4849 | ChoicE c; | ^ In file included from ../include/sqnutils.h:51, from ../include/dlogutil.h:50, from ../include/bspview.h:48, from e2docsum.c:53: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strucapi.h:52, from e2docsum.c:62: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchStructureViewer’: e2docsum.c:2981:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2981 | system (cmmd); | ^~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchSequin’: e2docsum.c:2838:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2838 | system (cmmd); | ^~~~~~~~~~~~~ e2docsum.c: At top level: e2docsum.c:2883:13: warning: ‘GetBiostrucMaxModels’ defined but not used [-Wunused-function] 2883 | static Int4 GetBiostrucMaxModels (void) | ^~~~~~~~~~~~~~~~~~~~ e2docsum.c:2850:13: warning: ‘GetBiostrucComplexity’ defined but not used [-Wunused-function] 2850 | static Int4 GetBiostrucComplexity (void) | ^~~~~~~~~~~~~~~~~~~~~ e2docsum.c:2154:20: warning: ‘cddDocProcs’ defined but not used [-Wunused-variable] 2154 | static DocPrntProc cddDocProcs [] = { Query_FetchDocSum, Query_FetchFields, FetchUid, NULL }; | ^~~~~~~~~~~ e2docsum.c: In function ‘LaunchStructureViewer’: e2docsum.c:2980:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4091 [-Wformat-overflow=] 2980 | sprintf (cmmd, "Cn3D %s &", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘LaunchStructureViewer’ at e2docsum.c:2980:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 4103 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ e2docsum.c: In function ‘LaunchSequin.isra.0’: e2docsum.c:2837:31: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4084 [-Wformat-overflow=] 2837 | sprintf (cmmd, "sequin -x < %s &", path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘LaunchSequin.isra.0’ at e2docsum.c:2837:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 15 and 4110 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF asn2graphic.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2graphic.h:45, from ../include/asn2graphicp.h:45, from asn2graphic.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2graphic.c: In function ‘ParseBioseqAppearanceItem’: asn2graphic.c:779:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 779 | if (buf != NULL) { | ^~ asn2graphic.c:740:28: note: ‘buf’ declared here 740 | Char buf [128]; | ^~~ asn2graphic.c:789:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 789 | if (buf != NULL) { | ^~ asn2graphic.c:740:28: note: ‘buf’ declared here 740 | Char buf [128]; | ^~~ asn2graphic.c: In function ‘ParseFeatureAppearanceItem’: asn2graphic.c:894:13: warning: the comparison will always evaluate as ‘true’ for the address of ‘buf’ will never be NULL [-Waddress] 894 | if (buf != NULL) { | ^~ asn2graphic.c:827:22: note: ‘buf’ declared here 827 | Char buf [128]; | ^~~ asn2graphic.c: In function ‘ParseFilterItem’: asn2graphic.c:1191:21: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 1191 | Int2 i, j; | ^ asn2graphic.c: In function ‘GeneProductsLayoutInternal’: asn2graphic.c:3730:36: warning: variable ‘featureStart’ set but not used [-Wunused-but-set-variable] 3730 | Int4 newLeft, featureStart, rowMaxRight; | ^~~~~~~~~~~~ asn2graphic.c: In function ‘ScaleSntDrawProc’: asn2graphic.c:4402:28: warning: variable ‘r’ set but not used [-Wunused-but-set-variable] 4402 | RecT r; | ^ asn2graphic.c: In function ‘GphSentProc’: asn2graphic.c:4997:16: warning: variable ‘scaleY’ set but not used [-Wunused-but-set-variable] 4997 | Int4 scaleY; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from asn2graphic.c:46: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In function ‘BuildClippedRFIP’, inlined from ‘BuildRenderInputFromRFIP’ at asn2graphic.c:2659:15: asn2graphic.c:2487:17: warning: ‘lastClippedRight’ may be used uninitialized [-Wmaybe-uninitialized] 2487 | } else if (lastClippedRight && useThis) { | ^ asn2graphic.c: In function ‘BuildRenderInputFromRFIP’: asn2graphic.c:2421:28: note: ‘lastClippedRight’ was declared here 2421 | Boolean lastClippedLeft, lastClippedRight; | ^~~~~~~~~~~~~~~~ In file included from ../include/asn2graphic.h:46: asn2graphic.c: In function ‘ProcessRows’: ../include/picture.h:499:23: warning: ‘SegmentTreeTop’ may be used uninitialized [-Wmaybe-uninitialized] 499 | #define CreateSegment Nlm_CreateSegment asn2graphic.c:4277:27: note: ‘SegmentTreeTop’ was declared here 4277 | SegmenT SegmentTreeTop; | ^~~~~~~~~~~~~~ ../include/picture.h:499:23: warning: ‘SegmentTreeMid’ may be used uninitialized [-Wmaybe-uninitialized] 499 | #define CreateSegment Nlm_CreateSegment asn2graphic.c:4278:27: note: ‘SegmentTreeMid’ was declared here 4278 | SegmenT SegmentTreeMid; | ^~~~~~~~~~~~~~ asn2graphic.c:4362:13: warning: ‘SegmentTreeBot’ may be used uninitialized [-Wmaybe-uninitialized] 4362 | if (! EnsureFeatureHasSegment (FPSP, featdeftype, SegmentTreeBot)) return 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asn2graphic.c:4279:27: note: ‘SegmentTreeBot’ was declared here 4279 | SegmenT SegmentTreeBot; | ^~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1198:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size 120 [-Wformat-overflow=] 1198 | sprintf (sect, "filters.%s", filterItemName); | ^~ ...... 1500 | FIP = ParseFilterItem (buf, defaultRowPadding, defaultGroupPadding, defaultLayout, VCP); | ~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ParseFilterItem’ at asn2graphic.c:1198:3, inlined from ‘ParseFilter’ at asn2graphic.c:1500:13, inlined from ‘ParseConfigFile’ at asn2graphic.c:1695:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 136 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:946:21: warning: ‘.master’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 946 | sprintf (sect, "%s.master", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:946:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1006:29: warning: ‘.bioseq’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1006 | sprintf (outputBuffer, "%s.bioseq", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1006:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1008:29: warning: ‘.imp’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1008 | sprintf (outputBuffer, "%s.imp", appearanceNameInFile); | ^~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1008:3, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 132 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1011:31: warning: ‘.import’ directive writing 7 bytes into a region of size between 1 and 128 [-Wformat-overflow=] 1011 | sprintf (outputBuffer, "%s.import", appearanceNameInFile); | ^~~~~~~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1011:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 135 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:34: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 129) into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:32: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 127 [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 134 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2graphic.c: In function ‘ParseConfigFile’: asn2graphic.c:1021:32: warning: ‘%s’ directive writing between 5 and 7 bytes into a region of size between 0 and 127 [-Wformat-overflow=] 1021 | sprintf (outputBuffer, "%s.%s", appearanceNameInFile, FindFeatStrFromFeatDefType (i)); | ^~ In function ‘sprintf’, inlined from ‘ParseAppearance’ at asn2graphic.c:1021:5, inlined from ‘ParseConfigFile’ at asn2graphic.c:1707:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 136 bytes into a destination of size 128 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF medview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/medview.h:48, from medview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medview.c: In function ‘PrintMedlineViewForm’: medview.c:588:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 588 | system (cmmd); | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bspview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from bspview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from bspview.c:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gbfview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from gbfview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gbfview.c: In function ‘RelModeFailText’: gbfview.c:1004:22: warning: variable ‘hasPubs’ set but not used [-Wunused-but-set-variable] 1004 | Boolean hasPubs; | ^~~~~~~ gbfview.c: In function ‘PopulateFlatFile’: gbfview.c:1292:22: warning: variable ‘doColors’ set but not used [-Wunused-but-set-variable] 1292 | Boolean doColors; | ^~~~~~~~ gbfview.c: In function ‘PopulateFasta’: gbfview.c:1717:33: warning: left-hand operand of comma expression has no effect [-Wunused-value] 1717 | if (ISA_na (bsp->mol)) {TRUE, | ^ gbfview.c:1649:20: warning: variable ‘group_segs’ set but not used [-Wunused-but-set-variable] 1649 | Uint1 group_segs; | ^~~~~~~~~~ gbfview.c: In function ‘PopulateAsnOrXML’: gbfview.c:1972:16: warning: variable ‘lookupFar’ set but not used [-Wunused-but-set-variable] 1972 | Boolean lookupFar = FALSE; | ^~~~~~~~~ gbfview.c:1971:16: warning: variable ‘lockFar’ set but not used [-Wunused-but-set-variable] 1971 | Boolean lockFar = FALSE; | ^~~~~~~ gbfview.c: In function ‘PrintFlatFileFastaOrAsn’: gbfview.c:2494:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2494 | system (cmmd); | ^~~~~~~~~~~~~ gbfview.c: In function ‘ReleaseIcon’: gbfview.c:667:21: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 667 | system (cmmd); | ^~~~~~~~~~~~~ gbfview.c: At top level: gbfview.c:1234:13: warning: ‘LookForFarProds’ defined but not used [-Wunused-function] 1234 | static void LookForFarProds ( | ^~~~~~~~~~~~~~~ gbfview.c:1215:13: warning: ‘LookForFarBsp’ defined but not used [-Wunused-function] 1215 | static void LookForFarBsp ( | ^~~~~~~~~~~~~ gbfview.c:944:13: warning: ‘LookForPubs’ defined but not used [-Wunused-function] 944 | static void LookForPubs (BioseqPtr bsp, Pointer userdata) | ^~~~~~~~~~~ gbfview.c:289:16: warning: ‘ColorIcon’ defined but not used [-Wunused-function] 289 | static Boolean ColorIcon ( | ^~~~~~~~~ gbfview.c: In function ‘ReleaseIcon’: gbfview.c:666:42: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 666 | sprintf (cmmd, "open %s", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ReleaseIcon’ at gbfview.c:666:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 4101 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gphview.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from gphview.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gphview.c: In function ‘ReleaseAlignment’: gphview.c:1306:18: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 1306 | SeqLocPtr slp; | ^~~ gphview.c: In function ‘DrawAlignOnAllSequences’: gphview.c:1391:17: warning: variable ‘vn’ set but not used [-Wunused-but-set-variable] 1391 | ValNode vn; | ^~ gphview.c: In function ‘ReleaseDesktop’: gphview.c:1836:18: warning: variable ‘seg’ set but not used [-Wunused-but-set-variable] 1836 | SegmenT seg; | ^~~ gphview.c: In function ‘AutoScrollGeneName’: gphview.c:2100:21: warning: variable ‘num’ set but not used [-Wunused-but-set-variable] 2100 | Int2 num; | ^~~ gphview.c: In function ‘DisplayGeneChoiceWindow’: gphview.c:2426:22: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 2426 | PrompT p; | ^ gphview.c: In function ‘PrintGraphical’: gphview.c:3268:14: warning: unused variable ‘ans’ [-Wunused-variable] 3268 | MsgAnswer ans; | ^~~ gphview.c: In function ‘PopulateAsn2GphGraphic’: gphview.c:3868:16: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 3868 | Int4 min; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gphdraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gphdraw.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gphdraw.c: In function ‘GraphSentProc’: gphdraw.c:195:18: warning: variable ‘scaleY’ set but not used [-Wunused-but-set-variable] 195 | Int4 scaleY; | ^~~~~~ gphdraw.c: In function ‘DrawGraphToPanel’: gphdraw.c:453:27: warning: variable ‘xp’ set but not used [-Wunused-but-set-variable] 453 | Int4Ptr xpoints, xp; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gxydraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gxydraw.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gxydraw.c: In function ‘DotXYPlot’: gxydraw.c:182:19: warning: ‘xaxiscount’ may be used uninitialized [-Wmaybe-uninitialized] 182 | Int4 xaxiscount, yaxiscount; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gtrdraw.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from gtrdraw.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/vibrant.h:130: In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curB’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:23: note: ‘curB’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curG’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:17: note: ‘curG’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:653:21: warning: ‘curR’ may be used uninitialized [-Wmaybe-uninitialized] 653 | #define SelectColor Nlm_SelectColor gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:83:11: note: ‘curR’ was declared here 83 | Uint1 curR, curG, curB; | ^~~~ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:685:20: warning: ‘f’ may be used uninitialized [-Wmaybe-uninitialized] 685 | #define DeleteFont Nlm_DeleteFont gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:82:11: note: ‘f’ was declared here 82 | FonT f, fx; | ^ In function ‘PlotTheTreePlot’, inlined from ‘TreeSentProc’ at gtrdraw.c:145:3: ../include/vibdefns.h:673:20: warning: ‘fx’ may be used uninitialized [-Wmaybe-uninitialized] 673 | #define SelectFont Nlm_SelectFont gtrdraw.c: In function ‘TreeSentProc’: gtrdraw.c:82:14: note: ‘fx’ was declared here 82 | FonT f, fx; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/bspview.h:48, from seqpanel.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqpanel.c: In function ‘FillFeatureInfo’: seqpanel.c:427:18: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 427 | Int4 j, start, stop; | ^~~~ seqpanel.c:427:11: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 427 | Int4 j, start, stop; | ^~~~~ seqpanel.c: In function ‘DrawFeatureCodonLines’: seqpanel.c:1897:21: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 1897 | Char tmp[2]; | ^~~ seqpanel.c: In function ‘DrawFeature’: seqpanel.c:2127:21: warning: variable ‘prot_len’ set but not used [-Wunused-but-set-variable] 2127 | Int4 prot_len; | ^~~~~~~~ seqpanel.c: In function ‘GetSeqChapterFeatureInfo’: seqpanel.c:3136:18: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 3136 | Int4 j, start, stop; | ^~~~ seqpanel.c:3136:11: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 3136 | Int4 j, start, stop; | ^~~~~ seqpanel.c: In function ‘onSeqEdVScrollBarSeqPanel’: seqpanel.c:3406:17: warning: variable ‘totallines’ set but not used [-Wunused-but-set-variable] 3406 | Int4 totallines; | ^~~~~~~~~~ seqpanel.c: In function ‘PrintFeature’: seqpanel.c:3812:28: warning: variable ‘fRight’ set but not used [-Wunused-but-set-variable] 3812 | Int4 fLeft, fRight, swap; | ^~~~~~ seqpanel.c:3812:21: warning: variable ‘fLeft’ set but not used [-Wunused-but-set-variable] 3812 | Int4 fLeft, fRight, swap; | ^~~~~ seqpanel.c: In function ‘PrintTranslatedFrame’: seqpanel.c:3966:17: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 3966 | Char tmp[2]; | ^~~ seqpanel.c: In function ‘ExportSequenceText’: seqpanel.c:4372:44: warning: pointer targets in passing argument 1 of ‘complement_string’ differ in signedness [-Wpointer-sign] 4372 | complement_string (file_line + SEQ_ED_PRINT_SEQ_OFFSET); | ^ | | | Nlm_Uint1Ptr {aka unsigned char *} In file included from ../include/alignmgr2.h:112, from seqpanel.c:39: ../include/salutil.h:78:47: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘Nlm_Uint1Ptr’ {aka ‘unsigned char *’} 78 | NLM_EXTERN CharPtr complement_string (CharPtr str); seqpanel.c:4236:17: warning: variable ‘curr_para_strings’ set but not used [-Wunused-but-set-variable] 4236 | ValNodePtr curr_para_strings = NULL; | ^~~~~~~~~~~~~~~~~ seqpanel.c:4229:17: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 4229 | Uint1Ptr buf; | ^~~ seqpanel.c: In function ‘SeqEdOnClick’: seqpanel.c:4946:21: warning: variable ‘direction’ set but not used [-Wunused-but-set-variable] 4946 | Int4 direction; | ^~~~~~~~~ seqpanel.c: In function ‘SeqAlnOnDrag’: seqpanel.c:5685:34: warning: variable ‘is_ctrl’ set but not used [-Wunused-but-set-variable] 5685 | Boolean is_double_click, is_ctrl; | ^~~~~~~ seqpanel.c:5685:17: warning: variable ‘is_double_click’ set but not used [-Wunused-but-set-variable] 5685 | Boolean is_double_click, is_ctrl; | ^~~~~~~~~~~~~~~ seqpanel.c: In function ‘ResizeSeqEdView’: seqpanel.c:5760:8: warning: variable ‘sequence_pos’ set but not used [-Wunused-but-set-variable] 5760 | Int4 sequence_pos = 0; | ^~~~~~~~~~~~ seqpanel.c:5755:8: warning: variable ‘height’ set but not used [-Wunused-but-set-variable] 5755 | Int4 height, width; | ^~~~~~ seqpanel.c: In function ‘WriteAlignmentInterleaveToFileEx’: seqpanel.c:8665:22: warning: passing argument 1 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8665 | fputs (fp, printed_line); | ^~ | | | FILE * In file included from ../include/ncbilcl.h:154: /usr/include/stdio.h:717:42: note: expected ‘const char * restrict’ but argument is of type ‘FILE *’ 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~~~~~~~^~~ seqpanel.c:8665:26: warning: passing argument 2 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8665 | fputs (fp, printed_line); | ^~~~~~~~~~~~ | | | Nlm_CharPtr {aka char *} /usr/include/stdio.h:717:64: note: expected ‘FILE * restrict’ but argument is of type ‘Nlm_CharPtr’ {aka ‘char *’} 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~^~~~~~~~ seqpanel.c: In function ‘WriteAlignmentContiguousToFile’: seqpanel.c:8761:20: warning: passing argument 1 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8761 | fputs (fp, printed_line); | ^~ | | | FILE * /usr/include/stdio.h:717:42: note: expected ‘const char * restrict’ but argument is of type ‘FILE *’ 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~~~~~~~^~~ seqpanel.c:8761:24: warning: passing argument 2 of ‘fputs’ from incompatible pointer type [-Wincompatible-pointer-types] 8761 | fputs (fp, printed_line); | ^~~~~~~~~~~~ | | | Nlm_CharPtr {aka char *} /usr/include/stdio.h:717:64: note: expected ‘FILE * restrict’ but argument is of type ‘Nlm_CharPtr’ {aka ‘char *’} 717 | extern int fputs (const char *__restrict __s, FILE *__restrict __stream) | ~~~~~~~~~~~~~~~~~^~~~~~~~ seqpanel.c: In function ‘ReverseSequenceStrandsInAlignment’: seqpanel.c:9008:17: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 9008 | SeqEntryPtr sep; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ seqpanel.c:1171:16: warning: ‘GetAlignmentColumnPercentIDsForAlignmentSection’ defined but not used [-Wunused-function] 1171 | static double *GetAlignmentColumnPercentIDsForAlignmentSection (BioseqViewPtr bvp, Int4 line, Int4 aln_idx) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: seqpanel.c: In function ‘SeqEdFindPatternDialog’: ../include/vibdefns.h:535:22: warning: ‘g1’ may be used uninitialized [-Wmaybe-uninitialized] 535 | #define AlignObjects Nlm_AlignObjects seqpanel.c:7632:25: note: ‘g1’ was declared here 7632 | GrouP h, g1, g2; | ^~ In file included from ../include/ncbi.h:62: In function ‘PrintPlusProtein’, inlined from ‘PrintFeature’ at seqpanel.c:3923:9: ../include/ncbistr.h:331:25: warning: ‘str_prot’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen seqpanel.c: In function ‘PrintFeature’: seqpanel.c:3810:21: note: ‘str_prot’ was declared here 3810 | CharPtr str_prot; | ^~~~~~~~ seqpanel.c: In function ‘SeqEdOnClick’: seqpanel.c:5026:10: warning: ‘is_left_end’ may be used uninitialized [-Wmaybe-uninitialized] 5026 | if (is_left_end) | ^ seqpanel.c:4952:21: note: ‘is_left_end’ was declared here 4952 | Boolean is_left_end, is_right_end; | ^~~~~~~~~~~ seqpanel.c:5030:15: warning: ‘is_right_end’ may be used uninitialized [-Wmaybe-uninitialized] 5030 | else if (is_right_end) | ^ seqpanel.c:4952:34: note: ‘is_right_end’ was declared here 4952 | Boolean is_left_end, is_right_end; | ^~~~~~~~~~~~ In function ‘ExportSequenceText’, inlined from ‘SeqEdExportProc’ at seqpanel.c:6972:7: seqpanel.c:4353:13: warning: ‘seq_pos’ may be used uninitialized [-Wmaybe-uninitialized] 4353 | SeqEdPrintTextLineToFile ((CharPtr)file_line, from, to, seq_pos, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘SeqEdExportProc’: seqpanel.c:4233:17: note: ‘seq_pos’ was declared here 4233 | Int4 seq_pos; | ^~~~~~~ In function ‘DrawAlignment’, inlined from ‘DrawSeqPanel’ at seqpanel.c:2551:11, inlined from ‘onDrawSeqPanel’ at seqpanel.c:2624:3: seqpanel.c:1252:3: warning: ‘seqbuf’ may be used uninitialized [-Wmaybe-uninitialized] 1252 | AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 | bvp->showAlnSubstitutions); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘onDrawSeqPanel’: seqpanel.c:2466:25: note: ‘seqbuf’ was declared here 2466 | Uint1Ptr buf, seqbuf, alnbuf; | ^~~~~~ In function ‘DrawAlignment’, inlined from ‘DrawSeqPanel’ at seqpanel.c:2551:11, inlined from ‘onDrawSeqPanel’ at seqpanel.c:2624:3: seqpanel.c:1252:3: warning: ‘alnbuf’ may be used uninitialized [-Wmaybe-uninitialized] 1252 | AlignmentIntervalToString (tmp_salp, row, start, stop, bvp->TargetRow, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1253 | bvp->viewWholeEntity, seqbuf, alnbuf, &alnbuf_len, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1254 | bvp->showAlnSubstitutions); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ seqpanel.c: In function ‘onDrawSeqPanel’: seqpanel.c:2466:33: note: ‘alnbuf’ was declared here 2466 | Uint1Ptr buf, seqbuf, alnbuf; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ingengraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from ../include/ingengraph.h:52, from ingengraph.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingengraph.c: In function ‘Ing_BigEncodeIdxFeat’: ingengraph.c:262:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 262 | return *((Uint8Ptr) index_g); | ~^~~~~~~~~~~~~~~~~~~ ingengraph.c: In function ‘Ing_AddOneAlignToOverviewPage’: ingengraph.c:355:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 355 | else | ^~~~ ingengraph.c:357:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 357 | prim = AddRectangle(seg, start, (row)*(-20), stop, (row)*(-20)+j, NO_ARROW, FALSE,0); | ^~~~ ingengraph.c:347:13: warning: unused variable ‘bsp’ [-Wunused-variable] 347 | BioseqPtr bsp=NULL; | ^~~ ingengraph.c: In function ‘Ing_AddAlignsToOverviewPage’: ingengraph.c:372:18: warning: unused variable ‘buf’ [-Wunused-variable] 372 | Char buf[41]={""}; | ^~~ ingengraph.c:367:18: warning: variable ‘NewLine’ set but not used [-Wunused-but-set-variable] 367 | Boolean NewLine=FALSE; | ^~~~~~~ ingengraph.c: In function ‘Ing_DrawOverviewPage’: ingengraph.c:492:14: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 492 | Int4 offset; | ^~~~~~ In file included from ../include/vibrant.h:130, from ../include/ingengraph.h:54: ../include/vibdefns.h:468:17: warning: unused variable ‘Nlm_Visible’ [-Wunused-variable] 468 | #define Visible Nlm_Visible | ^~~~~~~~~~~ ingengraph.c:488:14: note: in expansion of macro ‘Visible’ 488 | Boolean Visible=FALSE; | ^~~~~~~ ingengraph.c: In function ‘Ing_PopOverviewPage’: ingengraph.c:715:16: warning: variable ‘margin’ set but not used [-Wunused-but-set-variable] 715 | Int4 margin, len; | ^~~~~~ ingengraph.c:714:16: warning: unused variable ‘buf’ [-Wunused-variable] 714 | Char buf[50]={""}; | ^~~ ingengraph.c:708:16: warning: unused variable ‘sanp’ [-Wunused-variable] 708 | SeqAnnotPtr sanp=NULL; | ^~~~ ingengraph.c: In function ‘Ing_AddAlignsToDetailedPage’: ingengraph.c:1097:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1097 | if ((start - offset - (label_len - feat_len)/2)<0) | ^~ ingengraph.c:1099:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1099 | if (bOver_the_edge) | ^~ ingengraph.c: In function ‘Ing_PopDetailedPage’: ingengraph.c:1437:16: warning: variable ‘CurrentSeg’ set but not used [-Wunused-but-set-variable] 1437 | SegmenT CurrentSeg=NULL; | ^~~~~~~~~~ ingengraph.c: In function ‘Ing_ExploreSegments’: ingengraph.c:1829:22: warning: unused variable ‘isDraft’ [-Wunused-variable] 1829 | Boolean isDraft = FALSE; | ^~~~~~~ ingengraph.c:1827:22: warning: unused variable ‘vnp’ [-Wunused-variable] 1827 | ValNodePtr vnp = NULL; | ^~~ ingengraph.c:1826:22: warning: unused variable ‘gbp’ [-Wunused-variable] 1826 | GBBlockPtr gbp = NULL; | ^~~ ingengraph.c:1824:33: warning: variable ‘black’ set but not used [-Wunused-but-set-variable] 1824 | Uint1 orange[3], black[3]; | ^~~~~ ingengraph.c:1823:33: warning: variable ‘lime’ set but not used [-Wunused-but-set-variable] 1823 | Uint1 indigo[3], lime[3]; | ^~~~ ingengraph.c:1823:22: warning: variable ‘indigo’ set but not used [-Wunused-but-set-variable] 1823 | Uint1 indigo[3], lime[3]; | ^~~~~~ ingengraph.c: In function ‘Ing_AddGCRect’: ingengraph.c:1933:17: warning: variable ‘comp2’ set but not used [-Wunused-but-set-variable] 1933 | FloatHi comp2, comp_prev; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/ingengraph.h:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ ingengraph.c:71:13: warning: ‘Ing_GetNamesZoomedVal’ declared ‘static’ but never defined [-Wunused-function] 71 | static void Ing_GetNamesZoomedVal(VieweR vNames,Int4Ptr from, Int4Ptr to, | ^~~~~~~~~~~~~~~~~~~~~ ingengraph.c:602:28: warning: ‘Ing_CollectFeatures1’ defined but not used [-Wunused-function] 602 | static Boolean LIBCALLBACK Ing_CollectFeatures1(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) | ^~~~~~~~~~~~~~~~~~~~ ingengraph.c:583:24: warning: ‘Ing_SortByChoice’ defined but not used [-Wunused-function] 583 | static int LIBCALLBACK Ing_SortByChoice (VoidPtr ptr1, VoidPtr ptr2) | ^~~~~~~~~~~~~~~~ ingengraph.c: In function ‘Ing_BigEncodeIdxFeat’: ingengraph.c:262:16: warning: ‘index_g’ is used uninitialized [-Wuninitialized] 262 | return *((Uint8Ptr) index_g); | ^~~~~~~~~~~~~~~~~~~~~ ingengraph.c:257:7: note: ‘index_g’ declared here 257 | Uint4 index_g[2]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ingenext.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2ff.h:113, from ../include/ingenwin.h:58, from ../include/ingenext.h:53, from ingenext.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingenext.c: In function ‘Ing_KeepTheBestAlignments’: ingenext.c:167:20: warning: variable ‘amaip’ set but not used [-Wunused-but-set-variable] 167 | AMAlignIndex2Ptr amaip = NULL; | ^~~~~ ingenext.c: In function ‘Ing_HandleQBlastResults’: ingenext.c:272:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 272 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){ | ^~~~~~~ ingenext.c: In function ‘Ing_HandleResults’: ingenext.c:535:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 535 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE)){ | ^~~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:739:18: warning: unused variable ‘paramlist’ [-Wunused-variable] 739 | ValNodePtr paramlist = NULL; | ^~~~~~~~~ ingenext.c: In function ‘Ing_tRNAscanProc’: ingenext.c:915:22: warning: unused variable ‘moveMe’ [-Wunused-variable] 915 | ValNodePtr moveMe = NULL; | ^~~~~~ ingenext.c:906:22: warning: unused variable ‘first’ [-Wunused-variable] 906 | TexT first = NULL; | ^~~~~ ingenext.c:902:22: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 902 | ButtoN b; | ^ ingenext.c:896:17: warning: unused variable ‘args’ [-Wunused-variable] 896 | CharPtr args = NULL; | ^~~~ ingenext.c: In function ‘Ing_ReadtRNAConfigFile’: ingenext.c:1125:15: warning: variable ‘demomode’ set but not used [-Wunused-but-set-variable] 1125 | Boolean demomode = FALSE; | ^~~~~~~~ ingenext.c: In function ‘Ing_DoBlast2Seqs’: ingenext.c:1369:12: warning: the comparison will always evaluate as ‘true’ for the address of ‘eval’ will never be NULL [-Waddress] 1369 | if (eval != NULL) | ^~ ingenext.c:1313:23: note: ‘eval’ declared here 1313 | Char eval[8]; | ^~~~ ingenext.c:1376:12: warning: the comparison will always evaluate as ‘true’ for the address of ‘eval’ will never be NULL [-Waddress] 1376 | if (eval != NULL) | ^~ ingenext.c:1313:23: note: ‘eval’ declared here 1313 | Char eval[8]; | ^~~~ ingenext.c:1312:23: warning: variable ‘is_local’ set but not used [-Wunused-but-set-variable] 1312 | Boolean is_local, first_bsp=TRUE; | ^~~~~~~~ ingenext.c: In function ‘Ing_CreateDotMatrixForm’: ingenext.c:1834:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1834 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) | ^~~~~~~ ingenext.c: In function ‘Ing_RunSpidey’: ingenext.c:1994:20: warning: unused variable ‘sanp’ [-Wunused-variable] 1994 | SeqAnnotPtr sanp = NULL; | ^~~~ ingenext.c:1993:20: warning: unused variable ‘spidp_next’ [-Wunused-variable] 1993 | SPI_mRNAPtr spidp_next = NULL; | ^~~~~~~~~~ ingenext.c:1992:20: warning: unused variable ‘spidp_head’ [-Wunused-variable] 1992 | SPI_mRNAPtr spidp_head = NULL; | ^~~~~~~~~~ ingenext.c: In function ‘Ing_ReadmRNAs_ext’: ingenext.c:2025:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025 | while (dataptr = ReadAsnFastaOrFlatFile(fp, &datatype, NULL, FALSE, FALSE, TRUE, FALSE)) | ^~~~~~~ ingenext.c: In function ‘Ing_DeleteInsertInGenomic’: ingenext.c:2522:16: warning: unused variable ‘newsegs’ [-Wunused-variable] 2522 | Int2 newsegs = 0, offset = 0; | ^~~~~~~ ingenext.c: In function ‘Ing_ReplaceAllMismatchedInLocation’: ingenext.c:2777:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2777 | if (!All) | ^~ ingenext.c:2781:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2781 | SeqLocReplace(msip, mmis, mmis, mstrand, gsip, gmis, gmis, gstrand); | ^~~~~~~~~~~~~ ingenext.c:2615:21: warning: unused variable ‘str’ [-Wunused-variable] 2615 | Char str[200] = {""}; | ^~~ ingenext.c:2612:22: warning: unused variable ‘amaip’ [-Wunused-variable] 2612 | AMAlignIndex2Ptr amaip = NULL; | ^~~~~ ingenext.c: In function ‘Ing_MismatchProc’: ingenext.c:3025:15: warning: unused variable ‘sip’ [-Wunused-variable] 3025 | SeqIdPtr sip = NULL; | ^~~ ingenext.c: In function ‘Ing_PrintSpideyReport’: ingenext.c:3471:27: warning: variable ‘gmis’ set but not used [-Wunused-but-set-variable] 3471 | Int4 mmis, gmis, miscount = 0; | ^~~~ ingenext.c: In function ‘Ing_PrintBlastReport’: ingenext.c:3853:18: warning: unused variable ‘more’ [-Wunused-variable] 3853 | Boolean more = FALSE; | ^~~~ In file included from ../include/vibrant.h:130, from ../include/dlogutil.h:48, from ../include/import.h:48, from ../include/ingenwin.h:64: ../include/vibdefns.h:652:16: warning: variable ‘Nlm_DkGray’ set but not used [-Wunused-but-set-variable] 652 | #define DkGray Nlm_DkGray | ^~~~~~~~~~ ingenext.c:3850:18: note: in expansion of macro ‘DkGray’ 3850 | Uint1 DkGray[3]; | ^~~~~~ ingenext.c: In function ‘Ing_PopulateReport’: ingenext.c:4328:20: warning: unused variable ‘sip’ [-Wunused-variable] 4328 | SeqIdPtr sip=NULL; | ^~~ ingenext.c:4324:20: warning: unused variable ‘temp’ [-Wunused-variable] 4324 | CharPtr temp = NULL; | ^~~~ ingenext.c: In function ‘Ing_ResizeReportWindow’: ingenext.c:4484:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 4484 | BaR hsb; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/ingenwin.h:60: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ingenwin.h:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:135, from ../include/ingenwin.h:62: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ingenext.c:130:13: warning: ‘querytimercount’ defined but not used [-Wunused-variable] 130 | static Int4 querytimercount = 0; | ^~~~~~~~~~~~~~~ ingenext.c:129:13: warning: ‘querytimerlimit’ defined but not used [-Wunused-variable] 129 | static Int4 querytimerlimit = 100; | ^~~~~~~~~~~~~~~ ingenext.c:59:28: warning: ‘Ing_BlastCallback’ defined but not used [-Wunused-function] 59 | static Boolean LIBCALLBACK Ing_BlastCallback (BlastResponse *brp, | ^~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ ingenext.c: In function ‘Ing_SpideyCallback’: ingenext.c:2097:54: warning: ‘%%’ directive writing 1 byte into a region of size between 0 and 9 [-Wformat-overflow=] 2097 | sprintf(igvp->progress_counter, "Completed %d%%", progress->percentdone); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Ing_SpideyCallback’ at ingenext.c:2097:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 22 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_DoBlast2Seqs’: ingenext.c:1457:17: warning: ‘e_head’ may be used uninitialized [-Wmaybe-uninitialized] 1457 | e_tmp->next=e_head; | ~~~~~~~~~~~^~~~~~~ ingenext.c:1317:39: note: ‘e_head’ was declared here 1317 | IngEntityPtr e_list, e_next, e_head, e_tmp; | ^~~~~~ ingenext.c: In function ‘Ing_MismatchProc’: ingenext.c:3181:7: warning: ‘mstart’ may be used uninitialized [-Wmaybe-uninitialized] 3181 | SeqPortSeek(spp_mrna, mstart-start, SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenext.c:3020:15: note: ‘mstart’ was declared here 3020 | Int4 mstart, gstart; | ^~~~~~ ingenext.c:3170:32: warning: ‘gstart’ may be used uninitialized [-Wmaybe-uninitialized] 3170 | gstart = start + (stop - gstart); | ~~~~~~^~~~~~~~~ ingenext.c:3020:23: note: ‘gstart’ was declared here 3020 | Int4 mstart, gstart; | ^~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:780:32: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 780 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘Ing_AccepttRNAargsProc’ at ingenext.c:780:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_AccepttRNAargsProc’: ingenext.c:794:30: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 794 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘Ing_AccepttRNAargsProc’ at ingenext.c:794:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ingenext.c: In function ‘Ing_ReplaceAllMismatchedInLocation’: ingenext.c:2648:8: warning: ‘nmismatches’ may be used uninitialized [-Wmaybe-uninitialized] 2648 | if (nmismatches > 0){ | ^ ingenext.c:2617:33: note: ‘nmismatches’ was declared here 2617 | Int4 gmis, mmis, nmismatches, nkeep = 0; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ingenwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn2ff.h:113, from ../include/ingenwin.h:58, from ingenwin.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ingenwin.c: In function ‘Ing_PopulateDetailedPage’: ingenwin.c:134:22: warning: unused variable ‘bSelected’ [-Wunused-variable] 134 | Boolean bSelected = FALSE; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_DoRange’: ingenwin.c:394:22: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 394 | BioseqPtr bsp; | ^~~ ingenwin.c: In function ‘Ing_PopulateCpG’: ingenwin.c:576:19: warning: variable ‘nchars’ set but not used [-Wunused-but-set-variable] 576 | Int2 cxChar, nchars; | ^~~~~~ ingenwin.c: In function ‘Ing_ResizeCpGWindow’: ingenwin.c:642:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 642 | BaR hsb; | ^~~ ingenwin.c: In function ‘Ing_PopulateMotif’: ingenwin.c:718:26: warning: variable ‘nchars’ set but not used [-Wunused-but-set-variable] 718 | Int2 cxChar, nchars; | ^~~~~~ ingenwin.c:717:24: warning: variable ‘swidth’ set but not used [-Wunused-but-set-variable] 717 | Int4 slen, swidth; | ^~~~~~ ingenwin.c:717:18: warning: variable ‘slen’ set but not used [-Wunused-but-set-variable] 717 | Int4 slen, swidth; | ^~~~ ingenwin.c: In function ‘Ing_ResizeMotifWindow’: ingenwin.c:785:12: warning: unused variable ‘name’ [-Wunused-variable] 785 | CharPtr name = NULL; | ^~~~ ingenwin.c:783:12: warning: variable ‘hsb’ set but not used [-Wunused-but-set-variable] 783 | BaR hsb; | ^~~ ingenwin.c: In function ‘Ing_ShowComplexity’: ingenwin.c:1270:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1270 | while ((Boolean)(slp_feat=SeqLocFindNext(slp_dust,slp_feat))){ | ^ ingenwin.c: In function ‘Ing_CreateNewFeature’: ingenwin.c:1301:22: warning: unused variable ‘rnatype’ [-Wunused-variable] 1301 | Uint1 rnatype=0; | ^~~~~~~ ingenwin.c: In function ‘Ing_GetAlignmentIntervals’: ingenwin.c:1418:20: warning: unused variable ‘master’ [-Wunused-variable] 1418 | SeqIdPtr master = NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_OldGetAlignmentIntervals’: ingenwin.c:1494:20: warning: unused variable ‘master’ [-Wunused-variable] 1494 | SeqIdPtr master = NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_OldMakeLocListFromSAP’: ingenwin.c:1613:26: warning: unused variable ‘slp2’ [-Wunused-variable] 1613 | SeqLocPtr slp1 = NULL, slp2 = NULL; | ^~~~ ingenwin.c:1613:13: warning: unused variable ‘slp1’ [-Wunused-variable] 1613 | SeqLocPtr slp1 = NULL, slp2 = NULL; | ^~~~ ingenwin.c: In function ‘Ing_OM_MsgFunc’: ingenwin.c:2380:15: warning: the address of ‘sfc’ will always evaluate as ‘true’ [-Waddress] 2380 | if (&sfc) | ^ ingenwin.c:2284:22: warning: unused variable ‘segID’ [-Wunused-variable] 2284 | Uint2 segID=0; | ^~~~~ ingenwin.c:2280:22: warning: unused variable ‘sep’ [-Wunused-variable] 2280 | SeqEntryPtr sep=NULL; | ^~~ ingenwin.c:2271:31: warning: unused variable ‘number’ [-Wunused-variable] 2271 | Int4 score=0, number=0; | ^~~~~~ ingenwin.c:2271:22: warning: unused variable ‘score’ [-Wunused-variable] 2271 | Int4 score=0, number=0; | ^~~~~ ingenwin.c:2270:34: warning: unused variable ‘n’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^ ingenwin.c:2270:28: warning: unused variable ‘s2’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^~ ingenwin.c:2270:22: warning: unused variable ‘s1’ [-Wunused-variable] 2270 | Int4 s1=0, s2=0, n=1; | ^~ ingenwin.c: In function ‘Ing_MoveCursor’: ingenwin.c:2631:9: warning: variable ‘grayClr2’ set but not used [-Wunused-but-set-variable] 2631 | Uint1 grayClr2[3]; | ^~~~~~~~ ingenwin.c: In function ‘Ing_FeatViewerClickProc’: ingenwin.c:2814:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2814 | if (subSeg=FindSegPrim(v, pt, NULL, NULL, &prim)){ | ^~~~~~ ingenwin.c:2804:14: warning: unused variable ‘slp’ [-Wunused-variable] 2804 | SeqLocPtr slp=NULL; | ^~~ ingenwin.c: In function ‘Ing_SequenceClickProc’: ingenwin.c:2908:22: warning: variable ‘ssp’ set but not used [-Wunused-but-set-variable] 2908 | SelStructPtr ssp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInBlastAsn’: ingenwin.c:3077:19: warning: unused variable ‘Report’ [-Wunused-variable] 3077 | IngReportPtr Report=NULL; | ^~~~~~ ingenwin.c:3075:19: warning: unused variable ‘sip’ [-Wunused-variable] 3075 | SeqIdPtr sip=NULL; | ^~~ ingenwin.c:3074:19: warning: unused variable ‘salp’ [-Wunused-variable] 3074 | SeqAlignPtr salp=NULL; | ^~~~ ingenwin.c:3073:19: warning: unused variable ‘n_sap’ [-Wunused-variable] 3073 | SeqAlignPtr n_sap=NULL; | ^~~~~ ingenwin.c: In function ‘Ing_ParseSeqIdFile’: ingenwin.c:3142:20: warning: unused variable ‘bsp’ [-Wunused-variable] 3142 | BioseqPtr bsp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInFeatureTable’: ingenwin.c:3194:20: warning: variable ‘sanp’ set but not used [-Wunused-but-set-variable] 3194 | SeqAnnotPtr sanp; | ^~~~ ingenwin.c: In function ‘Ing_AssembleGenscanInfo’: ingenwin.c:3258:17: warning: unused variable ‘slp’ [-Wunused-variable] 3258 | SeqLocPtr slp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInGenscan’: ingenwin.c:3300:33: warning: unused variable ‘str’ [-Wunused-variable] 3300 | CharPtr letter=NULL, str=NULL; | ^~~ ingenwin.c:3300:20: warning: unused variable ‘letter’ [-Wunused-variable] 3300 | CharPtr letter=NULL, str=NULL; | ^~~~~~ ingenwin.c:3298:33: warning: unused variable ‘first_pass’ [-Wunused-variable] 3298 | Boolean found=FALSE, first_pass=FALSE; | ^~~~~~~~~~ ingenwin.c: In function ‘Ing_AssembleTabDelimited’: ingenwin.c:3519:17: warning: variable ‘score’ set but not used [-Wunused-but-set-variable] 3519 | Int4 score; | ^~~~~ ingenwin.c:3516:17: warning: unused variable ‘tmp’ [-Wunused-variable] 3516 | CharPtr tmp=NULL; | ^~~ ingenwin.c: In function ‘Ing_ReadInTabDelimited’: ingenwin.c:3659:40: warning: variable ‘label_str’ set but not used [-Wunused-but-set-variable] 3659 | CharPtr tmp=NULL, str=NULL, label_str=NULL; | ^~~~~~~~~ ingenwin.c:3659:20: warning: unused variable ‘tmp’ [-Wunused-variable] 3659 | CharPtr tmp=NULL, str=NULL, label_str=NULL; | ^~~ ingenwin.c:3653:20: warning: unused variable ‘lip_tmp’ [-Wunused-variable] 3653 | IngInfoPtr lip_tmp=NULL; | ^~~~~~~ ingenwin.c:3650:20: warning: unused variable ‘letter’ [-Wunused-variable] 3650 | CharPtr letter=NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_FileOpenSpecial’: ingenwin.c:3984:16: warning: unused variable ‘Report’ [-Wunused-variable] 3984 | IngReportPtr Report=NULL; | ^~~~~~ ingenwin.c: In function ‘Ing_FileOpenMain’: ingenwin.c:4078:21: warning: unused variable ‘sep_orig’ [-Wunused-variable] 4078 | SeqEntryPtr sep_orig=NULL, sep=NULL; | ^~~~~~~~ ingenwin.c: In function ‘Ing_ResizeMainWindow’: ingenwin.c:4187:25: warning: variable ‘InfoHeight’ set but not used [-Wunused-but-set-variable] 4187 | Int2 RulerHeight, InfoHeight; | ^~~~~~~~~~ ingenwin.c: In function ‘Ing_OpenFromFileORNetwork’: ingenwin.c:4491:25: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 4491 | ButtoN b,b2; | ^~ ingenwin.c: In function ‘Ing_EditFeature’: ingenwin.c:4640:22: warning: variable ‘igvp’ set but not used [-Wunused-but-set-variable] 4640 | IngGenomeViewerPtr igvp=NULL; | ^~~~ ingenwin.c: In function ‘Ing_MarkSeqAnnot’: ingenwin.c:4713:16: warning: unused variable ‘bNoParent’ [-Wunused-variable] 4713 | Boolean bNoParent = FALSE; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_PropagateClickProc’: ingenwin.c:5064:22: warning: unused variable ‘primID’ [-Wunused-variable] 5064 | Uint2 primID=0; | ^~~~~~ ingenwin.c:5063:22: warning: unused variable ‘itemtype’ [-Wunused-variable] 5063 | Uint2 itemtype=0; | ^~~~~~~~ ingenwin.c:5062:22: warning: unused variable ‘itemID’ [-Wunused-variable] 5062 | Uint4 itemID=0; | ^~~~~~ ingenwin.c:5061:22: warning: unused variable ‘entityID’ [-Wunused-variable] 5061 | Uint2 entityID=0; | ^~~~~~~~ ingenwin.c:5060:22: warning: unused variable ‘ssp’ [-Wunused-variable] 5060 | SelStructPtr ssp=NULL; | ^~~ ingenwin.c:5059:22: warning: unused variable ‘igvp’ [-Wunused-variable] 5059 | IngGenomeViewerPtr igvp=NULL; | ^~~~ ingenwin.c: In function ‘Ing_PrintCompProteins’: ingenwin.c:5146:32: warning: unused variable ‘str2’ [-Wunused-variable] 5146 | Char str1[200] = {""}, str2[10] = {""}; | ^~~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5282:14: warning: variable ‘ARROW’ set but not used [-Wunused-but-set-variable] 5282 | Uint1 ARROW=NO_ARROW; | ^~~~~ ingenwin.c:5279:14: warning: unused variable ‘stringwidth’ [-Wunused-variable] 5279 | Int4 stringwidth = 0; | ^~~~~~~~~~~ ingenwin.c:5277:14: warning: unused variable ‘left’ [-Wunused-variable] 5277 | Int4 left = 10; | ^~~~ ingenwin.c:5276:14: warning: variable ‘prim’ set but not used [-Wunused-but-set-variable] 5276 | PrimitivE prim; | ^~~~ ingenwin.c: In function ‘Ing_DoPropagate’: ingenwin.c:5596:14: warning: unused variable ‘strErr’ [-Wunused-variable] 5596 | Char strErr[50]={""}; | ^~~~~~ ingenwin.c: In function ‘Ing_GetFromNetwork’: ingenwin.c:7518:11: warning: unused variable ‘szAppName’ [-Wunused-variable] 7518 | Char szAppName [10]={"Ingenue"}; | ^~~~~~~~~ ingenwin.c: In function ‘Ing_SetupMainWindow’: ingenwin.c:7761:16: warning: unused variable ‘szAppName’ [-Wunused-variable] 7761 | Char szAppName [10]={"Ingenue"}; | ^~~~~~~~~ ingenwin.c:7760:48: warning: unused variable ‘str2’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~ ingenwin.c:7760:33: warning: unused variable ‘str1’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~ ingenwin.c:7760:16: warning: unused variable ‘title’ [-Wunused-variable] 7760 | Char title[100]={""}, str1[20]={""}, str2[20]={""}; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/ingenwin.h:60: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ingenwin.h:61: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:135, from ../include/ingenwin.h:62: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ingenwin.c:7552:13: warning: ‘Ing_ItemtoNetwork’ defined but not used [-Wunused-function] 7552 | static void Ing_ItemtoNetwork(IteM i){ | ^~~~~~~~~~~~~~~~~ ingenwin.c:6717:13: warning: ‘Ing_BspListProc’ defined but not used [-Wunused-function] 6717 | static void Ing_BspListProc(IteM i) | ^~~~~~~~~~~~~~~ ingenwin.c:5535:16: warning: ‘Ing_KeywordAlreadyInList’ defined but not used [-Wunused-function] 5535 | static Boolean Ing_KeywordAlreadyInList (ValNodePtr head, CharPtr kwd) | ^~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:1869:16: warning: ‘Ing_DeSelectPrim’ defined but not used [-Wunused-function] 1869 | static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) | ^~~~~~~~~~~~~~~~ ingenwin.c:1610:18: warning: ‘Ing_OldMakeLocListFromSAP’ defined but not used [-Wunused-function] 1610 | static SeqLocPtr Ing_OldMakeLocListFromSAP(SeqAlignPtr sap) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:1487:23: warning: ‘Ing_OldGetAlignmentIntervals’ defined but not used [-Wunused-function] 1487 | static IngIvalInfoPtr Ing_OldGetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ ingenwin.c: In function ‘Ing_ReplaceMismatchedProc’: ingenwin.c:4902:3: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 4902 | Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:4882:23: note: ‘start’ was declared here 4882 | Int4 start, stop; | ^~~~~ ingenwin.c:4902:3: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 4902 | Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c:4882:30: note: ‘stop’ was declared here 4882 | Int4 start, stop; | ^~~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5353:17: warning: ‘%s’ directive writing up to 299 bytes into a region of size 255 [-Wformat-overflow=] 5353 | sprintf(str, "%s", pfp->name); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Ing_PropagateReport’ at ingenwin.c:5353:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 1 and 300 bytes into a destination of size 255 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘Ing_PrintCompProteins’, inlined from ‘Ing_PropagateReport’ at ingenwin.c:5365:5: ingenwin.c:5224:12: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 5224 | last_pos = j; | ~~~~~~~~~^~~ ingenwin.c: In function ‘Ing_PropagateReport’: ingenwin.c:5137:17: note: ‘j’ was declared here 5137 | Int4 i, j, k, row; | ^ ingenwin.c: In function ‘Ing_DoPropagate’: ingenwin.c:5625:26: warning: ‘ already exists. Do you stil...’ directive writing 51 bytes into a region of size between 1 and 300 [-Wformat-overflow=] 5625 | sprintf (str_buf, "%s already exists. Do you still want to propagate it?", pfp->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘Ing_DoPropagate’ at ingenwin.c:5625:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 52 and 351 bytes into a destination of size 300 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘Ing_AssembleGenscanInfo’, inlined from ‘Ing_ReadInGenscan’ at ingenwin.c:3345:12, inlined from ‘Ing_FileOpenSpecial’ at ingenwin.c:4021:9: ingenwin.c:3290:13: warning: ‘strand’ may be used uninitialized [-Wmaybe-uninitialized] 3290 | slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ingenwin.c: In function ‘Ing_FileOpenSpecial’: ingenwin.c:3255:17: note: ‘strand’ was declared here 3255 | Uint1 strand; | ^~~~~~ In file included from ../include/vibrant.h:130, from ../include/dlogutil.h:48, from ../include/import.h:48, from ../include/ingenwin.h:64: ingenwin.c: In function ‘Ing_KozakProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:1006:22: note: ‘ReportW’ was declared here 1006 | WindoW ReportW; | ^~~~~~~ ingenwin.c:1048:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | if (ans == ANS_NO) | ^ ingenwin.c:1010:22: note: ‘ans’ was declared here 1010 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_SignalPeptideProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:1057:22: note: ‘ReportW’ was declared here 1057 | WindoW ReportW; | ^~~~~~~ ingenwin.c:1099:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 1099 | if (ans == ANS_NO) | ^ ingenwin.c:1061:22: note: ‘ans’ was declared here 1061 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_RepeatsProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:955:22: note: ‘ReportW’ was declared here 955 | WindoW ReportW; | ^~~~~~~ ingenwin.c:997:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 997 | if (ans == ANS_NO) | ^ ingenwin.c:959:22: note: ‘ans’ was declared here 959 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_PolyAProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:904:22: note: ‘ReportW’ was declared here 904 | WindoW ReportW; | ^~~~~~~ ingenwin.c:946:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 946 | if (ans == ANS_NO) | ^ ingenwin.c:908:22: note: ‘ans’ was declared here 908 | MsgAnswer ans; | ^~~ ingenwin.c: In function ‘Ing_CpGProc’: ../include/vibdefns.h:476:16: warning: ‘ReportW’ may be used uninitialized [-Wmaybe-uninitialized] 476 | #define Select Nlm_Select ingenwin.c:857:22: note: ‘ReportW’ was declared here 857 | WindoW ReportW; | ^~~~~~~ ingenwin.c:895:6: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 895 | if (ans == ANS_NO) | ^ ingenwin.c:860:22: note: ‘ans’ was declared here 860 | MsgAnswer ans; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF macrodlg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objseq.h:48, from macrodlg.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ macrodlg.c: In function ‘ExistingTextDialog’: macrodlg.c:1959:22: warning: variable ‘ppt’ set but not used [-Wunused-but-set-variable] 1959 | PrompT ppt; | ^~~ macrodlg.c: In function ‘EndDistanceToDialog’: macrodlg.c:3076:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3076 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:3082:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3082 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:3088:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 3088 | sprintf (buf, "%d", v->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘SourceQualChoiceDialog’: macrodlg.c:3757:48: warning: variable ‘b4’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c:3757:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 3757 | ButtoN b1, b2, b3 = NULL, b4 = NULL; | ^~ macrodlg.c: In function ‘SourceConstraintDialog’: macrodlg.c:3995:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c:3995:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c:3995:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 3995 | ButtoN b1, b2, b3; | ^~ macrodlg.c: In function ‘CDSGeneProtQualConstraintDialog’: macrodlg.c:4309:37: warning: variable ‘b3’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c:4309:33: warning: variable ‘b2’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c:4309:29: warning: variable ‘b1’ set but not used [-Wunused-but-set-variable] 4309 | ButtoN b1, b2, b3; | ^~ macrodlg.c: In function ‘QuantityConstraintToDialog’: macrodlg.c:7368:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7368 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:7373:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7373 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:7378:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 7378 | sprintf (buf, "%d", vnp->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘TestApplyActionDialog’: macrodlg.c:12965:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 12965 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘TestEditActionDialog’: macrodlg.c:13170:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 13170 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘TestRemoveOutsideActionDialog’: macrodlg.c:13328:8: warning: variable ‘field_type’ set but not used [-Wunused-but-set-variable] 13328 | Int2 field_type = 0; | ^~~~~~~~~~ macrodlg.c: In function ‘ApplyFeatureActionToDialog’: macrodlg.c:15186:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15186 | sprintf (num, "%d^", action->location->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:15188:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 15188 | sprintf (num, "%d", action->location->data.intvalue + 1); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: In function ‘AddMacroActions’: macrodlg.c:20523:25: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 20523 | Boolean rval = FALSE; | ^~~~ macrodlg.c: In function ‘PointerToSampleDialog’: macrodlg.c:20659:19: warning: variable ‘max_char_per_line’ set but not used [-Wunused-but-set-variable] 20659 | Int4 max_char_per_line; | ^~~~~~~~~~~~~~~~~ macrodlg.c: In function ‘SampleDialogCopy’: macrodlg.c:20779:53: warning: variable ‘last_col’ set but not used [-Wunused-but-set-variable] 20779 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~ macrodlg.c:20779:42: warning: variable ‘first_col’ set but not used [-Wunused-but-set-variable] 20779 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~~ macrodlg.c: In function ‘SingleMacroAcceptButton’: macrodlg.c:22071:33: warning: variable ‘num_features’ set but not used [-Wunused-but-set-variable] 22071 | Int4 num_fields, num_features; | ^~~~~~~~~~~~ macrodlg.c:22071:21: warning: variable ‘num_fields’ set but not used [-Wunused-but-set-variable] 22071 | Int4 num_fields, num_features; | ^~~~~~~~~~ macrodlg.c: In function ‘LaunchMacroTemplateEditor’: macrodlg.c:23785:23: warning: variable ‘bfp’ set but not used [-Wunused-but-set-variable] 23785 | BaseFormPtr bfp; | ^~~ macrodlg.c: In function ‘SearchFuncToDialog’: macrodlg.c:25755:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 25755 | sprintf (buf, "%d", func->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c:25776:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 25776 | sprintf (buf, "%d", func->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld macrodlg.c: At top level: macrodlg.c:20095:13: warning: ‘ChangeMacroActionPopup’ defined but not used [-Wunused-function] 20095 | static void ChangeMacroActionPopup (LisT t) | ^~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:20038:13: warning: ‘GetPopupChoiceForActionChoice’ defined but not used [-Wunused-function] 20038 | static Int2 GetPopupChoiceForActionChoice (Uint1 action_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:19715:13: warning: ‘GetCategoryForActionChoice’ defined but not used [-Wunused-function] 19715 | static Int2 GetCategoryForActionChoice (Uint1 action_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c:19698:14: warning: ‘GetActionChoiceForCategoryPopupChoice’ defined but not used [-Wunused-function] 19698 | static Uint1 GetActionChoiceForCategoryPopupChoice (Int2 category, Int2 popup_choice) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ macrodlg.c: In function ‘ActionToSingleMacroActionForm’: macrodlg.c:22273:30: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 22273 | Show (frm->action_dlgs[val - 1]); | ~~~~^~~ macrodlg.c:22216:25: note: ‘val’ was declared here 22216 | Int2 val, i; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF biosrc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/biosrc.h:48, from biosrc.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ biosrc.c: In function ‘CreateSimpleBioSourceDialog’: biosrc.c:2455:18: warning: variable ‘indexerVersion’ set but not used [-Wunused-but-set-variable] 2455 | Boolean indexerVersion; | ^~~~~~~~~~~~~~ biosrc.c: In function ‘CreateBioSourceDialog’: biosrc.c:3615:18: warning: variable ‘y’ set but not used [-Wunused-but-set-variable] 3615 | PrompT y; | ^ biosrc.c: At top level: biosrc.c:3291:26: warning: ‘EnumListFromQualNameAssoc’ defined but not used [-Wunused-function] 3291 | static EnumFieldAssocPtr EnumListFromQualNameAssoc (Nlm_QualNameAssocPtr qp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:3100:16: warning: ‘SubsourceDialogToSubSourcePtr’ defined but not used [-Wunused-function] 3100 | static Pointer SubsourceDialogToSubSourcePtr (DialoG d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2677:13: warning: ‘SubSourcePtrToSubsourceDialog’ defined but not used [-Wunused-function] 2677 | static void SubSourcePtrToSubsourceDialog (DialoG d, Pointer data) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2617:16: warning: ‘OrgmodDialogToOrgModPtr’ defined but not used [-Wunused-function] 2617 | static Pointer OrgmodDialogToOrgModPtr (DialoG d) | ^~~~~~~~~~~~~~~~~~~~~~~ biosrc.c:2568:13: warning: ‘OrgModPtrToOrgmodDialog’ defined but not used [-Wunused-function] 2568 | static void OrgModPtrToOrgmodDialog (DialoG d, Pointer data) | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cdrgn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/cdrgn.h:89, from cdrgn.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdrgn.c: In function ‘SetBestProteinFeature’: cdrgn.c:1003:21: warning: unused variable ‘prp’ [-Wunused-variable] 1003 | ProtRefPtr prp; | ^~~ cdrgn.c: In function ‘CdRegionPtrToForm’: cdrgn.c:1050:19: warning: unused variable ‘vnp’ [-Wunused-variable] 1050 | ValNodePtr vnp; | ^~~ cdrgn.c: In function ‘ProductToSeqLocPtr’: cdrgn.c:1293:19: warning: variable ‘rfp’ set but not used [-Wunused-but-set-variable] 1293 | RnaFormPtr rfp = NULL; | ^~~ cdrgn.c: In function ‘CreateCodeBreakAlist’: cdrgn.c:1926:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 1926 | Uint1 first; | ^~~~~ cdrgn.c: In function ‘CodeBreakPtrToCodeBreakDialog’: cdrgn.c:1977:19: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 1977 | Uint1 aa; | ^~ cdrgn.c: In function ‘PopulateAAPopup’: cdrgn.c:7041:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 7041 | Uint1 first; | ^~~~~ cdrgn.c: In function ‘RnaRefPtrToForm’: cdrgn.c:7557:17: warning: unused variable ‘is_iMet’ [-Wunused-variable] 7557 | Boolean is_iMet = FALSE; | ^~~~~~~ cdrgn.c:7556:17: warning: unused variable ‘is_fMet’ [-Wunused-variable] 7556 | Boolean is_fMet = FALSE; | ^~~~~~~ cdrgn.c: At top level: cdrgn.c:6851:13: warning: ‘ConvertRnaRefNameToProductQual’ defined but not used [-Wunused-function] 6851 | static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cdrgn.c:6789:13: warning: ‘RemoveQualByName’ defined but not used [-Wunused-function] 6789 | static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name) | ^~~~~~~~~~~~~~~~ cdrgn.c:6770:18: warning: ‘FindOrAddQual’ defined but not used [-Wunused-function] 6770 | static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name) | ^~~~~~~~~~~~~ cdrgn.c:6323:15: warning: ‘CreateMrnaUserObjectDialog’ defined but not used [-Wunused-function] 6323 | static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr sep, BaseFormPtr bfp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cdrgn.c:6246:14: warning: ‘check_rna_type’ defined but not used [-Wunused-function] 6246 | static Uint1 check_rna_type (Uint1 type) | ^~~~~~~~~~~~~~ cdrgn.c:3183:13: warning: ‘SetComment’ defined but not used [-Wunused-function] 3183 | static void SetComment (CharPtr new_comment, WindoW w) | ^~~~~~~~~~ cdrgn.c:2149:13: warning: ‘AccessionToGi’ defined but not used [-Wunused-function] 2149 | static Int4 AccessionToGi (CharPtr string) | ^~~~~~~~~~~~~ cdrgn.c:961:13: warning: ‘FormToProtRef’ defined but not used [-Wunused-function] 961 | static void FormToProtRef(CdRgnFormPtr cfp, ProtRefPtr prp) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF import.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/import.h:48, from import.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ import.c:3776:22: warning: ‘kDoNotEditTitle’ initialized and declared ‘extern’ 3776 | extern const CharPtr kDoNotEditTitle = "You are manually editing a title. If you continue, the title will not be automatically updated if the taxonomy information changes. Are you sure you want to do this? It is a very bad idea."; | ^~~~~~~~~~~~~~~ import.c: In function ‘ExpandSecondaries’: import.c:3394:30: warning: ‘%*ld’ directive writing between 1 and 32768 bytes into a region of size 32 [-Wformat-overflow=] 3394 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~ import.c:3394:29: note: directive argument in the range [-2147483648, 2147483647] 3394 | sprintf (numbers, "%*ld", digits, (long) idx); | ^~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ExpandSecondaries’ at import.c:3394:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 32769 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pubdesc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/pubdesc.h:48, from pubdesc.c:44: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pubdesc.c: In function ‘MakeReplaceAuthorsForm’: pubdesc.c:4303:24: warning: variable ‘pepp’ set but not used [-Wunused-but-set-variable] 4303 | PubdescEditProcsPtr pepp; | ^~~~ pubdesc.c: In function ‘DisplayDocSum’: pubdesc.c:4865:9: warning: variable ‘lineheight’ set but not used [-Wunused-but-set-variable] 4865 | Int2 lineheight; | ^~~~~~~~~~ pubdesc.c: In function ‘GetLastNameFromPersonId’: pubdesc.c:5592:21: warning: the comparison will always evaluate as ‘true’ for the address of ‘names’ will never be NULL [-Waddress] 5592 | if (nsp->names != NULL) { | ^~ In file included from ../include/objsset.h:51, from ../include/sequtil.h:43, from ../include/sqnutils.h:49, from ../include/dlogutil.h:50: ../include/objgen.h:212:17: note: ‘names’ declared here 212 | CharPtr names[7]; | ^~~~~ pubdesc.c: At top level: pubdesc.c:5377:13: warning: ‘Quit’ defined but not used [-Wunused-function] 5377 | static void Quit (ButtoN b) | ^~~~ pubdesc.c:5113:14: warning: ‘AddAll’ defined but not used [-Wunused-function] 5113 | static void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st) | ^~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5096:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5096 | sprintf (year_buf, "%d", year - 1); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5096:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5099:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5099 | sprintf (year_buf, "%d", year); | ^ In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5099:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pubdesc.c: In function ‘SendQuery’: pubdesc.c:5102:29: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5102 | sprintf (year_buf, "%d", year + 1); | ^ In function ‘sprintf’, inlined from ‘AddYear’ at pubdesc.c:5102:7, inlined from ‘QueryFromForm’ at pubdesc.c:5174:5, inlined from ‘SendQuery’ at pubdesc.c:5231:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqsub.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from ../include/seqsub.h:58, from seqsub.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqsub.c: In function ‘SeqSubmitFromTemplateEditor’: seqsub.c:3250:20: warning: variable ‘omdp’ set but not used [-Wunused-but-set-variable] 3250 | ObjMgrDataPtr omdp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mapgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from mapgene.c:2: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mapgene.c: In function ‘load_new_align’: mapgene.c:79:24: warning: variable ‘match_slp’ set but not used [-Wunused-but-set-variable] 79 | SeqLocPtr slp, match_slp, t_slp; | ^~~~~~~~~ mapgene.c: In function ‘figure_loc_by_position’: mapgene.c:1039:27: warning: variable ‘center’ set but not used [-Wunused-but-set-variable] 1039 | Int4 start, stop, center; | ^~~~~~ mapgene.c: In function ‘cvt_loc_for_single_gene’: mapgene.c:1958:36: warning: variable ‘p_align_offset’ set but not used [-Wunused-but-set-variable] 1958 | Int4 offset, align_offset, p_align_offset; | ^~~~~~~~~~~~~~ mapgene.c:1957:14: warning: unused variable ‘shift’ [-Wunused-variable] 1957 | Int4 shift = 0; | ^~~~~ mapgene.c: In function ‘print_header_for_center’: mapgene.c:2693:17: warning: variable ‘link’ set but not used [-Wunused-but-set-variable] 2693 | CharPtr link; | ^~~~ mapgene.c: In function ‘PrintGeneticMarkerForOneMap’: mapgene.c:3635:17: warning: variable ‘link’ set but not used [-Wunused-but-set-variable] 3635 | CharPtr link; | ^~~~ mapgene.c: At top level: mapgene.c:3207:16: warning: ‘convert_center_name_to_gifname’ defined but not used [-Wunused-function] 3207 | static Boolean convert_center_name_to_gifname (CharPtr center_name, CharPtr gif_name) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mapgene.c:1788:13: warning: ‘adjust_slp_list’ defined but not used [-Wunused-function] 1788 | static void adjust_slp_list(ValNodePtr slp_list) | ^~~~~~~~~~~~~~~ mapgene.c:1748:16: warning: ‘merge_slp_list’ defined but not used [-Wunused-function] 1748 | static Boolean merge_slp_list(ValNodePtr PNTR gene_slp_list, ValNodePtr slp_list) | ^~~~~~~~~~~~~~ mapgene.c:1280:13: warning: ‘change_anchor_to_front’ defined but not used [-Wunused-function] 1280 | static void change_anchor_to_front(ValNodePtr msp_list, SeqIdPtr anchor_id) | ^~~~~~~~~~~~~~~~~~~~~~ mapgene.c:200:13: warning: ‘get_center_pointer’ defined but not used [-Wunused-function] 200 | static Int4 get_center_pointer(SeqLocPtr slp) | ^~~~~~~~~~~~~~~~~~ mapgene.c:27:13: warning: ‘print_this_id’ defined but not used [-Wunused-function] 27 | static void print_this_id (SeqIdPtr sip) | ^~~~~~~~~~~~~ mapgene.c: In function ‘PrintHTMLContigAlign.isra.0’: mapgene.c:2798:51: warning: ‘%s’ directive writing up to 30 bytes into a region of size 25 [-Wformat-overflow=] 2798 | sprintf(link_name, "CONTIG%s", alpha_name); | ^~ ~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘FindEricContigMap’ at mapgene.c:2798:4, inlined from ‘create_CONTIG_link’ at mapgene.c:2817:10, inlined from ‘PrintHTMLContigAlign.isra.0’ at mapgene.c:3050:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 37 bytes into a destination of size 31 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘print_contig_info’, inlined from ‘PrintContigForOneMap’ at mapgene.c:3410:9, inlined from ‘PrintContigForOneMap’ at mapgene.c:3396:9: mapgene.c:3181:25: warning: ‘yac_num’ may be used uninitialized [-Wmaybe-uninitialized] 3181 | PrintHTMLContigAlign(band_name, contig_name, anp_list, fp, db, fish_list, yac_list, yac_num); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mapgene.c: In function ‘PrintContigForOneMap’: mapgene.c:3152:14: note: ‘yac_num’ was declared here 3152 | Int4 yac_num; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prtgene.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/tofile.h:66, from ../include/prtgene.h:3, from prtgene.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prtgene.c: In function ‘print_sfp_ext’: prtgene.c:108:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 108 | if(ufp->choice == 2) /*integer */ | ^~ prtgene.c:110:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 110 | print_store_buf(temp, buf, buf_size, &len, fp); | ^~~~~~~~~~~~~~~ prtgene.c: In function ‘print_store_for_html’: prtgene.c:749:14: warning: variable ‘white_sp’ set but not used [-Wunused-but-set-variable] 749 | Char white_sp; | ^~~~~~~~ prtgene.c: In function ‘PrintSequenceToFile.isra.0’: prtgene.c:950:49: warning: ‘ (bp) on the genome’ directive writing 19 bytes into a region of size between 16 and 96 [-Wformat-overflow=] 950 | sprintf(temp, ": %s - %s (bp) on the genome", temp_1, temp_2); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘PrintSequenceToFile.isra.0’ at prtgene.c:950:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 25 and 105 bytes into a destination of size 101 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbidesk.a ar cru libncbidesk.a drawseq.o dotmatrx.o fea2seg.o fstyle.o smdlg1.o smdlg2.o smdlg3.o smtools.o styleman.o stylemui.o glbpic.o layout.o saldist.o saled.o salfiles.o salpanel.o salparam.o salsa.o seqfltr.o seqgraph.o seqgrphx.o seqmtrx.o seqpcc.o seqanal.o aacomp.o seqscrl.o valdlg.o vsm.o vsmfile.o vsmutil.o udvgraph.o udvopen.o udvpanel.o dotvibrant.o dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbidesk.a ../lib ranlib ../lib/libncbidesk.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvclick.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvclick.c:248: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvclick.c: In function ‘DDV_SendBSPSelectMsg_OLD’: ddvclick.c:979:13: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 979 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ ddvclick.c: In function ‘DDV_SendBSPSelectMsg’: ddvclick.c:1090:18: warning: variable ‘bDeselectAll’ set but not used [-Wunused-but-set-variable] 1090 | Boolean bDeselectAll=TRUE; | ^~~~~~~~~~~~ ddvclick.c: In function ‘DDV_DragProc’: ddvclick.c:2013:13: warning: unused variable ‘cur_pgp’ [-Wunused-variable] 2013 | ParaGPtr cur_pgp=NULL; | ^~~~~~~ ddvclick.c: In function ‘DDV_HoldProc’: ddvclick.c:2494:13: warning: unused variable ‘Scroll’ [-Wunused-variable] 2494 | Boolean Scroll=FALSE; | ^~~~~~ ddvclick.c:2490:13: warning: unused variable ‘cur_pgp’ [-Wunused-variable] 2490 | ParaGPtr cur_pgp=NULL; | ^~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ../include/ddvpanel.h:150, from ddvclick.c:252: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvclick.c:1823:13: warning: ‘EraseOutline’ defined but not used [-Wunused-function] 1823 | static void EraseOutline(PaneL p) { | ^~~~~~~~~~~~ ddvclick.c:1811:16: warning: ‘RectanglesAreSame’ defined but not used [-Wunused-function] 1811 | static Boolean RectanglesAreSame(RecT rc1, RecT rc2) { | ^~~~~~~~~~~~~~~~~ ddvclick.c:970:13: warning: ‘DDV_SendBSPSelectMsg_OLD’ defined but not used [-Wunused-function] 970 | static void DDV_SendBSPSelectMsg_OLD(DdvMainPtr dmp,Int4 bsp_coord,Int4 SeqAlign_coord, | ^~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c:611:13: warning: ‘DDV_GetSeqAlignCoordGivenCol’ defined but not used [-Wunused-function] 611 | static Int4 DDV_GetSeqAlignCoordGivenCol(DdvMainPtr dmp, Int4 Disp_coord) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c: In function ‘DDV_GetSeqNameGivenRow’: ddvclick.c:956:6: warning: ‘sip’ may be used uninitialized [-Wmaybe-uninitialized] 956 | if (!sip) | ^ ddvclick.c:942:12: note: ‘sip’ was declared here 942 | SeqIdPtr sip; | ^~~ In function ‘DDV_SendBSPSelectMsg’, inlined from ‘DDV_SelectRegion’ at ddvclick.c:2974:7, inlined from ‘DDV_ReleaseProc’ at ddvclick.c:2289:13: ddvclick.c:1127:9: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 1127 | slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddvclick.c: In function ‘DDV_ReleaseProc’: ddvclick.c:1091:18: note: ‘pgp’ was declared here 1091 | ParaGPtr pgp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvgraph.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvgraph.c:210: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvgraph.c: In function ‘DDV_DrawSequence’: ddvgraph.c:701:31: warning: unused variable ‘pos’ [-Wunused-variable] 701 | Int2 decal=1,i,x,y,pos=0; | ^~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ddvgraph.c:215: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvopen.c:372: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvopen.c: In function ‘DDV_GetAndCheckSeqAlign’: ddvopen.c:1739:17: warning: variable ‘nRet’ set but not used [-Wunused-but-set-variable] 1739 | Uint2 nRet=DVV_MSG_M_OK; | ^~~~ ddvopen.c: In function ‘DDV_FOpenAcceptProc’: ddvopen.c:1932:33: warning: variable ‘nRet’ set but not used [-Wunused-but-set-variable] 1932 | Uint2 nRet=DVV_MSG_M_OK,The_entityID; | ^~~~ ddvopen.c: In function ‘DDV_NetOpen_okProc’: ddvopen.c:2141:25: warning: variable ‘AccessType’ set but not used [-Wunused-but-set-variable] 2141 | Int2 AccessType,procval; | ^~~~~~~~~~ ddvopen.c: In function ‘DDV_StartMainWin_Slave’: ddvopen.c:2411:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 2411 | else | ^~~~ ddvopen.c:2417:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 2417 | if (!w) return(NULL); | ^~ ddvopen.c: In function ‘DDV_ImportBioseqDlg’: ddvopen.c:2819:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 2819 | ButtoN b; | ^ ddvopen.c: In function ‘DDV_HideDlg’: ddvopen.c:3135:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 3135 | ButtoN b; | ^ In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from ddvopen.c:376: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ddvopen.c:377: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvopen.c:2111:16: warning: ‘DDV_IsInt’ defined but not used [-Wunused-function] 2111 | static Boolean DDV_IsInt(CharPtr szAccess) | ^~~~~~~~~ ddvopen.c:1285:13: warning: ‘DDV_NoConvert’ defined but not used [-Wunused-function] 1285 | static void DDV_NoConvert(ButtoN g) { | ^~~~~~~~~~~~~ ddvopen.c:1272:13: warning: ‘DDV_Convert’ defined but not used [-Wunused-function] 1272 | static void DDV_Convert(ButtoN g) { | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ddvpanel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvpanel.c:389: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvpanel.c: In function ‘DDV_CreateViewerPanel’: ddvpanel.c:1177:8: warning: variable ‘cxChar’ set but not used [-Wunused-but-set-variable] 1177 | Int2 cxChar,cyChar; | ^~~~~~ ddvpanel.c: In function ‘DDV_DispStyles_OkProc’: ddvpanel.c:1543:21: warning: unused variable ‘szBuf’ [-Wunused-variable] 1543 | Char szBuf[15]={""}; | ^~~~~ ddvpanel.c: In function ‘DDV_ExportTexte’: ddvpanel.c:2799:40: warning: variable ‘browse’ set but not used [-Wunused-but-set-variable] 2799 | ButtoN chk2,chk3,chk4,chk5,chk6,browse,ok; | ^~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/ddvopen.h:140, from ../include/ddvmain.h:202, from ../include/ddvpanel.h:150, from ddvpanel.c:392: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3377:13: warning: ‘write_annot’ defined but not used [-Wunused-function] 3377 | static void write_annot(SeqAlignPtr align) | ^~~~~~~~~~~ ddvpanel.c:3296:13: warning: ‘DDV_MoveRightBoundaryRight’ defined but not used [-Wunused-function] 3296 | static void DDV_MoveRightBoundaryRight(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3290:13: warning: ‘DDV_MoveRightBoundaryLeft’ defined but not used [-Wunused-function] 3290 | static void DDV_MoveRightBoundaryLeft(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3284:13: warning: ‘DDV_MoveLeftBoundaryRight’ defined but not used [-Wunused-function] 3284 | static void DDV_MoveLeftBoundaryRight(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3278:13: warning: ‘DDV_MoveLeftBoundaryLeft’ defined but not used [-Wunused-function] 3278 | static void DDV_MoveLeftBoundaryLeft(IteM i) | ^~~~~~~~~~~~~~~~~~~~~~~~ ddvpanel.c:3272:13: warning: ‘DDV_MoveRowRight’ defined but not used [-Wunused-function] 3272 | static void DDV_MoveRowRight(IteM i) | ^~~~~~~~~~~~~~~~ ddvpanel.c:3266:13: warning: ‘DDV_MoveRowLeft’ defined but not used [-Wunused-function] 3266 | static void DDV_MoveRowLeft(IteM i) | ^~~~~~~~~~~~~~~ ddvpanel.c:3024:13: warning: ‘DDV_DeleteRow’ defined but not used [-Wunused-function] 3024 | static void DDV_DeleteRow(IteM i) | ^~~~~~~~~~~~~ ddvpanel.c: In function ‘DDV_SortPGPLineNum’: ddvpanel.c:2441:23: warning: ‘pgp’ may be used uninitialized [-Wmaybe-uninitialized] 2441 | n+=pgp->nLines; | ~~~^~~~~~~~ ddvpanel.c:2431:12: note: ‘pgp’ was declared here 2431 | ParaGPtr pgp; | ^~~ rm -f libddvlib.a ar cru libddvlib.a ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libddvlib.a ../lib ranlib ../lib/libddvlib.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF corematx.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from corematx.c:135: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dvncode.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from dvncode.c:69: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmmdb1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb1.c: In function ‘BiostrucAsnRead’: objmmdb1.c:90:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 90 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucIdFree’: objmmdb1.c:323:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 323 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucIdAsnRead’: objmmdb1.c:358:12: warning: unused variable ‘isError’ [-Wunused-variable] 358 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucSetAsnRead’: objmmdb1.c:547:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 547 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucAnnotSetAsnRead’: objmmdb1.c:716:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 716 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucResidueGraphSetAsnRead’: objmmdb1.c:885:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 885 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiostrucDescrFree’: objmmdb1.c:1015:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1015 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucDescrAsnRead’: objmmdb1.c:1059:12: warning: unused variable ‘isError’ [-Wunused-variable] 1059 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucHistoryAsnRead’: objmmdb1.c:1270:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1270 | AsnReadFunc func; | ^~~~ objmmdb1.c:1269:12: warning: unused variable ‘isError’ [-Wunused-variable] 1269 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucReplaceAsnRead’: objmmdb1.c:1450:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1450 | AsnReadFunc func; | ^~~~ objmmdb1.c:1449:12: warning: unused variable ‘isError’ [-Wunused-variable] 1449 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘VersionOfDatabase_version_of_databaseFree’: objmmdb1.c:1618:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1618 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiostrucSourceAsnRead’: objmmdb1.c:1652:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1652 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘VersionOfDatabase_version_of_databaseAsnRead’: objmmdb1.c:1753:12: warning: unused variable ‘isError’ [-Wunused-variable] 1753 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucGraphAsnRead’: objmmdb1.c:2001:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2001 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘BiomolDescrFree’: objmmdb1.c:2139:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2139 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘BiomolDescrAsnRead’: objmmdb1.c:2189:12: warning: unused variable ‘isError’ [-Wunused-variable] 2189 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueGraphAsnRead’: objmmdb1.c:2446:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2446 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘MoleculeGraphAsnRead’: objmmdb1.c:2654:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2654 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘InterResidueBondAsnRead’: objmmdb1.c:2856:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2856 | AsnReadFunc func; | ^~~~ objmmdb1.c:2855:12: warning: unused variable ‘isError’ [-Wunused-variable] 2855 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueAsnRead’: objmmdb1.c:3037:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3037 | AsnReadFunc func; | ^~~~ objmmdb1.c:3036:12: warning: unused variable ‘isError’ [-Wunused-variable] 3036 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ResidueGraphPntrFree’: objmmdb1.c:3177:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3177 | Pointer pnt; | ^~~ objmmdb1.c: In function ‘ResidueGraphPntrAsnRead’: objmmdb1.c:3212:12: warning: unused variable ‘isError’ [-Wunused-variable] 3212 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucGraphPntrAsnRead’: objmmdb1.c:3399:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3399 | AsnReadFunc func; | ^~~~ objmmdb1.c:3398:12: warning: unused variable ‘isError’ [-Wunused-variable] 3398 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘BiostrucResidueGraphSetPntrAsnRead’: objmmdb1.c:3565:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3565 | AsnReadFunc func; | ^~~~ objmmdb1.c:3564:12: warning: unused variable ‘isError’ [-Wunused-variable] 3564 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomAsnRead’: objmmdb1.c:3732:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3732 | AsnReadFunc func; | ^~~~ objmmdb1.c: In function ‘IntraResidueBondAsnRead’: objmmdb1.c:3924:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3924 | AsnReadFunc func; | ^~~~ objmmdb1.c:3923:12: warning: unused variable ‘isError’ [-Wunused-variable] 3923 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘ChiralCenterAsnRead’: objmmdb1.c:4097:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4097 | AsnReadFunc func; | ^~~~ objmmdb1.c:4096:12: warning: unused variable ‘isError’ [-Wunused-variable] 4096 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomPntrAsnRead’: objmmdb1.c:4286:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4286 | AsnReadFunc func; | ^~~~ objmmdb1.c:4285:12: warning: unused variable ‘isError’ [-Wunused-variable] 4285 | Boolean isError = FALSE; | ^~~~~~~ objmmdb1.c: In function ‘AtomPntrSetAsnRead’: objmmdb1.c:4441:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4441 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:73, from objmmdb1.c:5: ../include/objmmdb2.h: At top level: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objmmdb1.c: In function ‘BiostrucIdAsnRead’: objmmdb1.c:411:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 411 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:357:10: note: ‘choice’ was declared here 357 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘BiostrucDescrAsnRead’: objmmdb1.c:1126:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1126 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:1058:10: note: ‘choice’ was declared here 1058 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘BiomolDescrAsnRead’: objmmdb1.c:2284:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2284 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:2188:10: note: ‘choice’ was declared here 2188 | Uint1 choice; | ^~~~~~ In function ‘VersionOfDatabase_version_of_databaseAsnRead’, inlined from ‘BiostrucSourceAsnRead’ at objmmdb1.c:1695:54: objmmdb1.c:1802:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1802 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c: In function ‘BiostrucSourceAsnRead’: objmmdb1.c:1752:10: note: ‘choice’ was declared here 1752 | Uint1 choice; | ^~~~~~ objmmdb1.c: In function ‘ResidueGraphPntrAsnRead’: objmmdb1.c:3265:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3265 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb1.c:3211:10: note: ‘choice’ was declared here 3211 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmmdb2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb2.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb2.c: In function ‘BiostrucModelAsnRead’: objmmdb2.c:88:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 88 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ModelDescrFree’: objmmdb2.c:242:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 242 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘ModelDescrAsnRead’: objmmdb2.c:289:12: warning: unused variable ‘isError’ [-Wunused-variable] 289 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘ModelSpaceAsnRead’: objmmdb2.c:512:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 512 | AsnReadFunc func; | ^~~~ objmmdb2.c:511:12: warning: unused variable ‘isError’ [-Wunused-variable] 511 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘Coordinates_coordinatesFree’: objmmdb2.c:709:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 709 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘ModelCoordinateSetAsnRead’: objmmdb2.c:743:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 743 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘Coordinates_coordinatesAsnRead’: objmmdb2.c:831:12: warning: unused variable ‘isError’ [-Wunused-variable] 831 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘ReferenceFrameAsnRead’: objmmdb2.c:1063:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1063 | AsnReadFunc func; | ^~~~ objmmdb2.c:1062:12: warning: unused variable ‘isError’ [-Wunused-variable] 1062 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘CoordinatesFree’: objmmdb2.c:1193:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1193 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘CoordinatesAsnRead’: objmmdb2.c:1231:12: warning: unused variable ‘isError’ [-Wunused-variable] 1231 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘AtomicCoordinatesAsnRead’: objmmdb2.c:1420:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1420 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘Surface_surfaceFree’: objmmdb2.c:1640:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1640 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘SurfaceCoordinatesAsnRead’: objmmdb2.c:1686:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1686 | AsnReadFunc func; | ^~~~ objmmdb2.c:1685:12: warning: unused variable ‘isError’ [-Wunused-variable] 1685 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘Surface_surfaceAsnRead’: objmmdb2.c:1766:12: warning: unused variable ‘isError’ [-Wunused-variable] 1766 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘DensityCoordinatesAsnRead’: objmmdb2.c:2030:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2030 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ModelSpacePointsAsnRead’: objmmdb2.c:2263:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2263 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsFree’: objmmdb2.c:2404:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2404 | Pointer pnt; | ^~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsAsnRead’: objmmdb2.c:2439:12: warning: unused variable ‘isError’ [-Wunused-variable] 2439 | Boolean isError = FALSE; | ^~~~~~~ objmmdb2.c: In function ‘AtomicOccupanciesAsnRead’: objmmdb2.c:2615:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2615 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AlternateConformationIdsAsnRead’: objmmdb2.c:2760:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2760 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘ConformationEnsembleAsnRead’: objmmdb2.c:2890:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2890 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘IsotropicTemperatureFactorsAsnRead’: objmmdb2.c:3054:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3054 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘AnisotropicTemperatureFactorsAsnRead’: objmmdb2.c:3221:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3221 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘TMeshAsnRead’: objmmdb2.c:3426:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3426 | AsnReadFunc func; | ^~~~ objmmdb2.c: In function ‘TrianglesAsnRead’: objmmdb2.c:3626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3626 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objmmdb2.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objmmdb2.c: In function ‘CoordinatesAsnRead’: objmmdb2.c:1281:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1281 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:1230:10: note: ‘choice’ was declared here 1230 | Uint1 choice; | ^~~~~~ objmmdb2.c: In function ‘ModelDescrAsnRead’: objmmdb2.c:366:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 366 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:288:10: note: ‘choice’ was declared here 288 | Uint1 choice; | ^~~~~~ objmmdb2.c: In function ‘AtomicTemperatureFactorsAsnRead’: objmmdb2.c:2485:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2485 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c:2438:10: note: ‘choice’ was declared here 2438 | Uint1 choice; | ^~~~~~ In function ‘Coordinates_coordinatesAsnRead’, inlined from ‘ModelCoordinateSetAsnRead’ at objmmdb2.c:794:40: objmmdb2.c:877:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 877 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c: In function ‘ModelCoordinateSetAsnRead’: objmmdb2.c:830:10: note: ‘choice’ was declared here 830 | Uint1 choice; | ^~~~~~ In function ‘Surface_surfaceAsnRead’, inlined from ‘SurfaceCoordinatesAsnRead’ at objmmdb2.c:1729:32: objmmdb2.c:1828:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1828 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb2.c: In function ‘SurfaceCoordinatesAsnRead’: objmmdb2.c:1765:10: note: ‘choice’ was declared here 1765 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmmdb3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmmdb3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureSetAsnRead’: objmmdb3.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphPntrsFree’: objmmdb3.c:220:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 220 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘AtomPntrsAsnRead’: objmmdb3.c:443:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 443 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphAlignmentAsnRead’: objmmdb3.c:626:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 626 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ChemGraphInteractionAsnRead’: objmmdb3.c:824:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 824 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘SphereAsnRead’: objmmdb3.c:1024:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1024 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ConeAsnRead’: objmmdb3.c:1192:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1192 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘CylinderAsnRead’: objmmdb3.c:1372:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1372 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BrickAsnRead’: objmmdb3.c:1557:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1557 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘TransformAsnRead’: objmmdb3.c:1796:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1796 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucFeatureSetDescrFree’: objmmdb3.c:1921:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1921 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘Location_locationFree’: objmmdb3.c:2161:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2161 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2206:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2206 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘Property_propertyFree’: objmmdb3.c:2722:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2722 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘ColorPropAsnRead’: objmmdb3.c:2798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2798 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘CameraAsnRead’: objmmdb3.c:2986:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2986 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucScriptAsnRead’: objmmdb3.c:3171:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3171 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionPntrsAsnRead’: objmmdb3.c:3330:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3330 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionSimilarityAsnRead’: objmmdb3.c:3648:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3648 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘OtherFeatureAsnRead’: objmmdb3.c:3825:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3825 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucMoleculePntrAsnRead’: objmmdb3.c:3999:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3999 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘MoleculePntrsAsnRead’: objmmdb3.c:4342:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4342 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ResidueExplicitPntrsAsnRead’: objmmdb3.c:4505:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4505 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ResidueIntervalPntrAsnRead’: objmmdb3.c:4673:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4673 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionCoordinatesAsnRead’: objmmdb3.c:4845:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4845 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RegionBoundaryFree’: objmmdb3.c:4981:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4981 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘AlignStatsAsnRead’: objmmdb3.c:5212:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5212 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘RealValueAsnRead’: objmmdb3.c:5454:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5454 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘ModelSpacePointAsnRead’: objmmdb3.c:5615:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5615 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘MoveFree’: objmmdb3.c:5759:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 5759 | Pointer pnt; | ^~~ objmmdb3.c: In function ‘RotMatrixAsnRead’: objmmdb3.c:5967:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5967 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘TransMatrixAsnRead’: objmmdb3.c:6200:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6200 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘GLMatrixAsnRead’: objmmdb3.c:6379:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6379 | AsnReadFunc func; | ^~~~ objmmdb3.c: In function ‘BiostrucScriptStepAsnRead’: objmmdb3.c:6680:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6680 | AsnReadFunc func; | ^~~~ In file included from ../include/strimprt.h:72, from objmmdb3.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ objmmdb3.c: In function ‘MoveAsnRead’: objmmdb3.c:5839:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5839 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:5793:10: note: ‘choice’ was declared here 5793 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘ChemGraphPntrsAsnRead’: objmmdb3.c:307:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 307 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:257:10: note: ‘choice’ was declared here 257 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘RegionBoundaryAsnRead’: objmmdb3.c:5075:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5075 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:5021:10: note: ‘choice’ was declared here 5021 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘ResiduePntrsAsnRead’: objmmdb3.c:4213:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4213 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:4162:10: note: ‘choice’ was declared here 4162 | Uint1 choice; | ^~~~~~ In function ‘Region_regionAsnRead’, inlined from ‘RegionPntrsAsnRead’ at objmmdb3.c:3373:30: objmmdb3.c:3464:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3464 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘RegionPntrsAsnRead’: objmmdb3.c:3409:10: note: ‘choice’ was declared here 3409 | Uint1 choice; | ^~~~~~ objmmdb3.c: In function ‘BiostrucFeatureSetDescrAsnRead’: objmmdb3.c:2024:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2024 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c:1961:10: note: ‘choice’ was declared here 1961 | Uint1 choice; | ^~~~~~ In function ‘Property_propertyAsnRead’, inlined from ‘BiostrucFeatureAsnRead’ at objmmdb3.c:2265:34: objmmdb3.c:2691:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2691 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2626:10: note: ‘choice’ was declared here 2626 | Uint1 choice; | ^~~~~~ In function ‘Location_locationAsnRead’, inlined from ‘BiostrucFeatureAsnRead’ at objmmdb3.c:2272:34: objmmdb3.c:2370:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2370 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmmdb3.c: In function ‘BiostrucFeatureAsnRead’: objmmdb3.c:2308:10: note: ‘choice’ was declared here 2308 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objcn3d.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objcn3d.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleDictionaryAsnRead’: objcn3d.c:87:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 87 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dUserAnnotationsAsnRead’: objcn3d.c:251:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 251 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dColorAsnRead’: objcn3d.c:415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 415 | AsnReadFunc func; | ^~~~ objcn3d.c:414:12: warning: unused variable ‘isError’ [-Wunused-variable] 414 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dBackboneStyleAsnRead’: objcn3d.c:605:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 605 | AsnReadFunc func; | ^~~~ objcn3d.c:604:12: warning: unused variable ‘isError’ [-Wunused-variable] 604 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dGeneralStyleAsnRead’: objcn3d.c:789:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 789 | AsnReadFunc func; | ^~~~ objcn3d.c:788:12: warning: unused variable ‘isError’ [-Wunused-variable] 788 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dBackboneLabelStyleAsnRead’: objcn3d.c:972:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 972 | AsnReadFunc func; | ^~~~ objcn3d.c:971:12: warning: unused variable ‘isError’ [-Wunused-variable] 971 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleSettingsAsnRead’: objcn3d.c:1175:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1175 | AsnReadFunc func; | ^~~~ objcn3d.c:1174:12: warning: unused variable ‘isError’ [-Wunused-variable] 1174 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dStyleSettingsSetAsnRead’: objcn3d.c:1578:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1578 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dStyleTableItemAsnRead’: objcn3d.c:1707:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1707 | AsnReadFunc func; | ^~~~ objcn3d.c:1706:12: warning: unused variable ‘isError’ [-Wunused-variable] 1706 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dResidueRangeAsnRead’: objcn3d.c:1872:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1872 | AsnReadFunc func; | ^~~~ objcn3d.c:1871:12: warning: unused variable ‘isError’ [-Wunused-variable] 1871 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dMoleculeLocationAsnRead’: objcn3d.c:2035:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2035 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dObjectLocationAsnRead’: objcn3d.c:2198:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2198 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dUserAnnotationAsnRead’: objcn3d.c:2363:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2363 | AsnReadFunc func; | ^~~~ objcn3d.c: In function ‘Cn3dGLMatrixAsnRead’: objcn3d.c:2555:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2555 | AsnReadFunc func; | ^~~~ objcn3d.c:2554:12: warning: unused variable ‘isError’ [-Wunused-variable] 2554 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dVectorAsnRead’: objcn3d.c:2843:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2843 | AsnReadFunc func; | ^~~~ objcn3d.c:2842:12: warning: unused variable ‘isError’ [-Wunused-variable] 2842 | Boolean isError = FALSE; | ^~~~~~~ objcn3d.c: In function ‘Cn3dViewSettingsAsnRead’: objcn3d.c:3016:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3016 | AsnReadFunc func; | ^~~~ objcn3d.c:3015:12: warning: unused variable ‘isError’ [-Wunused-variable] 3015 | Boolean isError = FALSE; | ^~~~~~~ In file included from ../include/mapcn3d.h:8, from objcn3d.c:5: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/mmdbapi1.h:232, from ../include/mmdbapi.h:92, from mmdbapi.c:116: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi.c: In function ‘MakeAModelstruc’: mmdbapi.c:192:11: warning: unused variable ‘iCount’ [-Wunused-variable] 192 | Int4 iCount = 0; | ^~~~~~ mmdbapi.c:189:11: warning: unused variable ‘pdnmsCount’ [-Wunused-variable] 189 | PDNMS pdnmsCount = NULL; | ^~~~~~~~~~ mmdbapi.c: In function ‘AddPFBSelect’: mmdbapi.c:532:11: warning: unused variable ‘pmsdStruc’ [-Wunused-variable] 532 | PMSD pmsdStruc = NULL; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbapi1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi1.c:294: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi1.c: In function ‘FreeAtomicModelAsnLists’: mmdbapi1.c:1037:41: warning: unused variable ‘pcoThis’ [-Wunused-variable] 1037 | CoordinatesPtr pcoThis = NULL; | ^~~~~~~ mmdbapi1.c: In function ‘FetchBS’: mmdbapi1.c:1242:13: warning: unused variable ‘bIsNetwork’ [-Wunused-variable] 1242 | Boolean bIsNetwork = FALSE; | ^~~~~~~~~~ mmdbapi1.c: In function ‘FreeSurfaceModelAsnList’: mmdbapi1.c:1627:16: warning: variable ‘pvnX’ set but not used [-Wunused-but-set-variable] 1627 | ValNodePtr pvnX = NULL; | ^~~~ mmdbapi1.c: In function ‘MakeChemGraphNodeList’: mmdbapi1.c:2343:16: warning: variable ‘pvnThis’ set but not used [-Wunused-but-set-variable] 2343 | ValNodePtr pvnThis = NULL; | ^~~~~~~ mmdbapi1.c: In function ‘DoApplyTransform’: mmdbapi1.c:2573:8: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2573 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘DoReverseTransform’: mmdbapi1.c:2713:8: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2713 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘InstBSAnnotSet’: mmdbapi1.c:2860:8: warning: unused variable ‘psfsThis’ [-Wunused-variable] 2860 | PSFS psfsThis = NULL; | ^~~~~~~~ mmdbapi1.c:2859:22: warning: unused variable ‘pbsfThis’ [-Wunused-variable] 2859 | BiostrucFeaturePtr pbsfThis = NULL; | ^~~~~~~~ mmdbapi1.c:2855:9: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 2855 | PMSD pmsdThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:2978:19: warning: unused variable ‘loc1’ [-Wunused-variable] 2978 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c:2967:22: warning: unused variable ‘pbsf’ [-Wunused-variable] 2967 | BiostrucFeaturePtr pbsf=NULL; | ^~~~ mmdbapi1.c: In function ‘fnPBSFtoPSA’: mmdbapi1.c:3174:19: warning: unused variable ‘loc1’ [-Wunused-variable] 3174 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3408:19: warning: unused variable ‘loc1’ [-Wunused-variable] 3408 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi1.c:3397:22: warning: unused variable ‘pbsf’ [-Wunused-variable] 3397 | BiostrucFeaturePtr pbsf=NULL; | ^~~~ mmdbapi1.c: In function ‘InstallAlignedSlave’: mmdbapi1.c:3877:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 3877 | Int2 iTest; | ^~~~~ mmdbapi1.c:3874:9: warning: unused variable ‘psfsThis’ [-Wunused-variable] 3874 | PSFS psfsThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiostrucAddFeature’: mmdbapi1.c:4184:11: warning: variable ‘ncbiVast’ set but not used [-Wunused-but-set-variable] 4184 | Boolean ncbiVast = FALSE; | ^~~~~~~~ mmdbapi1.c:4182:11: warning: variable ‘pdbFootnote’ set but not used [-Wunused-but-set-variable] 4182 | Boolean pdbFootnote = FALSE; | ^~~~~~~~~~~ mmdbapi1.c:4181:11: warning: variable ‘pdbSite’ set but not used [-Wunused-but-set-variable] 4181 | Boolean pdbSite = FALSE; | ^~~~~~~ mmdbapi1.c:4172:15: warning: unused variable ‘pdvnThis’ [-Wunused-variable] 4172 | DValNodePtr pdvnThis = NULL; | ^~~~~~~~ mmdbapi1.c: In function ‘BiostrucAsnGet’: mmdbapi1.c:5289:18: warning: variable ‘aop’ set but not used [-Wunused-but-set-variable] 5289 | AsnOptionPtr aop; | ^~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:3083:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3083 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BiosToSeq’ at mmdbapi1.c:3083:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiosToSeq’: mmdbapi1.c:3127:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 3127 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi1.c:2974:37: note: ‘slavesip’ was declared here 2974 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ mmdbapi1.c: In function ‘fnPBSFtoPSA’: mmdbapi1.c:3275:52: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3275 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘fnPBSFtoPSA’ at mmdbapi1.c:3275:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3515:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 3515 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘BiostrToSeqAnnotSet’ at mmdbapi1.c:3515:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi1.c: In function ‘BiostrToSeqAnnotSet’: mmdbapi1.c:3559:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 3559 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi1.c:3404:37: note: ‘slavesip’ was declared here 3404 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ mmdbapi1.c: In function ‘InstBSAnnotSet’: mmdbapi1.c:2885:15: warning: ‘iMMDBId’ may be used uninitialized [-Wmaybe-uninitialized] 2885 | pdnmsThis = FindLoadedBiostruc(NULL, iMMDBId); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mmdbapi1.c:2853:8: note: ‘iMMDBId’ was declared here 2853 | Int4 iMMDBId; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbapi2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi2.c:159: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi2.c: In function ‘GetAtomLocs’: mmdbapi2.c:1471:9: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1471 | if (pmadThis) | ^ mmdbapi2.c: In function ‘AssignAtomLocId’: mmdbapi2.c:1537:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1537 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignBackBone’: mmdbapi2.c:1686:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1686 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignVirtual’: mmdbapi2.c:1790:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1790 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘AssignIons’: mmdbapi2.c:1846:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1846 | Int2 iTest = 0; | ^~~~~ mmdbapi2.c: In function ‘MolFromPDBChain’: mmdbapi2.c:1931:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1931 | Int2 iTest; | ^~~~~ mmdbapi2.c: In function ‘SeqStringFromMol’: mmdbapi2.c:1948:9: warning: unused variable ‘iTest’ [-Wunused-variable] 1948 | Int4 iTest =0; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbapi3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbapi3.c:207: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi3.c: In function ‘WritePDBHeader’: mmdbapi3.c:840:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 840 | if(org) | ^~ mmdbapi3.c:845:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 845 | src = orgstring; | ^~~ mmdbapi3.c:840:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 840 | if(org) | ^ mmdbapi3.c: In function ‘WritePDBRemarks’: mmdbapi3.c:1389:8: warning: unused variable ‘len’ [-Wunused-variable] 1389 | int len; | ^~~ mmdbapi3.c:1388:9: warning: unused variable ‘pcThis’ [-Wunused-variable] 1388 | Char pcThis[81]; | ^~~~~~ mmdbapi3.c:1387:21: warning: unused variable ‘pbsdrLast’ [-Wunused-variable] 1387 | BiostrucDescrPtr pbsdrLast = NULL; | ^~~~~~~~~ mmdbapi3.c:1386:21: warning: unused variable ‘pbsdrThis’ [-Wunused-variable] 1386 | BiostrucDescrPtr pbsdrThis = NULL; | ^~~~~~~~~ mmdbapi3.c: In function ‘WritePDBConnect’: mmdbapi3.c:1610:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 1610 | Int2 iTest; | ^~~~~ mmdbapi3.c: In function ‘WritePDBModelList’: mmdbapi3.c:1625:10: warning: variable ‘iCount’ set but not used [-Wunused-but-set-variable] 1625 | Int4 iCount; | ^~~~~~ mmdbapi3.c: In function ‘WriteKinAtom’: mmdbapi3.c:2287:11: warning: unused variable ‘pcElName’ [-Wunused-variable] 2287 | CharPtr pcElName = NULL; | ^~~~~~~~ mmdbapi3.c: In function ‘WriteFASTAMolecule’: mmdbapi3.c:3537:9: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 3537 | Int4 iTest =0; | ^~~~~ mmdbapi3.c: In function ‘WriteKinAtom’: mmdbapi3.c:2313:19: warning: ‘iTemp’ may be used uninitialized [-Wmaybe-uninitialized] 2313 | if (iTemp > TempsKine[iIndex]) return; /* too high */ | ^ mmdbapi3.c:2284:8: note: ‘iTemp’ was declared here 2284 | Int4 iTemp; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbapi4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/mmdbapi1.h:232, from ../include/mmdbapi.h:92, from mmdbapi4.c:106: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mmdbapi4.c: In function ‘RefreshSurface’: mmdbapi4.c:147:10: warning: unused variable ‘iVal’ [-Wunused-variable] 147 | Int4 iVal = 0; | ^~~~ mmdbapi4.c: In function ‘FreeCoordinatesAsnLists’: mmdbapi4.c:335:41: warning: variable ‘pdcThis’ set but not used [-Wunused-but-set-variable] 335 | DensityCoordinatesPtr pdcThis = NULL; | ^~~~~~~ mmdbapi4.c: In function ‘FreeRedundantAsn’: mmdbapi4.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ mmdbapi4.c:370:11: warning: unused variable ‘pdnmmThis’ [-Wunused-variable] 370 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ mmdbapi4.c:367:22: warning: unused variable ‘pbsmThis’ [-Wunused-variable] 367 | BiostrucModelPtr pbsmThis = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘RefreshModelAsnMem’: mmdbapi4.c:474:41: warning: unused variable ‘iCoordSets’ [-Wunused-variable] 474 | Int4 iCoordSets = 0; | ^~~~~~~~~~ mmdbapi4.c:465:41: warning: unused variable ‘pappThis’ [-Wunused-variable] 465 | AtomPntrsPtr pappThis = NULL; | ^~~~~~~~ mmdbapi4.c:464:41: warning: unused variable ‘pmspThis’ [-Wunused-variable] 464 | ModelSpacePointsPtr pmspThis = NULL; | ^~~~~~~~ mmdbapi4.c:463:41: warning: unused variable ‘pocThis’ [-Wunused-variable] 463 | AtomicOccupanciesPtr pocThis = NULL; | ^~~~~~~ mmdbapi4.c:458:41: warning: unused variable ‘paciThis’ [-Wunused-variable] 458 | AlternateConformationIdsPtr paciThis = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘RebuildChemGraphAsn’: mmdbapi4.c:931:33: warning: unused variable ‘bOK’ [-Wunused-variable] 931 | Boolean bOK = TRUE; | ^~~ mmdbapi4.c: In function ‘WriteASNChemGraphOnly’: mmdbapi4.c:1192:10: warning: unused variable ‘iHash’ [-Wunused-variable] 1192 | Int4 iHash = 0; | ^~~~~ mmdbapi4.c: In function ‘FreeSingleModel’: mmdbapi4.c:1336:11: warning: unused variable ‘pdnml’ [-Wunused-variable] 1336 | PDNML pdnml = NULL; | ^~~~~ mmdbapi4.c:1332:22: warning: unused variable ‘pbsmTemp’ [-Wunused-variable] 1332 | BiostrucModelPtr pbsmTemp = NULL; | ^~~~~~~~ mmdbapi4.c: In function ‘WriteAsnModelList’: mmdbapi4.c:1505:14: warning: unused variable ‘paioAIP’ [-Wunused-variable] 1505 | AsnIoPtr paioAIP = NULL; | ^~~~~~~ mmdbapi4.c:1502:11: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1502 | PMLD pmldThis = NULL; | ^~~~~~~~ mmdbapi4.c:1498:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1498 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ mmdbapi4.c:1496:22: warning: unused variable ‘pbsmThis’ [-Wunused-variable] 1496 | BiostrucModelPtr pbsmThis = NULL; | ^~~~~~~~ mmdbapi4.c:1495:17: warning: unused variable ‘pBSThis’ [-Wunused-variable] 1495 | BiostrucPtr pBSThis = NULL; | ^~~~~~~ mmdbapi4.c:1494:13: warning: unused variable ‘bFirst’ [-Wunused-variable] 1494 | Boolean bFirst = TRUE; | ^~~~~~ mmdbapi4.c:1493:10: warning: unused variable ‘iTest’ [-Wunused-variable] 1493 | Int2 iTest = 0; | ^~~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1741:19: warning: unused variable ‘loc1’ [-Wunused-variable] 1741 | ValNodePtr loc1 = NULL; | ^~~~ mmdbapi4.c: In function ‘WriteAsnModelList’: mmdbapi4.c:1632:13: warning: ‘bRet’ may be used uninitialized [-Wmaybe-uninitialized] 1632 | return bRet; | ^~~~ mmdbapi4.c:1503:13: note: ‘bRet’ was declared here 1503 | Boolean bRet; | ^~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1828:54: warning: ‘, mapped to sequence alignment’ directive writing 30 bytes into a region of size between 21 and 70 [-Wformat-overflow=] 1828 | sprintf (buf, "VAST structural alignment for %s, mapped to sequence alignment", buf2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BiostrucAnnotSetToSeqAnnot’ at mmdbapi4.c:1828:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 61 and 110 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mmdbapi4.c: In function ‘BiostrucAnnotSetToSeqAnnot’: mmdbapi4.c:1872:20: warning: ‘slavesip’ may be used uninitialized [-Wmaybe-uninitialized] 1872 | dsp->ids->next = slavesip; | ~~~~~~~~~~~~~~~^~~~~~~~~~ mmdbapi4.c:1737:37: note: ‘slavesip’ was declared here 1737 | SeqIdPtr mastersip = NULL, slavesip; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mmdbentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mmdbentr.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vastsubs.c vastsubs.c: In function ‘LoadSubsetTable’: vastsubs.c:212:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | fscanf(fd, "%d", &ndoms); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:239:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 239 | fscanf(fd, "%d", &nsubs); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:258:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 258 | fscanf(fd, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~ vastsubs.c:287:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 287 | fscanf(fd, "%8c", domid); | ^~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:296:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 296 | fscanf(fd, "%d", &n); | ^~~~~~~~~~~~~~~~~~~~ vastsubs.c:302:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 302 | fscanf(fd, "%d %d %d", &subset[j], &grps[j], &ranks[j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vastsubs.c:304:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | fscanf(fd, "\n"); | ^~~~~~~~~~~~~~~~ vastsubs.c:277:59: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized] 277 | SubsetArray[strindex + len++] = '\0'; | ~~~^~ vastsubs.c:202:23: note: ‘len’ was declared here 202 | Int4 i, j, n, len, strindex, ndoms, nsubs; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF prunebsc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/prunebsc.h:10, from prunebsc.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ prunebsc.c: In function ‘PruneFeatureSet’: prunebsc.c:220:22: warning: variable ‘bsfpDie’ set but not used [-Wunused-but-set-variable] 220 | BiostrucFeaturePtr bsfpDie, bsfp, bsfpnew = NULL; | ^~~~~~~ prunebsc.c: In function ‘PruneModel’: prunebsc.c:272:30: warning: variable ‘mcsDie’ set but not used [-Wunused-but-set-variable] 272 | ModelCoordinateSetPtr mcs, mcsDie, mcsnew = NULL; | ^~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:559:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 559 | if (vnp = ValNodeFindNext(currentbp->descr, NULL, BiomolDescr_name)) | ^~~ prunebsc.c:574:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 574 | if (vnp = ValNodeFindNext(het->descr, NULL, BiomolDescr_name)) | ^~~ prunebsc.c:663:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 663 | if (vnp = ValNodeFindNext(bsfsp->descr, NULL, BiostrucFeatureSetDescr_name)) | ^~~ prunebsc.c:102:8: warning: ‘mtype’ may be used uninitialized [-Wmaybe-uninitialized] 102 | Int4 mtype; | ^~~~~ In function ‘MakeHetGraphPtr’, inlined from ‘PruneBiostruc’ at prunebsc.c:544:9: prunebsc.c:182:7: warning: ‘mtype’ may be used uninitialized [-Wmaybe-uninitialized] 182 | switch(mtype) | ^~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:173:8: note: ‘mtype’ was declared here 173 | Int4 mtype, molecule_id; | ^~~~~ In file included from ../include/ncbilcl.h:159: In function ‘atoi’, inlined from ‘MakeHetGraphPtr’ at prunebsc.c:189:25, inlined from ‘PruneBiostruc’ at prunebsc.c:544:9: /usr/include/stdlib.h:483:16: warning: ‘mname’ may be used uninitialized [-Wmaybe-uninitialized] 483 | return (int) strtol (__nptr, (char **) NULL, 10); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:174:11: note: ‘mname’ was declared here 174 | CharPtr mname; | ^~~~~ prunebsc.c:562:9: warning: ‘chnid’ may be used uninitialized [-Wmaybe-uninitialized] 562 | if (*chnid == *chain) | ^~~~~~ prunebsc.c:522:11: note: ‘chnid’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~ prunebsc.c:579:8: warning: ‘mol_id’ may be used uninitialized [-Wmaybe-uninitialized] 579 | if (hetnum == mol_id) | ^ prunebsc.c:523:8: note: ‘mol_id’ was declared here 523 | Int4 mol_id, hetnum, molId1, molId2; | ^~~~~~ prunebsc.c:591:26: warning: ‘currenthet’ may be used uninitialized [-Wmaybe-uninitialized] 591 | currenthet->next = het; | ~~~~~~~~~~~~~~~~~^~~~~ prunebsc.c:528:29: note: ‘currenthet’ was declared here 528 | MoleculeGraphPtr bp, het, currenthet, currentbp; | ^~~~~~~~~~ In function ‘atoi’, inlined from ‘PruneBiostruc’ at prunebsc.c:577:14: /usr/include/stdlib.h:483:16: warning: ‘hetid’ may be used uninitialized [-Wmaybe-uninitialized] 483 | return (int) strtol (__nptr, (char **) NULL, 10); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prunebsc.c: In function ‘PruneBiostruc’: prunebsc.c:522:18: note: ‘hetid’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~ prunebsc.c:649:23: warning: ‘pirbnew’ may be used uninitialized [-Wmaybe-uninitialized] 649 | pirbnew->next = pirb; | ~~~~~~~~~~~~~~^~~~~~ prunebsc.c:529:29: note: ‘pirbnew’ was declared here 529 | InterResidueBondPtr pirb, pirbnew; | ^~~~~~~ In file included from ../include/ncbi.h:62: ../include/ncbistr.h:339:25: warning: ‘feature_name’ may be used uninitialized [-Wmaybe-uninitialized] 339 | #define StringICmp Nlm_StringICmp prunebsc.c:522:25: note: ‘feature_name’ was declared here 522 | CharPtr chnid, hetid, feature_name; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objcdd.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objcdd.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objcdd.c: In function ‘CddIdFree’: objcdd.c:53:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 53 | Pointer pnt; | ^~~ objcdd.c: In function ‘CddIdAsnRead’: objcdd.c:85:12: warning: unused variable ‘isError’ [-Wunused-variable] 85 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddIdSetAsnRead’: objcdd.c:248:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 248 | AsnReadFunc func; | ^~~~ objcdd.c:245:12: warning: unused variable ‘av’ [-Wunused-variable] 245 | DataVal av; | ^~ objcdd.c: In function ‘CddAsnRead’: objcdd.c:402:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 402 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddSetAsnRead’: objcdd.c:798:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 798 | AsnReadFunc func; | ^~~~ objcdd.c:795:12: warning: unused variable ‘av’ [-Wunused-variable] 795 | DataVal av; | ^~ objcdd.c: In function ‘CddTreeAsnRead’: objcdd.c:935:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 935 | AsnReadFunc func; | ^~~~ objcdd.c:934:12: warning: unused variable ‘isError’ [-Wunused-variable] 934 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddTreeSetAsnRead’: objcdd.c:1147:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1147 | AsnReadFunc func; | ^~~~ objcdd.c:1144:12: warning: unused variable ‘av’ [-Wunused-variable] 1144 | DataVal av; | ^~ objcdd.c: In function ‘CddPrefNodesAsnRead’: objcdd.c:1281:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1281 | AsnReadFunc func; | ^~~~ objcdd.c:1280:12: warning: unused variable ‘isError’ [-Wunused-variable] 1280 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddProjectAsnRead’: objcdd.c:1478:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1478 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddOrgRefAsnRead’: objcdd.c:1668:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1668 | AsnReadFunc func; | ^~~~ objcdd.c:1667:12: warning: unused variable ‘isError’ [-Wunused-variable] 1667 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddOrgRefSetAsnRead’: objcdd.c:1838:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1838 | AsnReadFunc func; | ^~~~ objcdd.c:1835:12: warning: unused variable ‘av’ [-Wunused-variable] 1835 | DataVal av; | ^~ objcdd.c: In function ‘CddPrefNodeDescrFree’: objcdd.c:1932:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1932 | Pointer pnt; | ^~~ objcdd.c: In function ‘CddPrefNodeDescrAsnRead’: objcdd.c:1967:12: warning: unused variable ‘isError’ [-Wunused-variable] 1967 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddPrefNodeDescrSetAsnRead’: objcdd.c:2130:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2130 | AsnReadFunc func; | ^~~~ objcdd.c:2127:12: warning: unused variable ‘av’ [-Wunused-variable] 2127 | DataVal av; | ^~ objcdd.c: In function ‘GlobalIdAsnRead’: objcdd.c:2263:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2263 | AsnReadFunc func; | ^~~~ objcdd.c:2262:12: warning: unused variable ‘isError’ [-Wunused-variable] 2262 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddRepeatAsnRead’: objcdd.c:2450:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2450 | AsnReadFunc func; | ^~~~ objcdd.c:2449:12: warning: unused variable ‘isError’ [-Wunused-variable] 2449 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddBookRefAsnRead’: objcdd.c:2627:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2627 | AsnReadFunc func; | ^~~~ objcdd.c:2626:12: warning: unused variable ‘isError’ [-Wunused-variable] 2626 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddDescrSetAsnRead’: objcdd.c:3183:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3183 | AsnReadFunc func; | ^~~~ objcdd.c:3180:12: warning: unused variable ‘av’ [-Wunused-variable] 3180 | DataVal av; | ^~ objcdd.c: In function ‘MatrixAsnRead’: objcdd.c:3315:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3315 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘TriangleAsnRead’: objcdd.c:3504:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3504 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘UpdateCommentFree’: objcdd.c:3641:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 3641 | Pointer pnt; | ^~~ objcdd.c: In function ‘UpdateCommentAsnRead’: objcdd.c:3685:12: warning: unused variable ‘isError’ [-Wunused-variable] 3685 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘UpdateAlignAsnRead’: objcdd.c:3889:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3889 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘RejectIdAsnRead’: objcdd.c:4064:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4064 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘FeatureEvidenceFree’: objcdd.c:4188:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 4188 | Pointer pnt; | ^~~ objcdd.c: In function ‘FeatureEvidenceAsnRead’: objcdd.c:4232:12: warning: unused variable ‘isError’ [-Wunused-variable] 4232 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘AlignAnnotAsnRead’: objcdd.c:4437:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4437 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘AlignAnnotSetAsnRead’: objcdd.c:4606:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4606 | AsnReadFunc func; | ^~~~ objcdd.c:4603:12: warning: unused variable ‘av’ [-Wunused-variable] 4603 | DataVal av; | ^~ objcdd.c: In function ‘DomainParentAsnRead’: objcdd.c:4738:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4738 | AsnReadFunc func; | ^~~~ objcdd.c:4737:12: warning: unused variable ‘isError’ [-Wunused-variable] 4737 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘SequenceTreeAsnRead’: objcdd.c:4919:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4919 | AsnReadFunc func; | ^~~~ objcdd.c:4918:12: warning: unused variable ‘isError’ [-Wunused-variable] 4918 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘AlgorithmTypeAsnRead’: objcdd.c:5107:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5107 | AsnReadFunc func; | ^~~~ objcdd.c:5106:12: warning: unused variable ‘isError’ [-Wunused-variable] 5106 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘SeqTreeNodeAsnRead’: objcdd.c:5410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5410 | AsnReadFunc func; | ^~~~ objcdd.c:5409:12: warning: unused variable ‘isError’ [-Wunused-variable] 5409 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘Children_footprintAsnRead’: objcdd.c:5595:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5595 | AsnReadFunc func; | ^~~~ objcdd.c:5594:12: warning: unused variable ‘isError’ [-Wunused-variable] 5594 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘NodeAnnotationAsnRead’: objcdd.c:5887:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5887 | AsnReadFunc func; | ^~~~ objcdd.c:5886:12: warning: unused variable ‘isError’ [-Wunused-variable] 5886 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddViewerRectAsnRead’: objcdd.c:6053:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6053 | AsnReadFunc func; | ^~~~ objcdd.c:6052:12: warning: unused variable ‘isError’ [-Wunused-variable] 6052 | Boolean isError = FALSE; | ^~~~~~~ objcdd.c: In function ‘CddViewerAsnRead’: objcdd.c:6235:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6235 | AsnReadFunc func; | ^~~~ objcdd.c: In function ‘CddScriptAsnRead’: objcdd.c:6410:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 6410 | AsnReadFunc func; | ^~~~ objcdd.c:6409:12: warning: unused variable ‘isError’ [-Wunused-variable] 6409 | Boolean isError = FALSE; | ^~~~~~~ In file included from objcdd.c:6: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from objcdd.c:7: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ objcdd.c: In function ‘CddIdAsnRead’: objcdd.c:134:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 134 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:84:10: note: ‘choice’ was declared here 84 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘CddPrefNodeDescrAsnRead’: objcdd.c:2016:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 2016 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:1966:10: note: ‘choice’ was declared here 1966 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘UpdateCommentAsnRead’: objcdd.c:3746:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3746 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:3684:10: note: ‘choice’ was declared here 3684 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘FeatureEvidenceAsnRead’: objcdd.c:4293:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 4293 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:4231:10: note: ‘choice’ was declared here 4231 | Uint1 choice; | ^~~~~~ objcdd.c: In function ‘CddDescrAsnRead’: objcdd.c:3007:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 3007 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c:2868:10: note: ‘choice’ was declared here 2868 | Uint1 choice; | ^~~~~~ In function ‘Children_childrenAsnRead’, inlined from ‘SeqTreeNodeAsnRead’ at objcdd.c:5467:34: objcdd.c:5561:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 5561 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objcdd.c: In function ‘SeqTreeNodeAsnRead’: objcdd.c:5510:10: note: ‘choice’ was declared here 5510 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cddutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddutil.c:336: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cddutil.c: In function ‘CddGetPmIds’: cddutil.c:649:17: warning: unused variable ‘bRefOpen’ [-Wunused-variable] 649 | Boolean bRefOpen = FALSE; | ^~~~~~~~ cddutil.c: In function ‘CddGetAnnotNames’: cddutil.c:807:19: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 807 | ValNodePtr vnp, vnpHead = NULL; | ^~~ cddutil.c: In function ‘CddCheckForRepeats’: cddutil.c:1034:7: warning: the address of ‘CddHasConsensus’ will always evaluate as ‘true’ [-Waddress] 1034 | if (!CddHasConsensus) return FALSE; | ^ cddutil.c:1013:23: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 1013 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddMSLDenDiagToMSLDenSeg’: cddutil.c:1663:30: warning: variable ‘lasts’ set but not used [-Wunused-but-set-variable] 1663 | Int4 lastm, lasts; | ^~~~~ cddutil.c:1663:23: warning: variable ‘lastm’ set but not used [-Wunused-but-set-variable] 1663 | Int4 lastm, lasts; | ^~~~~ cddutil.c: In function ‘SeqAlignInform’: cddutil.c:1938:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 1938 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddAlignInform’: cddutil.c:2125:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2125 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddPssmInform’: cddutil.c:2248:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2248 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddPosFreqInform’: cddutil.c:2306:22: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2306 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComputation’: cddutil.c:2368:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 2368 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c:2365:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2365 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddCposComputation’: cddutil.c:2571:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 2571 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c:2568:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 2568 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddRetrieveBioseqById’: cddutil.c:3379:15: warning: unused variable ‘retcode’ [-Wunused-variable] 3379 | Int2 retcode = 1; | ^~~~~~~ cddutil.c:3377:15: warning: unused variable ‘uid’ [-Wunused-variable] 3377 | Int4 uid = 0; | ^~~ cddutil.c: In function ‘CddCalculateTriangle’: cddutil.c:3534:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3534 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c:3534:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3534 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c: In function ‘CddCalculateQuerySim’: cddutil.c:3653:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3653 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c:3653:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3653 | if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; | ^~ cddutil.c: In function ‘CddConsensus’: cddutil.c:3853:49: warning: variable ‘m_end’ set but not used [-Wunused-but-set-variable] 3853 | Int4 m_last, m_frst, s_insert, m_end; | ^~~~~ cddutil.c: In function ‘CddCposCompPart1’: cddutil.c:4247:25: warning: variable ‘iStatus’ set but not used [-Wunused-but-set-variable] 4247 | Int2 iStatus; | ^~~~~~~ cddutil.c: In function ‘CddGetNewIndexForThreading’: cddutil.c:4392:14: warning: unused variable ‘Index’ [-Wunused-variable] 4392 | Int4 i, Index=0; | ^~~~~ cddutil.c: In function ‘CddCposComp’: cddutil.c:4474:33: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 4474 | ValNodePtr newRow, RowHead; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComp2KBP’: cddutil.c:4838:14: warning: the comparison will always evaluate as ‘true’ for the address of ‘ckptFileName’ will never be NULL [-Waddress] 4838 | if (NULL != ckptFileName) | ^~ cddutil.c:4752:27: note: ‘ckptFileName’ declared here 4752 | Char ckptFileName[PATH_MAX]; | ^~~~~~~~~~~~ cddutil.c:4745:59: warning: variable ‘RowHead’ set but not used [-Wunused-but-set-variable] 4745 | ValNodePtr ColumnHead, LetterHead, newRow, RowHead, newLetter; | ^~~~~~~ cddutil.c: In function ‘CddDumpTaxLinks’: cddutil.c:5727:16: warning: unused variable ‘txid’ [-Wunused-variable] 5727 | Int4 txid = 0, gi = 0; | ^~~~ cddutil.c: At top level: cddutil.c:6267:1: warning: "/*" within comment [-Wcomment] 6267 | /*---------------------------------------------------------------------------*/ | In file included from ../include/cddutil.h:205, from cddutil.c:353: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:589:25: warning: ‘CddFindSeqIdInSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 589 | static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location); | ^~~~~~~~~~~~~~~~~~~~ cddutil.c:4661:16: warning: ‘CddtakeMatrixCheckpoint’ defined but not used [-Wunused-function] 4661 | static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from cddutil.c:349: ../include/cdd.h:343:21: warning: ‘amp’ defined but not used [-Wunused-variable] 343 | static AsnModulePtr amp = ampx; | ^~~ ../include/cdd.h:342:19: warning: ‘at’ defined but not used [-Wunused-variable] 342 | static AsnTypePtr at = atx; | ^~ ../include/cdd.h:341:23: warning: ‘avn’ defined but not used [-Wunused-variable] 341 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/cdd.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "cdd.h24"; | ^~~~~~~~~~~ In file included from ../include/ncbi.h:62: cddutil.c: In function ‘CddRegularizeFileName’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ ../include/ncbistr.h:279:25: note: length computed here 279 | #define Nlm_StrLen strlen cddutil.c: In function ‘CddCopyMSLDenDiag’: cddutil.c:3015:25: warning: ‘ddpTail’ may be used uninitialized [-Wmaybe-uninitialized] 3015 | ddpTail->next = ddpNew; | ~~~~~~~~~~~~~~^~~~~~~~ cddutil.c:2992:29: note: ‘ddpTail’ was declared here 2992 | DenseDiagPtr ddp, ddpNew, ddpTail; | ^~~~~~~ cddutil.c: In function ‘CddCalculateTriangle’: cddutil.c:3535:7: warning: ‘buffer1’ may be used uninitialized [-Wmaybe-uninitialized] 3535 | if (buffer1) MemFree(buffer1); | ^ cddutil.c:3415:19: note: ‘buffer1’ was declared here 3415 | Uint1Ptr buffer1, buffer2, buffer3; | ^~~~~~~ cddutil.c:3524:22: warning: ‘pscTail’ may be used uninitialized [-Wmaybe-uninitialized] 3524 | pscTail->next = psc; pscTail = psc; psc = NULL; | ~~~~~~~~~~~~~~^~~~~ cddutil.c:3413:38: note: ‘pscTail’ was declared here 3413 | ScorePtr pscHead=NULL, psc, pscTail; | ^~~~~~~ cddutil.c: In function ‘CddDenDiagCposComp2KBP’: cddutil.c:4974:11: warning: ‘pssm’ may be used uninitialized [-Wmaybe-uninitialized] 4974 | return(pssm); | ^ cddutil.c:4764:27: note: ‘pssm’ was declared here 4764 | Seq_Mtf* pssm; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cddposutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cddposutil.c:119: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cddposutil.c: In function ‘CddfindThreshSequences’: cddposutil.c:359:15: warning: variable ‘thisId’ set but not used [-Wunused-but-set-variable] 359 | SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */ | ^~~~~~ cddposutil.c: In function ‘CddfindDenseDiagThreshSequences’: cddposutil.c:386:16: warning: variable ‘thisId’ set but not used [-Wunused-but-set-variable] 386 | SeqIdPtr thisId; /* Ids of target sequences in current SeqAlign */ | ^~~~~~ cddposutil.c: In function ‘CddposFreqsToMatrix’: cddposutil.c:1038:45: warning: operation on ‘*(*(posSearch->posPrivateMatrix + (sizetype)((long unsigned int)length * 8)) + (sizetype)((long unsigned int)a * 4))’ may be undefined [-Wsequence-point] 1038 | posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN; cddposutil.c: In function ‘CddposDenseDiagDemographics’: cddposutil.c:1094:17: warning: unused variable ‘is_new_id’ [-Wunused-variable] 1094 | Boolean is_new_id = FALSE; | ^~~~~~~~~ cddposutil.c:1093:17: warning: unused variable ‘segIndex’ [-Wunused-variable] 1093 | Int4 segIndex; /*Index for which piece we are at*/ | ^~~~~~~~ cddposutil.c:1092:25: warning: variable ‘startS’ set but not used [-Wunused-but-set-variable] 1092 | Int4 startQ, startS; /*Indices into array of starting positions*/ | ^~~~~~ cddposutil.c:1092:17: warning: variable ‘startQ’ set but not used [-Wunused-but-set-variable] 1092 | Int4 startQ, startS; /*Indices into array of starting positions*/ | ^~~~~~ cddposutil.c:1091:17: warning: unused variable ‘curId’ [-Wunused-variable] 1091 | SeqIdPtr curId; /*Used to compare seq. coming from different SeqAligns*/ | ^~~~~ cddposutil.c: In function ‘CddSetUpSearchInternalByLoc’: cddposutil.c:1246:53: warning: unused variable ‘last_length_adjustment’ [-Wunused-variable] 1246 | index, length, length_adjustment=0, last_length_adjustment, min_query_length; | ^~~~~~~~~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddSetUpSearchWithReadDb’: cddposutil.c:2040:55: warning: variable ‘final_db_seq’ set but not used [-Wunused-but-set-variable] 2040 | Int4 final_virtual_db_seq=0, final_db_seq=0; | ^~~~~~~~~~~~ cddposutil.c:2006:44: warning: unused variable ‘virtual_oid_bit’ [-Wunused-variable] 2006 | Uint4 oid_bit, virtual_oid_bit; | ^~~~~~~~~~~~~~~ cddposutil.c:2006:35: warning: unused variable ‘oid_bit’ [-Wunused-variable] 2006 | Uint4 oid_bit, virtual_oid_bit; | ^~~~~~~ cddposutil.c:2005:47: warning: unused variable ‘virtual_mask_index’ [-Wunused-variable] 2005 | Int4 mask_index, virtual_mask_index; | ^~~~~~~~~~~~~~~~~~ cddposutil.c:2005:35: warning: unused variable ‘mask_index’ [-Wunused-variable] 2005 | Int4 mask_index, virtual_mask_index; | ^~~~~~~~~~ cddposutil.c:2004:31: warning: unused variable ‘alias_oidlist’ [-Wunused-variable] 2004 | OIDListPtr alias_oidlist; | ^~~~~~~~~~~~~ cddposutil.c:2003:33: warning: unused variable ‘use_private_gilist’ [-Wunused-variable] 2003 | Boolean use_private_gilist = FALSE; | ^~~~~~~~~~~~~~~~~~ cddposutil.c:2000:23: warning: unused variable ‘vnp’ [-Wunused-variable] 2000 | ValNodePtr vnp; | ^~~ cddposutil.c: In function ‘CddposReadAlignment’: cddposutil.c:2226:16: warning: variable ‘alignPos’ set but not used [-Wunused-but-set-variable] 2226 | Int4 alignPos, queryOffset, subjectOffset, matchLength; | ^~~~~~~~ In file included from ../include/cddutil.h:205, from cddposutil.c:131: ../include/objcdd.h: At top level: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:507:27: warning: ‘CddReadBlastOptions’ declared ‘static’ but never defined [-Wunused-function] 507 | static PGPBlastOptionsPtr CddReadBlastOptions(BioseqPtr bsp, Int4 iPseudo, CharPtr matrix_name); | ^~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:512:13: warning: ‘BlastKarlinBlkCopy’ declared ‘static’ but never defined [-Wunused-function] 512 | static void BlastKarlinBlkCopy(BLAST_KarlinBlkPtr kbp_in,BLAST_KarlinBlkPtr kbp_out); | ^~~~~~~~~~~~~~~~~~ ../include/cddutil.h:516:13: warning: ‘CddputMatrixKbp’ declared ‘static’ but never defined [-Wunused-function] 516 | static void CddputMatrixKbp(FILE *checkFile, BLAST_KarlinBlkPtr kbp, | ^~~~~~~~~~~~~~~ ../include/cddutil.h:518:13: warning: ‘CddputMatrixMatrix’ declared ‘static’ but never defined [-Wunused-function] 518 | static void CddputMatrixMatrix(FILE *checkFile, | ^~~~~~~~~~~~~~~~~~ ../include/cddutil.h:522:16: warning: ‘CddtakeMatrixCheckpoint’ declared ‘static’ but never defined [-Wunused-function] 522 | static Boolean CddtakeMatrixCheckpoint(compactSearchItems *compactSearch, | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:589:25: warning: ‘CddFindSeqIdInSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 589 | static SeqIdPtr CddFindSeqIdInSeqLoc(SeqLocPtr location); | ^~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:591:25: warning: ‘CddRelocateSeqLoc’ declared ‘static’ but never defined [-Wunused-function] 591 | static void CddRelocateSeqLoc(SeqLocPtr location, SeqIdPtr sip, Int4 *ali); | ^~~~~~~~~~~~~~~~~ ../include/cddutil.h:592:25: warning: ‘CddSeqLocInExpAlign’ declared ‘static’ but never defined [-Wunused-function] 592 | static Int4 CddSeqLocInExpAlign(SeqLocPtr location, CddExpAlignPtr eap); | ^~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:593:25: warning: ‘CddFindSeqIdInAlignAnnot’ declared ‘static’ but never defined [-Wunused-function] 593 | static SeqIdPtr CddFindSeqIdInAlignAnnot(AlignAnnotPtr oldannot); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/cddutil.h:623:24: warning: ‘HitYet’ declared ‘static’ but never defined [-Wunused-function] 623 | static Boolean HitYet(Int4Ptr retlist, Int4 index, Int4 i); | ^~~~~~ ../include/cddutil.h:649:16: warning: ‘CddFixForXML’ declared ‘static’ but never defined [-Wunused-function] 649 | static CharPtr CddFixForXML(CharPtr pc); | ^~~~~~~~~~~~ cddposutil.c:971:13: warning: ‘CddfreePosFreqs’ defined but not used [-Wunused-function] 971 | static void CddfreePosFreqs(Nlm_FloatHi ** posFreqs, Int4 length) | ^~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddposComputeSequenceWeights’: cddposutil.c:829:10: warning: ‘Sigma’ may be used uninitialized [-Wmaybe-uninitialized] 829 | if (Sigma > 0) { | ^ cddposutil.c:747:16: note: ‘Sigma’ was declared here 747 | Nlm_FloatHi Sigma; /*Number of different characters occurring in matches | ^~~~~ cddposutil.c:840:35: warning: ‘intervalSigma’ may be used uninitialized [-Wmaybe-uninitialized] 840 | posSearch->posSigma[qplace] = intervalSigma; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ cddposutil.c:749:16: note: ‘intervalSigma’ was declared here 749 | Nlm_FloatHi intervalSigma; /*Same as Sigma but includes identical columns*/ | ^~~~~~~~~~~~~ cddposutil.c: In function ‘CddposDemographics’: cddposutil.c:1199:24: warning: ‘retrievalOffset’ may be used uninitialized [-Wmaybe-uninitialized] 1199 | subjectOffset = curSegs->starts[startS] - retrievalOffset; | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cddposutil.c:1154:44: note: ‘retrievalOffset’ was declared here 1154 | Int4 queryOffset, subjectOffset, retrievalOffset; /*offsets needed to make a match align*/ | ^~~~~~~~~~~~~~~ cddposutil.c: In function ‘CddSetUpSearchWithReadDb’: cddposutil.c:2041:86: warning: ‘total_virtual_mask’ may be used uninitialized [-Wmaybe-uninitialized] 2041 | Int4 mask, oid, virtual_oid, maskindex, virtual_mask_index, total_virtual_mask, base; | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF objmime.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmime.c:76: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmime.c: In function ‘NcbiMimeAsn1Free’: objmime.c:126:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 126 | Pointer pnt; | ^~~ objmime.c: In function ‘NcbiMimeAsn1AsnRead’: objmime.c:173:12: warning: unused variable ‘isError’ [-Wunused-variable] 173 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘Data_dataFree’: objmime.c:382:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 382 | Pointer pnt; | ^~~ objmime.c: In function ‘EntrezGeneralAsnRead’: objmime.c:428:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 428 | AsnReadFunc func; | ^~~~ objmime.c:427:12: warning: unused variable ‘isError’ [-Wunused-variable] 427 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘Data_dataAsnRead’: objmime.c:522:12: warning: unused variable ‘isError’ [-Wunused-variable] 522 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘BiostrucAlignAsnRead’: objmime.c:801:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 801 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucAlignSeqAsnRead’: objmime.c:1027:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1027 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucSeqAsnRead’: objmime.c:1220:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1220 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘BiostrucSeqsAsnRead’: objmime.c:1415:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1415 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘SeqAlignData_seq_align_dataFree’: objmime.c:1613:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1613 | Pointer pnt; | ^~~ objmime.c: In function ‘BiostrucSeqsAlignsCddAsnRead’: objmime.c:1647:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1647 | AsnReadFunc func; | ^~~~ objmime.c: In function ‘SeqAlignData_seq_align_dataAsnRead’: objmime.c:1734:12: warning: unused variable ‘isError’ [-Wunused-variable] 1734 | Boolean isError = FALSE; | ^~~~~~~ objmime.c: In function ‘BundleSeqsAlignsAsnRead’: objmime.c:1973:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1973 | AsnReadFunc func; | ^~~~ In file included from ../include/mapmime.h:4, from objmime.c:81: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/mapmime.h:6: ../include/objcdd.h:642:37: warning: ‘Children_childrenFree’ declared ‘static’ but never defined [-Wunused-function] 642 | static Children_childrenPtr LIBCALL Children_childrenFree PROTO ((Children_childrenPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:643:37: warning: ‘Children_childrenAsnRead’ declared ‘static’ but never defined [-Wunused-function] 643 | static Children_childrenPtr LIBCALL Children_childrenAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:644:24: warning: ‘Children_childrenAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 644 | static Boolean LIBCALL Children_childrenAsnWrite PROTO (( Children_childrenPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:666:38: warning: ‘Children_footprintFree’ declared ‘static’ but never defined [-Wunused-function] 666 | static Children_footprintPtr LIBCALL Children_footprintFree PROTO ((Children_footprintPtr )); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:667:38: warning: ‘Children_footprintNew’ declared ‘static’ but never defined [-Wunused-function] 667 | static Children_footprintPtr LIBCALL Children_footprintNew PROTO (( void )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:668:38: warning: ‘Children_footprintAsnRead’ declared ‘static’ but never defined [-Wunused-function] 668 | static Children_footprintPtr LIBCALL Children_footprintAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objcdd.h:669:24: warning: ‘Children_footprintAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 669 | static Boolean LIBCALL Children_footprintAsnWrite PROTO (( Children_footprintPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ objmime.c: In function ‘NcbiMimeAsn1AsnRead’: objmime.c:235:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 235 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c:172:10: note: ‘choice’ was declared here 172 | Uint1 choice; | ^~~~~~ In function ‘Data_dataAsnRead’, inlined from ‘EntrezGeneralAsnRead’ at objmime.c:471:26: objmime.c:584:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 584 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c: In function ‘EntrezGeneralAsnRead’: objmime.c:521:10: note: ‘choice’ was declared here 521 | Uint1 choice; | ^~~~~~ In function ‘SeqAlignData_seq_align_dataAsnRead’, inlined from ‘BiostrucSeqsAlignsCddAsnRead’ at objmime.c:1683:44: objmime.c:1780:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1780 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmime.c: In function ‘BiostrucSeqsAlignsCddAsnRead’: objmime.c:1733:10: note: ‘choice’ was declared here 1733 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF strucapi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from strucapi.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdalgs.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdatd.c thrdatd.c: In function ‘atd’: thrdatd.c:859:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 859 | for(i=0;ial[i]); printf("sai->al\n"); | ^~~ thrdatd.c:859:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 859 | for(i=0;ial[i]); printf("sai->al\n"); | ^~~~~~ thrdatd.c:860:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 860 | for(i=0;inmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n"); | ^~~ thrdatd.c:860:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 860 | for(i=0;inmt;i++) printf("%d ",sai->sq[i]); printf("sai->sq\n"); | ^~~~~~ thrdatd.c:862:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 862 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~ thrdatd.c:862:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 862 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~~~~ thrdatd.c:863:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 863 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~ thrdatd.c:863:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 863 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~~~~ thrdatd.c:864:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 864 | for(i=0;inlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n"); | ^~~ thrdatd.c:864:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 864 | for(i=0;inlp;i++) printf("%d ",sli->lp[i]); printf("sli->lp\n"); | ^~~~~~ thrdatd.c:865:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 865 | for(i=0;inmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n"); | ^~~ thrdatd.c:865:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 865 | for(i=0;inmt;i++) printf("%d ",sli->cr[i]); printf("sli->cr\n"); | ^~~~~~ thrdatd.c:1014:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1014 | for(k=0;kal[k]); printf("sai->al\n"); | ^~~ thrdatd.c:1014:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1014 | for(k=0;kal[k]); printf("sai->al\n"); | ^~~~~~ thrdatd.c:1015:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1015 | for(k=0;ksq[k]); printf("sai->sq\n"); | ^~~ thrdatd.c:1015:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1015 | for(k=0;ksq[k]); printf("sai->sq\n"); | ^~~~~~ thrdatd.c:1017:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1017 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~ thrdatd.c:1017:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1017 | for(i=0;ino[i]); printf("sli->no\n"); | ^~~~~~ thrdatd.c:1018:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1018 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~ thrdatd.c:1018:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1018 | for(i=0;ico[i]); printf("sli->co\n"); | ^~~~~~ thrdatd.c:1019:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1019 | for(i=0;ilp[i]); printf("sli->lp\n"); | ^~~ thrdatd.c:1019:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1019 | for(i=0;ilp[i]); printf("sli->lp\n"); | ^~~~~~ thrdatd.c:1020:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1020 | for(i=0;icr[i]); printf("sli->cr\n"); | ^~~ thrdatd.c:1020:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1020 | for(i=0;icr[i]); printf("sli->cr\n"); | ^~~~~~ thrdatd.c:1244:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1244 | for(i=0;igss[i]); free(spe->gss); | ^~~ thrdatd.c:1244:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1244 | for(i=0;igss[i]); free(spe->gss); | ^~~~ thrdatd.c:1251:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1251 | for(i=0; inrr[i]); free(spn->nrr); | ^~~ thrdatd.c:1251:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1251 | for(i=0; inrr[i]); free(spn->nrr); | ^~~~ thrdatd.c:1255:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1255 | for(i=0; inrp[i]); free(spn->nrp); | ^~~ thrdatd.c:1255:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1255 | for(i=0; inrp[i]); free(spn->nrp); | ^~~~ thrdatd.c:1259:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1259 | for(i=0; inrf[i]); free(spn->nrf); | ^~~ thrdatd.c:1259:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1259 | for(i=0; inrf[i]); free(spn->nrf); | ^~~~ thrdatd.c:1260:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1260 | for(i=0; ifrf[i]); free(spn->frf); | ^~~ thrdatd.c:1260:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1260 | for(i=0; ifrf[i]); free(spn->frf); | ^~~~ thrdatd.c:201:8: warning: variable ‘hh’ set but not used [-Wunused-but-set-variable] 201 | float hh; | ^~ thrdatd.c:198:9: warning: variable ‘rf’ set but not used [-Wunused-but-set-variable] 198 | int rf; /* Reference position for a core element */ | ^~ thrdatd.c:188:17: warning: unused variable ‘m’ [-Wunused-variable] 188 | int i,j,k,l,m,n; /* Counters */ | ^ thrdatd.c:188:15: warning: unused variable ‘l’ [-Wunused-variable] 188 | int i,j,k,l,m,n; /* Counters */ | ^ thrdatd.c:171:9: warning: variable ‘nrp’ set but not used [-Wunused-but-set-variable] 171 | int nrp; /* Number of residue-peptide contacts in motif */ | ^~~ thrdatd.c:170:9: warning: variable ‘nrr’ set but not used [-Wunused-but-set-variable] 170 | int nrr; /* Number of residue-residue contacts in motif */ | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdbwfi.c thrdbwfi.c: In function ‘bwfi’: thrdbwfi.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] 114 | } | ^ thrdbwfi.c:89:30: warning: ‘nz’ may be used uninitialized [-Wmaybe-uninitialized] 89 | cw=0.; ct=ttb->mx; for(i=0; i<=nz; i++) { | ~^~~~ thrdbwfi.c:63:9: note: ‘nz’ was declared here 63 | int nz; /* Number of threads with non-zero Boltzmann weight */ | ^~ thrdbwfi.c:64:9: warning: ‘nt’ may be used uninitialized [-Wmaybe-uninitialized] 64 | int nt; /* Number of threads within specified ensemble cutoff */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdcpal.c thrdcpal.c: In function ‘cpal’: thrdcpal.c:210:1: warning: control reaches end of non-void function [-Wreturn-type] 210 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdcpll.c thrdcpll.c: In function ‘cpll’: thrdcpll.c:74:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 74 | int nrt; /* Number of residue types */ | ^~~ thrdcpll.c:229:1: warning: control reaches end of non-void function [-Wreturn-type] 229 | } | ^ thrdcpll.c:220:29: warning: ‘r2’ may be used uninitialized [-Wmaybe-uninitialized] 220 | cl->rf.t2[k]=r2; | ~~~~~~~~~~~~^~~ thrdcpll.c:78:12: note: ‘r2’ was declared here 78 | int r1,r2; /* Motif residue positions */ | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdcprl.c thrdcprl.c: In function ‘cprl’: thrdcprl.c:261:1: warning: control reaches end of non-void function [-Wreturn-type] 261 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdcxei.c thrdcxei.c: In function ‘cxei’: thrdcxei.c:94:15: warning: variable ‘ms’ set but not used [-Wunused-but-set-variable] 94 | int ntot, ms; | ^~ thrdcxei.c:205:1: warning: control reaches end of non-void function [-Wreturn-type] 205 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrddgri.c thrddgri.c: In function ‘g’: thrddgri.c:72:9: warning: variable ‘s0’ set but not used [-Wunused-but-set-variable] 72 | int s0; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdrsmp.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdsal0.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdsalr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdsalu.c thrdsalu.c: In function ‘salu’: thrdsalu.c:83:1: warning: control reaches end of non-void function [-Wreturn-type] 83 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdsgoi.c thrdsgoi.c: In function ‘sgoi’: thrdsgoi.c:98:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 98 | for(i=0; i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdslo0.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdslor.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdslou.c thrdslou.c: In function ‘slou’: thrdslou.c:114:1: warning: control reaches end of non-void function [-Wreturn-type] 114 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdspci.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdspea.c thrdspea.c: In function ‘spea’: thrdspea.c:91:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 91 | int nrt; /* Number of residue types in potential */ | ^~~ thrdspea.c:189:1: warning: control reaches end of non-void function [-Wreturn-type] 189 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdspel.c thrdspel.c: In function ‘spel’: thrdspel.c:88:9: warning: variable ‘nrt’ set but not used [-Wunused-but-set-variable] 88 | int nrt; /* Number of residue types in potential */ | ^~~ thrdspel.c:188:1: warning: control reaches end of non-void function [-Wreturn-type] 188 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdspni.c thrdspni.c: In function ‘spni’: thrdspni.c:238:1: warning: control reaches end of non-void function [-Wreturn-type] 238 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdttb0.c thrdttb0.c: In function ‘ttb0’: thrdttb0.c:75:1: warning: control reaches end of non-void function [-Wreturn-type] 75 | } | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdttbi.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF thrdzsc.c thrdzsc.c: In function ‘zsc’: thrdzsc.c:107:11: warning: unused variable ‘gs’ [-Wunused-variable] 107 | int g,gs; | ^~ thrdzsc.c:102:20: warning: unused variable ‘zsc’ [-Wunused-variable] 102 | float tg,tgp,tgm,zsc; /* Energy of shuffled sequence */ | ^~~ thrdzsc.c:95:9: warning: unused variable ‘ps’ [-Wunused-variable] 95 | int ps,ms,cs, | ^~ thrdzsc.c:80:9: warning: unused variable ‘temp’ [-Wunused-variable] 80 | int temp; /* Random index of the query sequence */ | ^~~~ thrdzsc.c:79:9: warning: unused variable ‘kk’ [-Wunused-variable] 79 | kk,itr,ii,jj; /* Counters */ | ^~ thrdzsc.c:369:1: warning: control reaches end of non-void function [-Wreturn-type] 369 | } | ^ thrdzsc.c:357:46: warning: ‘tg_max’ may be used uninitialized [-Wmaybe-uninitialized] 357 | ttb->zsc[i_max]=ScalingFactor*(tg_max-avg)/disp; | ~~~~~~~^~~~~ thrdzsc.c:103:9: note: ‘tg_max’ was declared here 103 | float tg_max; /* Energy of a given thread */ | ^~~~~~ rm -f libncbimmdb.a ar cru libncbimmdb.a corematx.o dvncode.o objmmdb1.o objmmdb2.o objmmdb3.o objcn3d.o mmdbapi.o mmdbapi1.o mmdbapi2.o mmdbapi3.o mmdbapi4.o mmdbentr.o vastsubs.o prunebsc.o objcdd.o cddutil.o cddposutil.o objmime.o strucapi.o thrdalgs.o thrdatd.o thrdbwfi.o thrdcpal.o thrdcpll.o thrdcprl.o thrdcxei.o thrddgri.o thrdrsmp.o thrdsal0.o thrdsalr.o thrdsalu.o thrdsgoi.o thrdslo0.o thrdslor.o thrdslou.o thrdspci.o thrdspea.o thrdspel.o thrdspni.o thrdttb0.o thrdttbi.o thrdzsc.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbimmdb.a ../lib ranlib ../lib/libncbimmdb.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF csim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from csim.c:74: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ csim.c: In function ‘set_pam_200’: csim.c:163:29: warning: missing braces around initializer [-Wmissing-braces] 163 | static Int2 wgts[23][23] = { /* the PAM200 matrix */ | ^ 164 | 165 | 2,-2, 0, 0,-2,-1, 0, 1,-1,-1,-2,-1,-1,-3, 1, 1, 1,-5,-3, 0, 1, 1, 0, | { } 166 | -2, 5, 0,-1,-3, 1,-1,-3, 1,-2,-2, 2, 0,-3, 0, 0,-1, 1,-4,-2, 0, 1, 0, | { } 167 | 0, 0, 2, 2,-3, 0, 1, 0, 1,-1,-2, 1,-2,-2, 0, 1, 0,-4,-1,-2, 3, 2, 0, | { } 168 | 0,-1, 2, 3,-4, 1, 3, 0, 0,-2,-3, 0,-2,-4,-1, 0, 0,-6,-3,-2, 4, 3, 0, | { } 169 | -2,-3,-3,-4, 8,-4,-4,-3,-3,-2,-5,-4,-4,-4,-2, 0,-2,-6, 0,-2,-3,-3, 0, | { } 170 | -1, 1, 0, 1,-4, 4, 2,-1, 2,-2,-1, 0,-1,-4, 0,-1,-1,-4,-3,-2, 2, 4, 0, | { } 171 | 0,-1, 1, 3,-4, 2, 3, 0, 0,-2,-3, 0,-2,-4, 0, 0, 0,-6,-3,-2, 3, 4, 0, | { } 172 | 1,-3, 0, 0,-3,-1, 0, 4,-2,-2,-3,-2,-3,-3,-1, 1, 0,-5,-4,-1, 1, 0, 0, | { } 173 | -1, 1, 1, 0,-3, 2, 0,-2, 5,-2,-2, 0,-2,-1, 0,-1,-1,-3, 0,-2, 2, 2, 0, | { } 174 | -1,-2,-1,-2,-2,-2,-2,-2,-2, 4, 2,-1, 2, 1,-2,-1, 0,-5,-1, 3,-1,-1, 0, | { } 175 | -2,-2,-2,-3,-5,-1,-3,-3,-2, 2, 4,-2, 3, 1,-2,-2,-1,-4,-1, 1,-2,-1, 0, | { } 176 | -1, 2, 1, 0,-4, 0, 0,-2, 0,-1,-2, 4, 1,-4,-1, 0, 0,-3,-4,-2, 1, 1, 0, | { } 177 | -1, 0,-2,-2,-4,-1,-2,-3,-2, 2, 3, 1, 5, 0,-2,-1, 0,-4,-2, 1,-1, 0, 0, | { } 178 | -3,-3,-2,-4,-4,-4,-4,-3,-1, 1, 1,-4, 0, 7,-4,-2,-2, 0, 5,-1,-2,-3, 0, | { } 179 | 1, 0, 0,-1,-2, 0, 0,-1, 0,-2,-2,-1,-2,-4, 5, 1, 0,-5,-4,-1, 0, 1, 0, | { } 180 | 1, 0, 1, 0, 0,-1, 0, 1,-1,-1,-2, 0,-1,-2, 1, 2, 1,-2,-2,-1, 1, 1, 0, | { } 181 | 1,-1, 0, 0,-2,-1, 0, 0,-1, 0,-1, 0, 0,-2, 0, 1, 3,-4,-2, 0, 1, 0, 0, | { } 182 | -5, 1,-4,-6,-6,-4,-6,-5,-3,-5,-4,-3,-4, 0,-5,-2,-4,12, 0,-6,-3,-4, 0, | { } 183 | -3,-4,-1,-3, 0,-3,-3,-4, 0,-1,-1,-4,-2, 5,-4,-2,-2, 0, 7,-2,-1,-2, 0, | { } 184 | 0,-2,-2,-2,-2,-2,-2,-1,-2, 3, 1,-2, 1,-1,-1,-1, 0,-6,-2, 4,-1,-1, 0, | { } 185 | 1, 0, 3, 4,-3, 2, 3, 1, 2,-1,-2, 1,-1,-2, 0, 1, 1,-3,-1,-1, 4, 4, 0, | { } 186 | 1, 1, 2, 3,-3, 4, 4, 0, 2,-1,-1, 1, 0,-3, 1, 1, 0,-4,-2,-1, 4, 5, 0, | { } 187 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, | { 188 | }; | } csim.c:196:16: warning: array subscript has type ‘char’ [-Wchar-subscripts] 196 | V[achars[i]][achars[j]]=10*(wgts[i][j]); | ~~~~~~^~~ csim.c:196:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 196 | V[achars[i]][achars[j]]=10*(wgts[i][j]); | ~~~~~~^~~ csim.c: In function ‘set_pam_file’: csim.c:228:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 228 | V[alph[i]][alph[j]]=(Int2)(10*weight); | ~~~~^~~ csim.c:228:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 228 | V[alph[i]][alph[j]]=(Int2)(10*weight); | ~~~~^~~ csim.c: In function ‘big_pass’: csim.c:668:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 668 | va = v[A[i]]; | ~^~~ csim.c:692:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 692 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c: In function ‘diff1’: csim.c:799:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 799 | va = v[A[1]]; | ~^~~ csim.c:805:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 805 | { c = va[B[j]] - ( GAP(j-1) + GAP(N-j) ); | ~^~~ csim.c:849:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 849 | va = v[A[i]]; | ~^~~ csim.c:853:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 853 | DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:853:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 853 | DIAG(i+(s_ptr->I), (s_ptr->J)+j, c, s+v[A[i]][B[j]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:874:15: warning: array subscript has type ‘char’ [-Wchar-subscripts] 874 | va = v[A[i+1]]; | ~^~~~~ csim.c:878:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]]) | ~^~~~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:878:60: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | DIAG(i+1+s_ptr->I, j+1+s_ptr->J, c, s+v[A[i+1]][B[j+1]]) | ~^~~~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:893:38: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 893 | if (c > midc || CC[j] != DD[j] && RR[j] == SS[j]) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ csim.c: In function ‘locate’: csim.c:974:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 974 | va = v[A[i]]; | ~^~~ csim.c:991:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 991 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1030:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1030 | va = v[A[(plist->m1)]]; | ~^~~~~~~~~~~~~ csim.c:1043:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1043 | DIAG((plist->m1), j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1061:45: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1061 | if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1062:64: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1062 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1071:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1071 | if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1072:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1072 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1084:23: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1084 | va = v[B[(plist->n1)]]; | ~^~~~~~~~~~~~~ csim.c:1110:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1110 | DIAG(i, (plist->n1), c, p+va[A[i]]) | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c:1128:45: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1128 | if ( ! cflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1129:43: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1129 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1138:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1138 | if ( ! rflag && ( ci > rl && cj > cl || di > rl && dj > cl | ~~~~~~~~^~~~~~~~~~ csim.c:1139:61: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1139 | || fi > rl && fj > cl ) ) | ~~~~~~~~^~~~~~~~~~ csim.c:1144:29: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 1144 | if ( (plist->m1) == 1 && (plist->n1) == 1 || no_cross(flag, plist, &rl, &cl) ) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ csim.c: In function ‘small_pass’: csim.c:1186:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1186 | va = v[A[i]]; | ~^~~ csim.c:1212:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1212 | DIAG(i, j, c, p+va[B[j]]) /* diagonal */ | ~^~~ csim.c:440:11: note: in definition of macro ‘DIAG’ 440 | x = ( pvalue ); \ | ^~~~~~ csim.c: In function ‘display’: csim.c:1360:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1360 | if (i < M || j < N) | ^ csim.c: In function ‘set_pam_file’: csim.c:227:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 227 | fscanf(fp, "%f", &weight); /**get the matrix**/ | ^~~~~~~~~~~~~~~~~~~~~~~~~ csim.c: At top level: csim.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: csim.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF db_slist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/list.h:56, from db_slist.c:97: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ db_slist.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: db_slist.c,v 6.2 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from dust.c:102: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dust.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: dust.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_dust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from blast_dust.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_dust.c:39:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 39 | static char const rcsid[] = | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF falign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from falign.c:92: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ falign.c: In function ‘fbld_table’: falign.c:490:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 490 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:494:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 494 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘bbld_table’: falign.c:517:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 517 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:521:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 521 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rcbld_table’: falign.c:544:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 544 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:548:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 548 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘ex_table’: falign.c:567:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 567 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘free_all’: falign.c:668:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 668 | if (df = cdiag_prev[l]) { | ^~ falign.c: In function ‘scan’: falign.c:688:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 688 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:694:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 694 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c:710:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 710 | if (df = diag_prev[len1+len2-1-pos]) { | ^~ falign.c:719:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 719 | if (df=diag_prev[l]) { | ^~ falign.c: In function ‘fscan’: falign.c:763:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 763 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:769:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 769 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘bscan’: falign.c:794:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 794 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:800:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 800 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rfscan’: falign.c:870:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 870 | ecode = (ecode << 2) + encoding[*++q]; | ^~~~ falign.c:876:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 876 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c:881:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 881 | if (df = diag_prev[len1+se2-pos]) { | ^~ falign.c:889:21: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 889 | if (df = diag_prev[len1+se2-pos]) { | ^~ falign.c: In function ‘trcscan’: falign.c:1476:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1476 | ecode = (ecode << 2) + encoding[*--q]; | ^~~~ falign.c:1482:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1482 | ecode = ((ecode & mask) << 2) + encoding[*q]; | ^~ falign.c: In function ‘rclocal’: falign.c:1547:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1547 | if (pf = diag_prev[ocur_diag]) { | ^~ falign.c: In function ‘enterS’: falign.c:1897:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1897 | if (s = findS(f->bgf)) { | ^ falign.c: In function ‘local’: falign.c:1958:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1958 | if (pf = diag_prev[cur_diag]) { | ^~ falign.c: In function ‘align’: falign.c:1999:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1999 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: In function ‘calign’: falign.c:2054:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2054 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: In function ‘malign’: falign.c:2109:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2109 | if (pf = cdiag_prev[cur_diag]) { | ^~ falign.c: At top level: falign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: falign.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF g_any.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from g_any.c:89: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ g_any.c: In function ‘k_align’: g_any.c:212:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 212 | va = vv[A[i+1]]; | ~^~~~~ g_any.c:229:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 229 | if (j < J2) c = s + va[B[j+1]]; | ~^~~~~ g_any.c:319:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 319 | b2 = PP[t1][b1]; | ^ g_any.c:322:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 322 | t2 = PT[t1][b1]; | ^ g_any.c: In function ‘z_ALIGN’: g_any.c:367:14: warning: variable ‘check_score’ set but not used [-Wunused-but-set-variable] 367 | Int4 check_score; | ^~~~~~~~~~~ g_any.c: In function ‘CHECK_SCORE’: g_any.c:492:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 492 | score = vv[A[++i]][B[++j]] + score; | ~^~~~~ g_any.c:492:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] 492 | score = vv[A[++i]][B[++j]] + score; | ~^~~~~ g_any.c: At top level: g_any.c:428:35: warning: ‘CLINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:428:24: warning: ‘BLINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:428:13: warning: ‘ALINE’ defined but not used [-Wunused-variable] 428 | static Char ALINE[51], BLINE[51], CLINE[51]; | ^~~~~ g_any.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: g_any.c,v 6.5 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sim2.c sim2.c: In function ‘SIM2’: sim2.c:19:23: warning: unused variable ‘compB’ [-Wunused-variable] 19 | CharPtr A, B, compB = NULL; | ^~~~~ sim2.c:17:33: warning: unused variable ‘sapC’ [-Wunused-variable] 17 | SeqAlignPtr sap = NULL, sapC=NULL, out_sap, out_sapC; | ^~~~ sim2.c: At top level: sim2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim2.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sim3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from sim3.c:28: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sim3.c: In function ‘locate’: sim3.c:103:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 103 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:105:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 105 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:113:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 113 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:115:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 115 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:129:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 129 | ecode = (ecode << 2) + encoding[*p++]; | ^~~~ sim3.c:133:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 133 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c:152:60: warning: array subscript has type ‘char’ [-Wchar-subscripts] 152 | ecode1 = ((ecode1 & mask) << 2) + encoding[*q++]; | ^~~~ sim3.c:155:58: warning: array subscript has type ‘char’ [-Wchar-subscripts] 155 | ecode = ((ecode & mask) << 2) + encoding[*p++]; | ^~~~ sim3.c: At top level: sim3.c:1067:16: warning: ‘is_end_seg’ defined but not used [-Wunused-function] 1067 | static Boolean is_end_seg(EditScriptPtr curr, EditScriptPtr head) | ^~~~~~~~~~ sim3.c:1056:13: warning: ‘get_current_pos’ defined but not used [-Wunused-function] 1056 | static Int4 get_current_pos(Int4Ptr pos, Int4 length) | ^~~~~~~~~~~~~~~ sim3.c:1048:13: warning: ‘get_start_pos’ defined but not used [-Wunused-function] 1048 | static Int4 get_start_pos(SeqLocPtr slp) | ^~~~~~~~~~~~~ sim3.c:806:13: warning: ‘Print_Script’ defined but not used [-Wunused-function] 806 | static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, CharPtr A, CharPtr B) | ^~~~~~~~~~~~ sim3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim3.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sim3.c: In function ‘locate’: sim3.c:229:13: warning: ‘paired_fj’ may be used uninitialized [-Wmaybe-uninitialized] 229 | *j1 = paired_fj; | ~~~~^~~~~~~~~~~ sim3.c:79:14: note: ‘paired_fj’ was declared here 79 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim3.c:230:24: warning: ‘paired_bj’ may be used uninitialized [-Wmaybe-uninitialized] 230 | *j2 = paired_bj+1; | ~~~~~~~~~^~ sim3.c:79:25: note: ‘paired_bj’ was declared here 79 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim3.c: In function ‘path’: sim3.c:720:12: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 720 | if(head2) | ^~~~~ sim3.c:481:37: note: ‘head2’ declared here 481 | EditScriptPtr head1, tail1, head2, tail2; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sim4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from sim4.c:18: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sim4.c: In function ‘sim4x’: sim4.c:630:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 630 | while(i1 = sgp->Blist[i].next) { | ^~ sim4.c: In function ‘greedy’: sim4.c:1770:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1770 | if (row == 0 && col == 0) | ^ sim4.c:1794:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1794 | if (row == 0) | ^ sim4.c:1838:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1838 | if (col == 0) | ^ sim4.c:1962:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1962 | if (row == m && col == n) | ^ sim4.c:1991:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1991 | if (row == m) | ^ sim4.c:2037:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2037 | if (col == n) | ^ sim4.c: In function ‘DISPLAY’: sim4.c:2625:35: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 2625 | if (a >= ALINE+50 || i >= M && j >= N) | ~~~~~~~^~~~~~~~~ sim4.c: At top level: sim4.c:2592:13: warning: ‘DISPLAY’ defined but not used [-Wunused-function] 2592 | static void DISPLAY(Int1 A[], Int1 B[], Int4 M, Int4 N, Int4 S[], Int4 AP, Int4 BP) | ^~~~~~~ sim4.c:2563:13: warning: ‘S2A’ defined but not used [-Wunused-function] 2563 | static void S2A(EditScriptPtr head, Int4Ptr S) | ^~~ sim4.c:2499:13: warning: ‘Print_Script’ defined but not used [-Wunused-function] 2499 | static void Print_Script(EditScriptPtr head, Int4 M, Int4 N, data_t *data) | ^~~~~~~~~~~~ sim4.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sim4.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sim4.c: In function ‘path’: sim4.c:2467:7: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 2467 | if (head2) *tail = tail2; | ^~~~~ sim4.c:2262:31: note: ‘head2’ declared here 2262 | EditScriptPtr head1, tail1, head2, tail2; | ^~~~~ sim4.c: In function ‘locate’: sim4.c:2918:7: warning: ‘paired_fj’ may be used uninitialized [-Wmaybe-uninitialized] 2918 | *j1 = paired_fj; | ~~~~^~~~~~~~~~~ sim4.c:2765:8: note: ‘paired_fj’ was declared here 2765 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ sim4.c:2919:19: warning: ‘paired_bj’ may be used uninitialized [-Wmaybe-uninitialized] 2919 | *j2 = paired_bj + 1; | ~~~~~~~~~~^~~ sim4.c:2765:19: note: ‘paired_bj’ was declared here 2765 | Int4 paired_fj, paired_bj, best_range, t; | ^~~~~~~~~ In function ‘greedy’, inlined from ‘sim4x’ at sim4.c:703:12: sim4.c:2112:22: warning: ‘back’ may be used uninitialized [-Wmaybe-uninitialized] 2112 | if (m-min_row[back]>=max_row[forth]) { | ^ sim4.c: In function ‘sim4x’: sim4.c:1609:12: note: ‘back’ was declared here 1609 | Int4 back, forth; /* backward and forward limits at exit */ | ^~~~ In function ‘greedy’, inlined from ‘sim4x’ at sim4.c:703:12: sim4.c:2112:37: warning: ‘forth’ may be used uninitialized [-Wmaybe-uninitialized] 2112 | if (m-min_row[back]>=max_row[forth]) { | ^ sim4.c: In function ‘sim4x’: sim4.c:1609:18: note: ‘forth’ was declared here 1609 | Int4 back, forth; /* backward and forward limits at exit */ | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF simutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from simutil.c:103: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ simutil.c: In function ‘make_align’: simutil.c:495:9: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 495 | Uint1 strand; | ^~~~~~ simutil.c: At top level: simutil.c:848:16: warning: ‘is_alu_seq’ defined but not used [-Wunused-function] 848 | static Boolean is_alu_seq(CharPtr name) | ^~~~~~~~~~ simutil.c:814:16: warning: ‘re_cal_score’ defined but not used [-Wunused-function] 814 | static FloatHi re_cal_score(RecordEndsPtr o_rep, RecordEndsPtr n_rep) | ^~~~~~~~~~~~ simutil.c:344:17: warning: ‘convert’ defined but not used [-Wunused-function] 344 | static ScorePtr convert(Int4Ptr x, Int4Ptr y, Int4Ptr start, Int4Ptr length, Int4 n, SeqLocPtr locx, SeqLocPtr locy, Int2Ptr numseg, FloatHiPtr SegScores) | ^~~~~~~ simutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: simutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ simutil.c: In function ‘sort_align_list’: simutil.c:602:20: warning: ‘score1’ may be used uninitialized [-Wmaybe-uninitialized] 602 | if (score2 > score1) { /* swap */ | ^ simutil.c:591:17: note: ‘score1’ was declared here 591 | FloatHi score1, score2; | ^~~~~~ simutil.c:602:20: warning: ‘score2’ may be used uninitialized [-Wmaybe-uninitialized] 602 | if (score2 > score1) { /* swap */ | ^ simutil.c:591:25: note: ‘score2’ was declared here 591 | FloatHi score1, score2; | ^~~~~~ simutil.c: In function ‘get_top_K_alignment’: simutil.c:659:20: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 659 | if (score < cut_off) break; | ^ simutil.c:646:17: note: ‘score’ was declared here 646 | FloatHi score; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF slist.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/list.h:56, from slist.c:101: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ slist.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: slist.c,v 6.2 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF sec.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/simutil.h:77, from sec.c:67: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sec.c: In function ‘Region’: sec.c:268:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 268 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:268:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 268 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:292:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 292 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:292:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 292 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:321:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 321 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:321:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 321 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:345:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 345 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:345:61: warning: array subscript has type ‘char’ [-Wchar-subscripts] 345 | ext_score += V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:428:68: warning: array subscript has type ‘char’ [-Wchar-subscripts] 428 | diag_score = diag_score + V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c:428:77: warning: array subscript has type ‘char’ [-Wchar-subscripts] 428 | diag_score = diag_score + V[seq1[i]][seq2[j]]; | ~~~~^~~ sec.c: At top level: sec.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: sec.c,v 6.1 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ sec.c: In function ‘Region’: sec.c:504:39: warning: ‘LB’ may be used uninitialized [-Wmaybe-uninitialized] 504 | LB[i] = old_l; | ~~~~~~^~~~~~~ sec.c:158:17: note: ‘LB’ was declared here 158 | Int4Ptr LB; | ^~ sec.c:505:39: warning: ‘RB’ may be used uninitialized [-Wmaybe-uninitialized] 505 | RB[i] = tr; | ~~~~~~^~~~ sec.c:159:17: note: ‘RB’ was declared here 159 | Int4Ptr RB; | ^~ sec.c:405:47: warning: ‘bi’ may be used uninitialized [-Wmaybe-uninitialized] 405 | c = ((FloatHi)z_ALIGN(seq1-1,seq2-1,bi,bj,ei,ej,LB,RB,V,G,H,S+fk))/DIGIT + (FloatHi)fk + (FloatHi)lk; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sec.c:163:14: note: ‘bi’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:71:37: warning: ‘bj’ may be used uninitialized [-Wmaybe-uninitialized] 71 | #define Max(x,y) ((x) >= (y) ? (x) : (y)) | ~~~~~~~~~~~~~~~~~~^~~~~~ sec.c:163:18: note: ‘bj’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:400:51: warning: ‘ei’ may be used uninitialized [-Wmaybe-uninitialized] 400 | for (i = pi; i <= ei; ++i) { | ~~^~~~~ sec.c:163:22: note: ‘ei’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:502:31: warning: ‘ej’ may be used uninitialized [-Wmaybe-uninitialized] 502 | tr = Min(cj + Width, ej); | ^ sec.c:163:26: note: ‘ej’ was declared here 163 | Int4 bi, bj, ei, ej, t; | ^~ sec.c:503:43: warning: ‘pi’ may be used uninitialized [-Wmaybe-uninitialized] 503 | for (i = pi; i <= ci; ++i) { | ~~^~~~~ sec.c:172:14: note: ‘pi’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~ sec.c:493:44: warning: ‘ppi’ may be used uninitialized [-Wmaybe-uninitialized] 493 | for (i = ppi; i <= ci; ++i) { | ~~^~~~~ sec.c:172:22: note: ‘ppi’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~~ sec.c:72:37: warning: ‘ppj’ may be used uninitialized [-Wmaybe-uninitialized] 72 | #define Min(x,y) ((x) <= (y) ? (x) : (y)) | ~~~~~~~~~~~~~~~~~~^~~~~~ sec.c:172:27: note: ‘ppj’ was declared here 172 | Int4 pi, pj, ppi, ppj; | ^~~ sec.c:504:39: warning: ‘old_l’ may be used uninitialized [-Wmaybe-uninitialized] 504 | LB[i] = old_l; | ~~~~~~^~~~~~~ sec.c:185:14: note: ‘old_l’ was declared here 185 | Int4 old_l, tl, tr; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF tfuns.c tfuns.c: In function ‘find_orf’: tfuns.c:866:33: warning: unused variable ‘into’ [-Wunused-variable] 866 | IntFuzzPtr infrom=NULL, into=NULL; | ^~~~ tfuns.c:866:20: warning: unused variable ‘infrom’ [-Wunused-variable] 866 | IntFuzzPtr infrom=NULL, into=NULL; | ^~~~~~ tfuns.c: At top level: tfuns.c:977:13: warning: ‘find_orf_from_circle’ defined but not used [-Wunused-function] 977 | static void find_orf_from_circle (SeqPortPtr spp, Boolean flagIsCircle, | ^~~~~~~~~~~~~~~~~~~~ tfuns.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: tfuns.c,v 6.17 2015/08/17 17:15:09 bollin Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF toasn3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/gather.h:169, from toasn3.c:10: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ toasn3.c: In function ‘FindOrg’: toasn3.c:1444:17: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 1444 | Int4 len; | ^~~ toasn3.c: In function ‘CheckQualsWithComm’: toasn3.c:1731:18: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 1731 | OrgRefPtr orp; | ^~~ toasn3.c: In function ‘CheckQuals’: toasn3.c:1768:18: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 1768 | OrgRefPtr orp; | ^~~ toasn3.c: In function ‘CountSourceFeat’: toasn3.c:2570:13: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 2570 | Pointer pnt; | ^~~ toasn3.c:2561:19: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 2561 | ValNodePtr vnp; | ^~~ toasn3.c: In function ‘TASNTrimInternalSemicolons’: toasn3.c:4155:12: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 4155 | CharPtr tmp; | ^~~ toasn3.c: In function ‘ImpFeatToProtRef’: toasn3.c:4861:13: warning: variable ‘lfree’ set but not used [-Wunused-but-set-variable] 4861 | Boolean lfree = FALSE, partial5, partial3; | ^~~~~ toasn3.c: In function ‘RemovePeptideImpFeats’: toasn3.c:5160:24: warning: variable ‘ifp’ set but not used [-Wunused-but-set-variable] 5160 | ImpFeatPtr ifp; | ^~~ toasn3.c: At top level: toasn3.c:1711:16: warning: ‘GetQualValue’ defined but not used [-Wunused-function] 1711 | static CharPtr GetQualValue(GBQualPtr gbqual, CharPtr qual) | ^~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from toasn3.c:19: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ toasn3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: toasn3.c,v 6.150 2016/11/02 23:36:09 kans Exp $"; | ^~~~~ toasn3.c: In function ‘CdEndCheck’: toasn3.c:4662:15: warning: ‘oldfrom’ may be used uninitialized [-Wmaybe-uninitialized] 4662 | sip->from = oldfrom; | ~~~~~~~~~~^~~~~~~~~ toasn3.c:4441:31: note: ‘oldfrom’ was declared here 4441 | Int4 len, remainder, aas, oldfrom, oldto, protlen, i, oldnum; | ^~~~~~~ toasn3.c:4663:13: warning: ‘oldto’ may be used uninitialized [-Wmaybe-uninitialized] 4663 | sip->to = oldto; | ~~~~~~~~^~~~~~~ toasn3.c:4441:40: note: ‘oldto’ was declared here 4441 | Int4 len, remainder, aas, oldfrom, oldto, protlen, i, oldnum; | ^~~~~ toasn3.c:4665:18: warning: ‘m_oldfrom’ may be used uninitialized [-Wmaybe-uninitialized] 4665 | msip->from = m_oldfrom; | ~~~~~~~~~~~^~~~~~~~~~~ toasn3.c:4442:10: note: ‘m_oldfrom’ was declared here 4442 | Int4 m_oldfrom, m_oldto; | ^~~~~~~~~ toasn3.c:4666:16: warning: ‘m_oldto’ may be used uninitialized [-Wmaybe-uninitialized] 4666 | msip->to = m_oldto; | ~~~~~~~~~^~~~~~~~~ toasn3.c:4442:21: note: ‘m_oldto’ was declared here 4442 | Int4 m_oldfrom, m_oldto; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF toporg.c toporg.c: In function ‘ChkSegset’: toporg.c:64:51: warning: variable ‘is_title’ set but not used [-Wunused-but-set-variable] 64 | Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE; | ^~~~~~~~ toporg.c:63:17: warning: variable ‘orp’ set but not used [-Wunused-but-set-variable] 63 | OrgRefPtr orp; | ^~~ toporg.c:60:17: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 60 | Pointer pnt; | ^~~ toporg.c:55:17: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 55 | ValNodePtr vnp = NULL, set_vnp = NULL, upd_date_vnp = NULL; | ^~~ toporg.c: In function ‘ChkNucProt’: toporg.c:608:51: warning: variable ‘is_title’ set but not used [-Wunused-but-set-variable] 608 | Boolean is_org = FALSE, is_modif = FALSE, is_title = FALSE; | ^~~~~~~~ toporg.c: In function ‘StripBSfromParts’: toporg.c:1330:17: warning: variable ‘empty’ set but not used [-Wunused-but-set-variable] 1330 | Boolean empty; | ^~~~~ toporg.c:1329:17: warning: variable ‘bsmp’ set but not used [-Wunused-but-set-variable] 1329 | BSMapPtr bsmp; | ^~~~ toporg.c:1328:29: warning: variable ‘set_vnp’ set but not used [-Wunused-but-set-variable] 1328 | ValNodePtr descr, vnp, set_vnp; | ^~~~~~~ toporg.c: In function ‘MapsToGenref’: toporg.c:2021:17: warning: variable ‘loc’ set but not used [-Wunused-but-set-variable] 2021 | SeqLocPtr loc; | ^~~ toporg.c:2016:17: warning: variable ‘descr’ set but not used [-Wunused-but-set-variable] 2016 | ValNodePtr descr = NULL, head, last, vnp; | ^~~~~ toporg.c: In function ‘FindOldLineage’: toporg.c:2606:17: warning: variable ‘lineage’ set but not used [-Wunused-but-set-variable] 2606 | CharPtr lineage; | ^~~~~~~ toporg.c: In function ‘ArePubsMergeableForFig’: toporg.c:4796:36: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^~ toporg.c:4796:12: note: add parentheses around left hand side expression to silence this warning 4796 | || !cgp_fig->serial_number != cgp_nofig->serial_number) { | ^~~~~~~~~~~~~~~~~~~~~~~ | ( ) toporg.c: In function ‘StripBadTitleFromProteinProducts’: toporg.c:5311:22: warning: variable ‘tech’ set but not used [-Wunused-but-set-variable] 5311 | Uint1 tech; | ^~~~ toporg.c: In function ‘FindPubWithFig’: toporg.c:5647:10: warning: variable ‘a’ set but not used [-Wunused-but-set-variable] 5647 | Int4 a = 0; | ^ toporg.c: In function ‘AddMissingGeneXref’: toporg.c:5955:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 5955 | Int2 count; | ^~~~~ toporg.c: In function ‘ConvertSegSetToDeltaSeqInt’: toporg.c:7093:18: warning: unused variable ‘str’ [-Wunused-variable] 7093 | CharPtr str, ttl = NULL; | ^~~ toporg.c:7086:18: warning: unused variable ‘ovp’ [-Wunused-variable] 7086 | ObjValNodePtr ovp; | ^~~ toporg.c: At top level: toporg.c:5475:13: warning: ‘SynchronizePseudogenesProc’ defined but not used [-Wunused-function] 5475 | static void SynchronizePseudogenesProc ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~ toporg.c:3119:13: warning: ‘BarCodeTechToKeyword’ defined but not used [-Wunused-function] 3119 | static void BarCodeTechToKeyword (BioseqPtr bsp, Pointer userdata) | ^~~~~~~~~~~~~~~~~~~~ toporg.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: toporg.c,v 6.251 2016/11/02 23:36:10 kans Exp $"; | ^~~~~ In function ‘CitSubsMatch’, inlined from ‘MergeEquivCitSubs’ at toporg.c:3952:13: toporg.c:3905:7: warning: ‘csp1’ may be used uninitialized [-Wmaybe-uninitialized] 3905 | if (DateMatch (csp1->date, csp2->date, FALSE) != 0) return FALSE; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ toporg.c: In function ‘MergeEquivCitSubs’: toporg.c:3925:18: note: ‘csp1’ was declared here 3925 | CitSubPtr csp1, csp2; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pobutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/pobutil.h:7, from pobutil.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pobutil.c: In function ‘build_repeat_feat’: pobutil.c:187:14: warning: unused variable ‘c’ [-Wunused-variable] 187 | Char c='%'; | ^ pobutil.c: In function ‘merge_StdSeg’: pobutil.c:1033:14: warning: variable ‘start_1’ set but not used [-Wunused-but-set-variable] 1033 | Int4 start_1, stop_1, start_2, stop_2; | ^~~~~~~ pobutil.c:1031:14: warning: unused variable ‘overlap’ [-Wunused-variable] 1031 | Int4 overlap = -1; | ^~~~~~~ In file included from ../include/ncbi.h:59: pobutil.c: In function ‘FindHumanRepeats’: ../include/ncbimem.h:191:21: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ pobutil.c:2380:9: note: in expansion of macro ‘MemSet’ 2380 | MemSet((Pointer) (&tmp), sizeof(ValNode), 0); | ^~~~~~ ../include/ncbimem.h:191:21: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ pobutil.c:2381:9: note: in expansion of macro ‘MemSet’ 2381 | MemSet((Pointer) (&si), sizeof(SeqInt), 0); | ^~~~~~ pobutil.c: In function ‘AluFeat’: pobutil.c:2431:17: warning: variable ‘my_userdata’ set but not used [-Wunused-but-set-variable] 2431 | Pointer my_userdata; | ^~~~~~~~~~~ pobutil.c: At top level: pobutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pobutil.c,v 6.10 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF stsutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from stsutil.c:88: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ stsutil.c: In function ‘InitSTSSearch_r’: stsutil.c:270:10: warning: unused variable ‘StsCount’ [-Wunused-variable] 270 | Int4 StsCount=0; | ^~~~~~~~ stsutil.c: In function ‘GetSTSEntry’: stsutil.c:635:13: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 635 | CharPtr p; | ^ stsutil.c: In function ‘STSCalculateHash’: stsutil.c:753:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 753 | if ((j = HashCode[*p++]) < 0) | ^~~~ stsutil.c: In function ‘STSReverse’: stsutil.c:771:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 771 | if ((*t = ComplCode[*s]) == 0) | ^~ stsutil.c: In function ‘InitHashTable’: stsutil.c:910:21: warning: variable ‘sts_uid’ set but not used [-Wunused-but-set-variable] 910 | CharPtr gb_uid, sts_uid; | ^~~~~~~ stsutil.c:910:13: warning: variable ‘gb_uid’ set but not used [-Wunused-but-set-variable] 910 | CharPtr gb_uid, sts_uid; | ^~~~~~ stsutil.c:908:23: warning: variable ‘gi’ set but not used [-Wunused-but-set-variable] 908 | Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0; | ^~ stsutil.c:908:10: warning: variable ‘id_sts’ set but not used [-Wunused-but-set-variable] 908 | Int4 id_sts, len, gi, StsCount = 0, StsInvalid =0; | ^~~~~~ stsutil.c:907:23: warning: unused variable ‘error’ [-Wunused-variable] 907 | Int4 LineLength, error= FALSE; | ^~~~~ stsutil.c: At top level: stsutil.c:892:13: warning: ‘STSHashInitFree’ defined but not used [-Wunused-function] 892 | static void STSHashInitFree(STSHashInitPtr sts) | ^~~~~~~~~~~~~~~ stsutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: stsutil.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF suggadj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggadj.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggadj.c: In function ‘score_possible_splice_sites’: suggadj.c:874:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 874 | score = ( vx[seq_or_rev[putative_donor]]==3) ?10:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:875:24: warning: array subscript has type ‘char’ [-Wchar-subscripts] 875 | score += (vx[seq_or_rev[putative_acceptor]]==3 )?10:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ suggadj.c:878:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 878 | score += ( vx[seq_or_rev[putative_donor+1]]==0 )?3:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ suggadj.c:879:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 879 | score += ( vx[seq_or_rev[putative_acceptor-1]]==2 )?3:0; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c: In function ‘check_split_codon’: suggadj.c:985:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 985 | val_assuming_1_from_left= vx[seq_or_rev[left_ends+1]] * 16 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:986:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 986 | vx[seq_or_rev[right_starts-2]]*4+ | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:987:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 987 | vx[seq_or_rev[right_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:998:40: warning: array subscript has type ‘char’ [-Wchar-subscripts] 998 | val_assuming_2_from_left= vx[seq_or_rev[left_ends+1]] * 16 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:999:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 999 | vx[seq_or_rev[left_ends+2]] * 4 + | ~~~~~~~~~~^~~~~~~~~~~~~ suggadj.c:1000:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1000 | vx[seq_or_rev[right_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c: In function ‘overlapping_fixer’: suggadj.c:1370:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1370 | test_val = vx[seq_or_rev[left_exon_ends]]*16 + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ suggadj.c:1371:54: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1371 | vx[seq_or_rev[right_exon_starts-1]]; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c:1373:66: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1373 | test_val += vx[seq_or_rev[right_exon_starts-2]]*4; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ suggadj.c:1375:66: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1375 | test_val += vx[seq_or_rev[left_exon_ends+1]]*4; | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ suggadj.c: At top level: suggadj.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggadj.c,v 6.3 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF suggest.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggest.c:199: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggest.c: In function ‘get_frames’: suggest.c:458:35: warning: array subscript has type ‘char’ [-Wchar-subscripts] 458 | val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]]; | ~^~~ suggest.c:458:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 458 | val = vx[t[0]]*16 + vx[t[1]]*4 + vx[(t==t_max)?'N':t[2]]; | ~^~~ suggest.c: At top level: suggest.c:1331:13: warning: ‘ReportSuggestIntervalsError’ defined but not used [-Wunused-function] 1331 | static void ReportSuggestIntervalsError (SeqRecPtr srp, CharPtr gen_txt) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ suggest.c:1222:1: warning: ‘fprintf_m_stk_entry’ defined but not used [-Wunused-function] 1222 | fprintf_m_stk_entry(FILE *fp, Int4 index, char *msg) | ^~~~~~~~~~~~~~~~~~~ suggest.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggest.c,v 6.14 2009/04/10 17:22:14 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF suggslp.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from suggslp.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ suggslp.c: In function ‘MakeReverseSequence’: suggslp.c:190:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 190 | *t++ = r[*--s]; | ^~~~ suggslp.c: At top level: suggslp.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: suggslp.c,v 6.6 2009/04/16 18:35:41 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blast.c:2572: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast.c: In function ‘BlastReevaluateWithAmbiguities’: blast.c:2954:31: warning: variable ‘query_end’ set but not used [-Wunused-but-set-variable] 2954 | Uint1Ptr query_start, query_end, subject_real_start=NULL; | ^~~~~~~~~ blast.c:2949:23: warning: variable ‘hspcnt’ set but not used [-Wunused-but-set-variable] 2949 | Int4 context, hspcnt, hspcnt_max, index, index1, status; | ^~~~~~ blast.c: In function ‘BlastGetVirtualOIDList’: blast.c:3179:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3179 | if (virtual_oidlist = rdfp_chain->oidlist) { | ^~~~~~~~~~~~~~~ blast.c: In function ‘BlastGetDbChunk’: blast.c:3210:13: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3210 | if (virtual_oidlist = BlastGetVirtualOIDList(rdfp)) { | ^~~~~~~~~~~~~~~ blast.c: In function ‘BlastCreateQueryDNAP’: blast.c:4100:11: warning: variable ‘strand_option’ set but not used [-Wunused-but-set-variable] 4100 | Uint1 strand_option; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastReapPartialHitlistByEvalue’: blast.c:6486:10: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 6486 | else | ^~~~ blast.c:6490:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 6490 | if( !search->mult_queries ) | ^~ blast.c: In function ‘BlastWordFinder_contig’: blast.c:7094:23: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 7094 | register Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastWordExtend’: blast.c:7835:64: warning: variable ‘leftscore’ set but not used [-Wunused-but-set-variable] 7835 | BLAST_Score leftsum, rightsum, rightscore, leftscore; | ^~~~~~~~~ blast.c: In function ‘BlastNewWordExtend’: blast.c:7982:64: warning: variable ‘leftscore’ set but not used [-Wunused-but-set-variable] 7982 | BLAST_Score leftsum, rightsum, rightscore, leftscore; | ^~~~~~~~~ blast.c: In function ‘BlastNtWordFinder_mh’: blast.c:8843:23: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 8843 | register Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c:8842:103: warning: variable ‘compression_factor’ set but not used [-Wunused-but-set-variable] 8842 | Int4 s_pos, q_off, s_off, offset, virtual_wordsize, wordsize, compressed_wordsize, compression_factor; | ^~~~~~~~~~~~~~~~~~ blast.c: In function ‘BlastNtWordFinder’: blast.c:9076:14: warning: variable ‘bits_to_shift’ set but not used [-Wunused-but-set-variable] 9076 | Int4 bits_to_shift, min_diag_length, min_diag_mask; | ^~~~~~~~~~~~~ blast.c: In function ‘BlastSaveCurrentHitlist’: blast.c:10115:25: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 10115 | if( hitlist_max > 1 ) | ^ blast.c:9785:14: warning: variable ‘query_length’ set but not used [-Wunused-but-set-variable] 9785 | Int4 query_length; | ^~~~~~~~~~~~ blast.c: In function ‘SumHSPEvalue’: blast.c:10588:9: warning: variable ‘gap_size’ set but not used [-Wunused-but-set-variable] 10588 | Int4 gap_size, num, subject_length; | ^~~~~~~~ blast.c: In function ‘link_hsps’: blast.c:11267:17: warning: variable ‘frame_change’ set but not used [-Wunused-but-set-variable] 11267 | Boolean frame_change, linked_set, ignore_small_gaps; | ^~~~~~~~~~~~ blast.c: At top level: blast.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $"; | ^~~~~ blast.c: In function ‘blastMergeFilterLocs’: blast.c:3969:9: warning: ‘dup_slp’ may be used uninitialized [-Wmaybe-uninitialized] 3969 | BlastConvertDNASeqLoc(dup_slp, frame, length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast.c:3933:20: note: ‘dup_slp’ was declared here 3933 | SeqLocPtr slp, dup_slp, dup_head; | ^~~~~~~ blast.c: In function ‘BlastLinkHsps’: blast.c:10455:41: warning: ‘orig_hitlist’ may be used uninitialized [-Wmaybe-uninitialized] 10455 | search->current_hitlist = orig_hitlist; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blast.c:10401:35: note: ‘orig_hitlist’ was declared here 10401 | BLAST_HitListPtr hitlist, orig_hitlist; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blastutl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastutl.c:1836: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastutl.c: In function ‘BlastSeqLocFilterEx’: blastutl.c:7554:11: warning: statement with no effect [-Wunused-value] 7554 | stop_timer("after repeat filtering"); | ^ blastutl.c: In function ‘BlastPreliminaryGappedScore’: blastutl.c:9853:37: warning: variable ‘query_length’ set but not used [-Wunused-but-set-variable] 9853 | Int4 index, max_offset = 0, query_length, min_score; | ^~~~~~~~~~~~ blastutl.c: In function ‘BlastGetGappedScore’: blastutl.c:10282:11: warning: statement with no effect [-Wunused-value] 10282 | stop_timer("after BlastGappedScoreInternal"); | ^ blastutl.c: At top level: blastutl.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastutl.c,v 6.472 2010/12/10 18:47:12 madden Exp $"; | ^~~~~ blastutl.c: In function ‘BlastNtFindWords’: blastutl.c:11445:17: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 11445 | end = MIN(end, len-initial_wordsize); blastutl.c:11396:14: note: ‘end’ was declared here 11396 | Int4 end, index, index_addition, lookup_index, stop; | ^~~ blastutl.c: In function ‘BlastFindWords’: blastutl.c:11623:22: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 11623 | stop = MIN(stop, len); blastutl.c:11522:66: note: ‘stop’ was declared here 11522 | Int4 loop_increment, loop_increment2, stop; | ^~~~ blastutl.c:11695:39: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 11695 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11512:58: note: ‘diff’ was declared here 11512 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:11704:45: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 11704 | start_score = second_score+first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11512:71: note: ‘first_score’ was declared here 11512 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:11711:46: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 11711 | start_score2 += matrix[(Int4) *(str+index2)][*(words+index2)]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11513:47: note: ‘start_score’ was declared here 11513 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘BlastNewFindWords_Old’: blastutl.c:11915:39: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 11915 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11777:58: note: ‘diff’ was declared here 11777 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:11924:45: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 11924 | start_score = second_score+first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11777:71: note: ‘first_score’ was declared here 11777 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:11931:46: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 11931 | start_score2 += MtrxScorePosSearch(search->sbp, blastutl.c:11778:47: note: ‘start_score’ was declared here 11778 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘BlastNewFindWordsEx’: blastutl.c:12110:23: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 12110 | diff2 += diff; | ~~~~~~^~~~~~~ blastutl.c:11989:50: note: ‘diff’ was declared here 11989 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~ blastutl.c:12118:29: warning: ‘first_score’ may be used uninitialized [-Wmaybe-uninitialized] 12118 | start_score = second_score + first_score; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11989:63: note: ‘first_score’ was declared here 11989 | BLAST_Score best_total, delta_score, diff, diff2, first_score; | ^~~~~~~~~~~ blastutl.c:12124:30: warning: ‘start_score’ may be used uninitialized [-Wmaybe-uninitialized] 12124 | start_score2 += posMatrix[offset+index2][*(words+index2)]; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blastutl.c:11990:39: note: ‘start_score’ was declared here 11990 | BLAST_Score second_score, start_score, start_score2, score; | ^~~~~~~~~~~ blastutl.c: In function ‘SumBlastGetGappedAlignmentEx’: blastutl.c:9662:40: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 9662 | for (index=start; index>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blastool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastool.c:946: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastool.c: In function ‘BlastScaleMatrix’: blastool.c:3032:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 3032 | else | ^~~~ blastool.c:3035:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 3035 | if (new_lambda > lambda) | ^~ blastool.c: In function ‘OOFBlastHSPGetNumIdentical’: blastool.c:6081:9: warning: variable ‘context’ set but not used [-Wunused-but-set-variable] 6081 | Int2 context; | ^~~~~~~ blastool.c: At top level: blastool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastool.c,v 6.292 2007/03/15 20:39:17 madden Exp $"; | ^~~~~ blastool.c: In function ‘BlastCreateVirtualOIDList’: blastool.c:2556:24: warning: ‘gilist’ may be used uninitialized [-Wmaybe-uninitialized] 2556 | BlastDoubleInt4Ptr gilist, real_gilist = NULL, *real_gilist_ptrs = NULL; | ^~~~~~ blastool.c: In function ‘BlastInsertList2Heap’: blastool.c:3595:38: warning: ‘query_length’ may be used uninitialized [-Wmaybe-uninitialized] 3595 | context = hsp->query_offset / query_length; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blastool.c:3575:30: note: ‘query_length’ was declared here 3575 | Int4 begin, end, hspcnt, query_length; | ^~~~~~~~~~~~ blastool.c: In function ‘BlastFreeHeap’: blastool.c:3687:38: warning: ‘query_length’ may be used uninitialized [-Wmaybe-uninitialized] 3687 | context = hsp->query_offset / query_length; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ blastool.c:3670:33: note: ‘query_length’ was declared here 3670 | Int4 begin, end, i, hspcnt, query_length; | ^~~~~~~~~~~~ blastool.c: In function ‘BlastPrintAlignInfo’: blastool.c:4800:23: warning: ‘sap’ may be used uninitialized [-Wmaybe-uninitialized] 4800 | sap->next = SeqAlignNew(); | ~~~~~~~~~~^~~~~~~~~~~~~~~ blastool.c:4589:33: note: ‘sap’ was declared here 4589 | SeqAlignPtr seqalign = NULL, sap; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blastconcat.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastconcat.c:89: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastconcat.c: In function ‘BlastMakeFakeBspConcat’: blastconcat.c:648:19: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 648 | SeqLocPtr slp = NULL; | ^~~ blastconcat.c: At top level: blastconcat.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastconcat.c,v 1.14 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF splutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from splutil.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ splutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: splutil.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gapxdrop.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/gapxdrop.h:150, from gapxdrop.c:368: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gapxdrop.c: In function ‘ALIGN_EX’: gapxdrop.c:864:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 864 | if (s == 1) | ^ gapxdrop.c:867:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 867 | if (s == 2) | ^ gapxdrop.c: At top level: gapxdrop.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: gapxdrop.c,v 6.76 2003/11/07 21:52:52 dondosha Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg0.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg0.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg0.c: In function ‘g_band0_align’: bandalg0.c:273:9: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 273 | if(leftd >= 1) | ^ bandalg0.c: At top level: bandalg0.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg0.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg1.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg1.c: In function ‘gband_quadratic’: bandalg1.c:54:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 54 | Int4 c, i, j; | ^ bandalg1.c: In function ‘g_band1_align’: bandalg1.c:205:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 205 | if(leftd >= 1) | ^ bandalg1.c: At top level: bandalg1.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg1.c,v 6.3 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg2.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg2.c: In function ‘gb_linear_align’: bandalg2.c:208:24: warning: variable ‘misma’ set but not used [-Wunused-but-set-variable] 208 | register Int4 match, misma; | ^~~~~ bandalg2.c:208:17: warning: variable ‘match’ set but not used [-Wunused-but-set-variable] 208 | register Int4 match, misma; | ^~~~~ bandalg2.c:207:18: warning: variable ‘AA’ set but not used [-Wunused-but-set-variable] 207 | register Uint1 AA; | ^~ bandalg2.c: At top level: bandalg2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg2.c,v 6.5 2003/05/30 17:25:35 coulouri Exp $"; | ^~~~~ bandalg2.c: In function ‘gb_linear_align’: bandalg2.c:494:22: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 494 | if (rmid > Y - X) { | ~~^~~ bandalg2.c:202:35: note: ‘X’ was declared here 202 | Int4 rmid, k =0, l=0, r, v, kt, X, Y; | ^ bandalg2.c:494:22: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 494 | if (rmid > Y - X) { | ~~^~~ bandalg2.c:202:38: note: ‘Y’ was declared here 202 | Int4 rmid, k =0, l=0, r, v, kt, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg3.c:37: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:54:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 54 | Int4 c, i, j; | ^ bandalg3.c: At top level: bandalg3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg3.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ In function ‘g_band3_align’, inlined from ‘gband_linear_qgap’ at bandalg3.c:111:7: bandalg3.c:291:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 291 | for (i = X, j = Y, e=0, c = 0; i>=0; i--, c++) { | ~^~~ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:185:25: note: ‘X’ was declared here 185 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band3_align’, inlined from ‘gband_linear_qgap’ at bandalg3.c:111:7: bandalg3.c:314:23: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 314 | else if(Y != rightd) _INS(rightd-Y) | ^ bandalg3.c: In function ‘gband_linear_qgap’: bandalg3.c:185:28: note: ‘Y’ was declared here 185 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg4.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg4.c:37: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg4.c: In function ‘g_band4_align_small’: bandalg4.c:826:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 826 | if (e == 1) | ^ bandalg4.c:829:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 829 | if (e == 2) | ^ bandalg4.c:630:8: warning: variable ‘band’ set but not used [-Wunused-but-set-variable] 630 | Int4 band, j; | ^~~~ bandalg4.c: At top level: bandalg4.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg4.c,v 6.4 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:534:12: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 534 | if(X != M || Y != N) regA = regB = 1; | ~~^~~~ bandalg4.c:183:30: note: ‘X’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ bandalg4.c:534:22: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 534 | if(X != M || Y != N) regA = regB = 1; | ~~^~~~ bandalg4.c:183:33: note: ‘Y’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ bandalg4.c:544:11: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 544 | for(; k > -1; r = k, k = data->MP[l][r], l = data->MT[l][r]){ | ~~^~~~ bandalg4.c:183:14: note: ‘k’ was declared here 183 | Int4 rmid, k, l, r, v, kt, X, Y; | ^ In function ‘g_band4_align_small’, inlined from ‘g_band4_align’ at bandalg4.c:208:14: bandalg4.c:823:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 823 | for (i = X, j = Y, e=l, c = 0; i>=0; i--, c++) { | ~^~~ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:640:25: note: ‘X’ was declared here 640 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band4_align_small’, inlined from ‘g_band4_align’ at bandalg4.c:208:14: bandalg4.c:857:11: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 857 | else if (Y != rightd) _INS(rightd - Y); | ^ bandalg4.c: In function ‘g_band4_align’: bandalg4.c:640:28: note: ‘Y’ was declared here 640 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalg5.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/bandalgn.h:73, from bandalg5.c:36: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:56:14: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 56 | Int4 c, i, j; | ^ bandalg5.c: In function ‘g_band5_align’: bandalg5.c:292:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 292 | if (e == 1) | ^ bandalg5.c:295:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 295 | if (e == 2) | ^ bandalg5.c: At top level: bandalg5.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalg5.c,v 6.3 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ In function ‘g_band5_align’, inlined from ‘gband_q3gap’ at bandalg5.c:109:7: bandalg5.c:289:35: warning: ‘X’ may be used uninitialized [-Wmaybe-uninitialized] 289 | for (i = X, j = Y, e=0, c = 0; i>=0; i--, c++) { | ~^~~ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:146:25: note: ‘X’ was declared here 146 | Int4 ib, best=MININT, X, Y; | ^ In function ‘g_band5_align’, inlined from ‘gband_q3gap’ at bandalg5.c:109:7: bandalg5.c:320:6: warning: ‘Y’ may be used uninitialized [-Wmaybe-uninitialized] 320 | if (Y != rightd) _INS(rightd - Y); | ^ bandalg5.c: In function ‘gband_q3gap’: bandalg5.c:146:28: note: ‘Y’ was declared here 146 | Int4 ib, best=MININT, X, Y; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bandalgn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from bandalgn.c:118: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bandalgn.c: In function ‘ExtendSeqAlign’: bandalgn.c:1113:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 1113 | DenseDiagPtr ddp; | ^~~ bandalgn.c: In function ‘CC_ExtendSeqAlign’: bandalgn.c:1188:22: warning: variable ‘ddp’ set but not used [-Wunused-but-set-variable] 1188 | DenseDiagPtr ddp; | ^~~ bandalgn.c: At top level: bandalgn.c:699:14: warning: ‘HSblastna_to_ncbi4na’ defined but not used [-Wunused-variable] 699 | static Uint1 HSblastna_to_ncbi4na[] = { 1, /* A, 0 */ | ^~~~~~~~~~~~~~~~~~~~ bandalgn.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bandalgn.c,v 6.17 2003/05/30 17:25:36 coulouri Exp $"; | ^~~~~ bandalgn.c: In function ‘LocalBandToEditBlock’: bandalgn.c:463:20: warning: ‘edit_block’ may be used uninitialized [-Wmaybe-uninitialized] 463 | lbsp->edit_block = edit_block; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ bandalgn.c:435:20: note: ‘edit_block’ was declared here 435 | GapXEditBlockPtr edit_block; | ^~~~~~~~~~ bandalgn.c: In function ‘SetLowUpFromBlast’: bandalgn.c:1053:28: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 1053 | if (maxsc < val) { | ^ bandalgn.c:943:17: note: ‘val’ was declared here 943 | FloatHi val, maxsc = 0; | ^~~ bandalgn.c:1056:38: warning: ‘mindi’ may be used uninitialized [-Wmaybe-uninitialized] 1056 | miny = mindi - width; | ~~~~~^~~~~~~~~~~~~~~ bandalgn.c:939:28: note: ‘mindi’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~ bandalgn.c:1055:38: warning: ‘maxdi’ may be used uninitialized [-Wmaybe-uninitialized] 1055 | maxy = maxdi + width; | ~~~~~^~~~~~~~~~~~~~~ bandalgn.c:939:34: note: ‘maxdi’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~ bandalgn.c:1060:28: warning: ‘alnlen’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | if (maxlen < alnlen) { | ^ bandalgn.c:940:37: note: ‘alnlen’ was declared here 940 | Int4 len,len1,len2,maxlen=0,alnlen,lastx,lowestx,diag; | ^~~~~~ bandalgn.c:1069:16: warning: ‘mindi_low’ may be used uninitialized [-Wmaybe-uninitialized] 1069 | miny = MIN(miny,mindi_low); bandalgn.c:939:40: note: ‘mindi_low’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~~~~~ bandalgn.c:1070:16: warning: ‘maxdi_up’ may be used uninitialized [-Wmaybe-uninitialized] 1070 | maxy = MAX(maxy,maxdi_up); bandalgn.c:939:50: note: ‘maxdi_up’ was declared here 939 | Int4 x,y,maxy,miny,mindi,maxdi,mindi_low,maxdi_up; | ^~~~~~~~ bandalgn.c: In function ‘GetAlignExtremes’: bandalgn.c:1306:14: warning: ‘x1’ may be used uninitialized [-Wmaybe-uninitialized] 1306 | *xx1 = x1; | ~~~~~^~~~ bandalgn.c:1281:39: note: ‘x1’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1307:14: warning: ‘x2’ may be used uninitialized [-Wmaybe-uninitialized] 1307 | *xx2 = x2; | ~~~~~^~~~ bandalgn.c:1281:43: note: ‘x2’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1308:14: warning: ‘y1’ may be used uninitialized [-Wmaybe-uninitialized] 1308 | *yy1 = y1; | ~~~~~^~~~ bandalgn.c:1281:47: note: ‘y1’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ bandalgn.c:1309:14: warning: ‘y2’ may be used uninitialized [-Wmaybe-uninitialized] 1309 | *yy2 = y2; | ~~~~~^~~~ bandalgn.c:1281:51: note: ‘y2’ was declared here 1281 | Int4 index1, x, y, x1, x2, y1, y2; | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blastkar.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blastkar.c:648: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blastkar.c:2373:25: warning: ‘Altschul_prob’ defined but not used [-Wunused-variable] 2373 | static BLAST_LetterProb Altschul_prob[] = { | ^~~~~~~~~~~~~ blastkar.c:2347:25: warning: ‘Dayhoff_prob’ defined but not used [-Wunused-variable] 2347 | static BLAST_LetterProb Dayhoff_prob[] = { | ^~~~~~~~~~~~ blastkar.c:1121:13: warning: ‘blosum62_20_prefs’ defined but not used [-Wunused-variable] 1121 | static Int4 blosum62_20_prefs[BLOSUM62_20_VALUES_MAX] = { | ^~~~~~~~~~~~~~~~~ blastkar.c:1053:21: warning: ‘blosum62_20_values’ defined but not used [-Wunused-variable] 1053 | static Nlm_FloatHi blosum62_20_values[BLOSUM62_20_VALUES_MAX][8] = { | ^~~~~~~~~~~~~~~~~~ blastkar.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blastkar.c,v 6.115 2006/12/14 17:08:19 madden Exp $"; | ^~~~~ blastkar.c: In function ‘BlastScoreBlkMatCreate’: blastkar.c:1574:43: warning: ‘ ’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1574 | sprintf(buffer, "blastn matrix:%ld %ld", (long) sbp->reward, (long) sbp->penalty); | ^ blastkar.c:1574:25: note: directive argument in the range [-2147483648, 2147483647] 1574 | sprintf(buffer, "blastn matrix:%ld %ld", (long) sbp->reward, (long) sbp->penalty); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BlastScoreBlkMatCreate’ at blastkar.c:1574:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 18 and 38 bytes into a destination of size 25 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF actutils.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/actutils.h:103, from actutils.c:232: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ actutils.c: In function ‘SlideToHit’: actutils.c:346:23: warning: variable ‘done’ set but not used [-Wunused-but-set-variable] 346 | Boolean inIsland, done; | ^~~~ actutils.c:346:13: warning: variable ‘inIsland’ set but not used [-Wunused-but-set-variable] 346 | Boolean inIsland, done; | ^~~~~~~~ actutils.c: In function ‘ResolveSpinConflict’: actutils.c:1484:35: warning: unused variable ‘row2_conflict’ [-Wunused-variable] 1484 | Boolean row1_conflict = FALSE, row2_conflict = FALSE; | ^~~~~~~~~~~~~ actutils.c:1484:12: warning: unused variable ‘row1_conflict’ [-Wunused-variable] 1484 | Boolean row1_conflict = FALSE, row2_conflict = FALSE; | ^~~~~~~~~~~~~ actutils.c: In function ‘ACT_FindBestAlnByDotPlot’: actutils.c:2002:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 2002 | Uint1 strand; | ^~~~~~ actutils.c:2001:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2001 | Int4 start2; | ^~~~~~ actutils.c:2000:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2000 | Int4 start1; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ actutils.c:3132:13: warning: ‘DumpAlignments’ defined but not used [-Wunused-function] 3132 | static void DumpAlignments (SeqAlignPtr salp) | ^~~~~~~~~~~~~~ actutils.c:2927:13: warning: ‘MapBioseqToBioseqSpecial’ defined but not used [-Wunused-function] 2927 | static Int4 MapBioseqToBioseqSpecial(SeqAlignPtr sap, Int4 begin, Int4 fin, Int4 pos, Int4 which_end) | ^~~~~~~~~~~~~~~~~~~~~~~~ actutils.c:1654:16: warning: ‘SpinsConflict’ defined but not used [-Wunused-function] 1654 | static Boolean SpinsConflict (SQN_nPtr spin1, SQN_nPtr spin2, Int4 fuzz, Int4 strand) | ^~~~~~~~~~~~~ actutils.c:1392:13: warning: ‘am_fix_strand’ defined but not used [-Wunused-function] 1392 | static void am_fix_strand(SeqAlignPtr sap, Uint1 strand1, Uint1 strand2) | ^~~~~~~~~~~~~ actutils.c:1375:16: warning: ‘am_isa_gap’ defined but not used [-Wunused-function] 1375 | static Boolean am_isa_gap(Int4 start, Int4 prevstop, Uint1 strand) | ^~~~~~~~~~ actutils.c:749:13: warning: ‘StateTableSearch’ defined but not used [-Wunused-function] 749 | static void StateTableSearch (TextFsaPtr tbl, CharPtr txt, Int4Ptr state, Int4 pos, ACT_sitelistPtr PNTR asp_prev, ACT_sitelistPtr PNTR asp_head) | ^~~~~~~~~~~~~~~~ actutils.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: actutils.c,v 6.56 2008/10/22 17:19:22 bollin Exp $"; | ^~~~~ In file included from ../include/ncbi.h:59: actutils.c: In function ‘GetOldBlastAlignmentPiece’: ../include/ncbimem.h:232:23: warning: ‘program’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree actutils.c:3089:25: note: ‘program’ was declared here 3089 | CharPtr program; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF posit.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from posit.c:402: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ posit.c: In function ‘posDemographics’: posit.c:1110:17: warning: variable ‘numSeqAligns’ set but not used [-Wunused-but-set-variable] 1110 | Int4 numseq, numSeqAligns; /*number of matching sequences and SeqAligns*/ | ^~~~~~~~~~~~ posit.c: In function ‘posFreqsToMatrix’: posit.c:1679:45: warning: operation on ‘*(*(posSearch->posPrivateMatrix + (sizetype)((long unsigned int)length * 8)) + (sizetype)((long unsigned int)a * 4))’ may be undefined [-Wsequence-point] 1679 | posSearch->posPrivateMatrix[length][a] = posSearch->posPrivateMatrix[length][a] = BLAST_SCORE_MIN; posit.c: In function ‘posComputePseudoFreqs’: posit.c:1840:16: warning: variable ‘lambda’ set but not used [-Wunused-but-set-variable] 1840 | Nlm_FloatHi lambda; /*Karlin-Altschul parameter*/ | ^~~~~~ posit.c: In function ‘WposComputation’: posit.c:1988:13: warning: variable ‘numSeqAligns’ set but not used [-Wunused-but-set-variable] 1988 | Int4 i, numSeqAligns, numseq, qlength; | ^~~~~~~~~~~~ posit.c: In function ‘posPrintInformation’: posit.c:2319:8: warning: variable ‘querySize’ set but not used [-Wunused-but-set-variable] 2319 | Int4 querySize; | ^~~~~~~~~ posit.c: In function ‘posFindAlignmentDimensions’: posit.c:3064:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3064 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3070:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3070 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3079:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3079 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3086:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3086 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posPreprocessAlignment’: posit.c:3137:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3137 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c:3152:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3152 | fgets(nextLine, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posReadAlignment’: posit.c:3253:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3253 | fgets(nextline, ALIGN_LINE_LENGTH,checkFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ posit.c: At top level: posit.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: posit.c,v 6.88 2011/10/25 14:33:16 boratyng Exp $"; | ^~~~~ posit.c: In function ‘posFindAlignmentDimensions’: posit.c:3087:20: warning: ‘testCountSeqs’ may be used uninitialized [-Wmaybe-uninitialized] 3087 | testCountSeqs++; | ~~~~~~~~~~~~~^~ posit.c:3052:8: note: ‘testCountSeqs’ was declared here 3052 | Int4 testCountSeqs; /*counts number of sequences in each block | ^~~~~~~~~~~~~ posit.c: In function ‘posComputeSequenceWeights’: posit.c:1424:11: warning: ‘Sigma’ may be used uninitialized [-Wmaybe-uninitialized] 1424 | if (Sigma > 0) { | ^ posit.c:1314:16: note: ‘Sigma’ was declared here 1314 | Nlm_FloatHi Sigma; /*Number of different characters occurring in matches within | ^~~~~ posit.c:1447:36: warning: ‘intervalSigma’ may be used uninitialized [-Wmaybe-uninitialized] 1447 | posSearch->posSigma[qplace] = intervalSigma; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ posit.c:1316:16: note: ‘intervalSigma’ was declared here 1316 | Nlm_FloatHi intervalSigma; /*Same as Sigma but includes identical columns*/ | ^~~~~~~~~~~~~ In function ‘posReadPosFreqsScoremat’, inlined from ‘posReadCheckpoint’ at posit.c:2994:17: posit.c:2873:28: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 2873 | if (i < pssm->numColumns || j < pssm->numRows) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ posit.c: In function ‘posReadCheckpoint’: posit.c:2702:11: note: ‘j’ was declared here 2702 | Int4 i, j, c; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF lookup.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from lookup.c:308: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/blastdef.h:922, from ../include/blast.h:470, from lookup.c:309: lookup.c: In function ‘MegaBlastBuildLookupTable’: ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1047:35: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1047 | GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1051:35: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1051 | GET_EXTRA_CODE_18_OPT(seq)) & no_bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1078:31: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1078 | GET_EXTRA_CODE_18_OPT(seq) | bit0; | ^~~~~~~~~~~~~~~~~~~~~ ../include/lookup.h:299:61: warning: suggest parentheses around arithmetic in operand of ‘|’ [-Wparentheses] 299 | #define GET_EXTRA_CODE_18_OPT(s) (((*(s+1))<<2) | (*(s+2))) & MASK_EXTRA_OPT | ^ lookup.c:1082:31: note: in expansion of macro ‘GET_EXTRA_CODE_18_OPT’ 1082 | GET_EXTRA_CODE_18_OPT(seq) | bit0; | ^~~~~~~~~~~~~~~~~~~~~ lookup.c:914:25: warning: variable ‘extra_code’ set but not used [-Wunused-but-set-variable] 914 | register Int4 ecode, extra_code; | ^~~~~~~~~~ lookup.c: At top level: lookup.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: lookup.c,v 6.59 2005/07/28 14:57:10 coulouri Exp $"; | ^~~~~ lookup.c: In function ‘MegaBlastBuildLookupTable’: lookup.c:1004:37: warning: ‘extra_length’ may be used uninitialized [-Wmaybe-uninitialized] 1004 | last_offset = query_length - extra_length; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ lookup.c:923:22: note: ‘extra_length’ was declared here 923 | Int2 word_length, extra_length, word_weight; | ^~~~~~~~~~~~ lookup.c:975:10: warning: ‘word_weight’ may be used uninitialized [-Wmaybe-uninitialized] 975 | if (word_weight >= 12) { | ^ lookup.c:923:36: note: ‘word_weight’ was declared here 923 | Int2 word_length, extra_length, word_weight; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF readdb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from readdb.c:2057: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ readdb.c: In function ‘readdb_parse_db_names’: readdb.c:2503:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2503 | if (**filenames == '"') | ^ readdb.c: In function ‘s_GetBlastDirInfo’: readdb.c:2734:32: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 2734 | memset(blast_dir, 0, sizeof(blast_dir)); | ^ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3167:33: warning: format ‘%lld’ expects argument of type ‘long long int *’, but argument 3 has type ‘Nlm_Int8 *’ {aka ‘long int *’} [-Wformat=] 3167 | sscanf(ptr, "%lld", &(rdbap->len)); | ~~~^ ~~~~~~~~~~~~~ | | | | | Nlm_Int8 * {aka long int *} | long long int * | %ld readdb.c: In function ‘IndexFileExists’: readdb.c:3320:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3320 | if (rdfp->cih) | ^~ readdb.c:3326:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3326 | if (rdbap->first_oid > 0) { | ^~ readdb.c:3400:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3400 | if (rdfp->cih && rdfp->aliasfilebit == 0) | ^~ readdb.c:3406:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3406 | if (rdbap->first_oid > 0) { | ^~ readdb.c: In function ‘FindBlastDBFileEx’: readdb.c:3480:33: warning: unused variable ‘envp’ [-Wunused-variable] 3480 | CharPtr buffer, buffer1, envp = NULL; | ^~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3558:25: warning: unused variable ‘envp’ [-Wunused-variable] 3558 | CharPtr charptr, envp = NULL; | ^~~~ readdb.c: In function ‘readdb_get_link’: readdb.c:4752:12: warning: variable ‘loaded_new’ set but not used [-Wunused-but-set-variable] 4752 | Boolean loaded_new = FALSE; | ^~~~~~~~~~ readdb.c:4751:24: warning: variable ‘last_used’ set but not used [-Wunused-but-set-variable] 4751 | ReadDBFILEPtr last, last_used, rdfp_var; | ^~~~~~~~~ readdb.c: In function ‘readdb_check_oid’: readdb.c:4896:45: warning: comparisons like ‘X<=Y<=Z’ do not have their mathematical meaning [-Wparentheses] 4896 | if (rdfp_var->start <= oid <= rdfp_var->stop) | ~~~~~~~~~~~~~~~~^~~~~~ readdb.c: In function ‘readdb_seqid2fasta’: readdb.c:5236:22: warning: unused variable ‘dummy_gi’ [-Wunused-variable] 5236 | Int4 dummy_gi = 0; /* Not used, should have been handled above. */ | ^~~~~~~~ readdb.c:5180:13: warning: unused variable ‘chptr’ [-Wunused-variable] 5180 | CharPtr chptr = NULL; | ^~~~~ readdb.c: In function ‘FDBuildOldStyleDefline’: readdb.c:6366:33: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 6366 | MemSet(defline, '\0', sizeof(defline)); | ^ readdb.c: In function ‘PrintDbInformationWithRID’: readdb.c:7571:14: warning: comparison between pointer and zero character constant [-Wpointer-compare] 7571 | if (rdfp == FALSE) | ^~ readdb.c:7571:9: note: did you mean to dereference the pointer? 7571 | if (rdfp == FALSE) | ^ readdb.c: In function ‘FDBLoadMembershipsTable’: readdb.c:8265:21: warning: variable ‘fn_name’ set but not used [-Wunused-but-set-variable] 8265 | const char* fn_name = NULL; | ^~~~~~~ readdb.c: In function ‘SeqIdE2Index’: readdb.c:8613:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 8613 | if ((tsip->version > 0) && (tsip->release == NULL)) | ^~ readdb.c:8615:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 8615 | break; | ^~~~~ readdb.c:8618:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 8618 | if (tsip->version > 0) | ^~ readdb.c:8620:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 8620 | break; | ^~~~~ readdb.c:8577:13: warning: unused variable ‘tmp’ [-Wunused-variable] 8577 | CharPtr tmp, ptr=NULL; | ^~~ readdb.c:8576:11: warning: unused variable ‘tmptype’ [-Wunused-variable] 8576 | Uint1 tmptype; | ^~~~~~~ readdb.c: In function ‘SeqIdSetE2Index’: readdb.c:8881:14: warning: variable ‘oldanp’ set but not used [-Wunused-but-set-variable] 8881 | SeqIdPtr oldanp; | ^~~~~~ readdb.c: In function ‘FDBAddSequence2’: readdb.c:9804:30: warning: the comparison will always evaluate as ‘true’ for the address of ‘div’ will never be NULL [-Waddress] 9804 | srp->div ? srp->div : "N/A", (long) SequenceLen, | ^ ../include/readdb.h:1073:13: note: ‘div’ declared here 1073 | char div[4]; | ^~~ readdb.c:9853:49: warning: the comparison will always evaluate as ‘true’ for the address of ‘div’ will never be NULL [-Waddress] 9853 | (long) direc.owner, pc->div ? pc->div : "N/A", | ^ ../include/readdb.h:1073:13: note: ‘div’ declared here 1073 | char div[4]; | ^~~ readdb.c: In function ‘FindDBbyGI’: readdb.c:11397:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 11397 | if (gi > cih->maxgi) | ^~ readdb.c:11400:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 11400 | cigi = cih->ci + gi; | ^~~~ readdb.c: In function ‘Fastacmd_PrintTaxonomyInfo’: readdb.c:11875:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 11875 | if ( gi && (rdfp->gi_target != 0) && (gi->data.intvalue != rdfp->gi_target) ) | ^~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:191:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 191 | #define Nlm_MemSet memset | ^~~~~~ ../include/ncbimem.h:210:17: note: in expansion of macro ‘Nlm_MemSet’ 210 | #define MemSet Nlm_MemSet | ^~~~~~~~~~ readdb.c:11878:9: note: in expansion of macro ‘MemSet’ 11878 | MemSet(buf, 0, sizeof(buf)); | ^~~~~~ readdb.c: In function ‘Fastacmd_Search_ex’: readdb.c:12080:22: warning: variable ‘guess_gi’ set but not used [-Wunused-but-set-variable] 12080 | Int4 guess_gi = -1; | ^~~~~~~~ readdb.c: In function ‘DumpOneSequence’: readdb.c:12407:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 12407 | fprintf(fp, "%d\n", gi->data.intvalue); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int Nlm_Int8 {aka long int} | %ld readdb.c:12417:21: warning: unused variable ‘numeric_id’ [-Wunused-variable] 12417 | Boolean numeric_id = GetAccessionVersionFromSeqId(accn, &gi, &id, TRUE); | ^~~~~~~~~~ In file included from ../include/sqnutils.h:51, from readdb.c:2067: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ readdb.c:12829:1: warning: ‘readdb_preload_index’ defined but not used [-Wunused-function] 12829 | readdb_preload_index (ReadDBFILEPtr rdfp, Int4 first_db_seq, | ^~~~~~~~~~~~~~~~~~~~ In file included from readdb.c:2060: ../include/ncbisami.h:191:14: warning: ‘OneBit’ defined but not used [-Wunused-variable] 191 | static Uint1 OneBit[] = {0x80 , 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1}; | ^~~~~~ ../include/ncbisami.h:183:14: warning: ‘PowersOfTwo’ defined but not used [-Wunused-variable] 183 | static Uint4 PowersOfTwo[] = {01,02,04,010,020,040,0100,0200,0400,01000, | ^~~~~~~~~~~ readdb.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: readdb.c,v 6.549 2016/09/02 15:04:59 ucko Exp $"; | ^~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3084:53: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3084 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:3084:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:3090:57: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3090 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:3090:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_read_alias_file’: readdb.c:2994:57: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2994 | sprintf(full_buffer, "%s%c%s", file_path, | ^ In function ‘sprintf’, inlined from ‘readdb_read_alias_file’ at readdb.c:2994:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘Int4ListReadFromFile’: readdb.c:2656:31: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2656 | sprintf(file_name, "%s%s%s", blast_dir, DIRDELIMSTR, FileNameFind(fname)); | ^ In function ‘sprintf’, inlined from ‘Int4ListReadFromFileEx’ at readdb.c:2656:5, inlined from ‘Int4ListReadFromFile’ at readdb.c:2764:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2277:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2277 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2277:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2296:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2296 | sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2296:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2252:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2252 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2252:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2252:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2252 | sprintf(buffer, "%s.%csq", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2252:6: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘ReadDBOpenMHdrAndSeqFiles’: readdb.c:2259:27: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 2259 | sprintf(buffer, "%s.%chr", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘ReadDBOpenMHdrAndSeqFiles’ at readdb.c:2259:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_get_taxonomy_names’: readdb.c:5679:28: warning: ‘ufp_last’ may be used uninitialized [-Wmaybe-uninitialized] 5679 | ufp_last->next = ufp; | ~~~~~~~~~~~~~~~^~~~~ readdb.c:5627:23: note: ‘ufp_last’ was declared here 5627 | UserFieldPtr ufp, ufp_last; | ^~~~~~~~ readdb.c: In function ‘readdb_get_descriptor’: ../include/ncbimem.h:192:21: warning: ‘new_defline_length’ may be used uninitialized [-Wmaybe-uninitialized] 192 | #define Nlm_MemCpy memcpy readdb.c:6622:26: note: ‘new_defline_length’ was declared here 6622 | Int4 defline_length, new_defline_length; | ^~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3600:33: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3600 | sprintf(buffer1, "%s%s%s", buffer, DIRDELIMSTR, filename); | ^ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3600:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3671:25: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3671 | sprintf(buffer, "%s.%cin", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3671:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3811:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3811 | sprintf(buffer, "%s.%cnd", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3811:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3812:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3812 | sprintf(buffer1, "%s.%cni", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3812:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3825:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3825 | sprintf(buffer, "%s.%csd", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3825:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3826:26: warning: ‘%c’ directive writing 1 byte into a region of size between 0 and 4095 [-Wformat-overflow=] 3826 | sprintf(buffer1, "%s.%csi", rdfp->full_filename, is_prot? 'p':'n'); | ^~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3826:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3845:29: warning: ‘.ppd’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 3845 | sprintf(buffer, "%s.ppd", rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3845:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘readdb_new_internalEx’: readdb.c:3846:29: warning: ‘.ppi’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 3846 | sprintf(buffer1, "%s.ppi", rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘readdb_new_internalEx’ at readdb.c:3846:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ readdb.c: In function ‘GetAccList’: readdb.c:11821:29: warning: ‘AccListLast’ may be used uninitialized [-Wmaybe-uninitialized] 11821 | AccListLast->next = AccListTmp; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ readdb.c:11705:32: note: ‘AccListLast’ was declared here 11705 | FCMDAccListPtr AccListTmp, AccListLast; | ^~~~~~~~~~~ readdb.c: In function ‘FD_ConstructMultivolumeDBList’: readdb.c:12690:31: warning: ‘%03ld’ directive writing between 3 and 10 bytes into a region of size 9 [-Wformat-overflow=] 12690 | sprintf(numstr, ".%03ld ", (long) i); | ^~~~~ readdb.c:12690:29: note: directive argument in the range [100, 2147483646] 12690 | sprintf(numstr, ".%03ld ", (long) i); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘FD_ConstructMultivolumeDBList’ at readdb.c:12690:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 13 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbisam.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ncbisam.c:198: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisam.c: In function ‘ISAMMakeStringIndex’: ncbisam.c:842:22: warning: unused variable ‘file_pos’ [-Wunused-variable] 842 | Int4 file_pos = ftell(data->db_fd); | ^~~~~~~~ ncbisam.c: In function ‘ISAMInitSearch’: ncbisam.c:1399:10: warning: variable ‘reserved2’ set but not used [-Wunused-but-set-variable] 1399 | Int4 reserved2; | ^~~~~~~~~ ncbisam.c: At top level: ncbisam.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $"; | ^~~~~ In file included from ../include/ncbierr.h:105, from ../include/ncbimsg.h:78, from ../include/ncbi.h:60: ncbisam.c: In function ‘ISAMMakeNumericIndex’: ../include/ncbimisc.h:342:41: warning: ‘KeyInfo’ may be used uninitialized [-Wmaybe-uninitialized] 342 | #define Nlm_SwapUint4(value) Nlm_SwitchUint4(value) | ^~~~~~~~~~~~~~~~~~~~~~ ncbisam.c:983:14: note: ‘KeyInfo’ was declared here 983 | Uint4Ptr KeyInfo, KeySamples; | ^~~~~~~ ../include/ncbimisc.h:342:41: warning: ‘KeyDataInfo’ may be used uninitialized [-Wmaybe-uninitialized] 342 | #define Nlm_SwapUint4(value) Nlm_SwitchUint4(value) | ^~~~~~~~~~~~~~~~~~~~~~ ncbisam.c:984:21: note: ‘KeyDataInfo’ was declared here 984 | NISAMKeyDataPtr KeyDataInfo, KeyDataSamples; | ^~~~~~~~~~~ ncbisam.c:1060:27: warning: ‘KeySamples’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | KeySamples[SampleCount] = KeyInfo[i]; | ^ ncbisam.c:983:23: note: ‘KeySamples’ was declared here 983 | Uint4Ptr KeyInfo, KeySamples; | ^~~~~~~~~~ ncbisam.c:1062:31: warning: ‘KeyDataSamples’ may be used uninitialized [-Wmaybe-uninitialized] 1062 | KeyDataSamples[SampleCount] = KeyDataInfo[i]; | ^ ncbisam.c:984:34: note: ‘KeyDataSamples’ was declared here 984 | NISAMKeyDataPtr KeyDataInfo, KeyDataSamples; | ^~~~~~~~~~~~~~ ncbisam.c: In function ‘ISAMCreateDatabase’: ../include/ncbierr.h:246:23: warning: ‘field_in’ may be used uninitialized [-Wmaybe-uninitialized] 246 | #define ErrLogPrintf Nlm_ErrLogPrintf ncbisam.c:1177:37: note: ‘field_in’ was declared here 1177 | unsigned long uid_in, uid_last, field_in; | ^~~~~~~~ In file included from ../include/ncbi.h:59: ../include/ncbimem.h:232:23: warning: ‘prevterm’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1181:13: note: ‘prevterm’ was declared here 1181 | CharPtr prevterm; | ^~~~~~~~ ncbisam.c: In function ‘NISAMSearch’: ncbisam.c:1681:11: warning: ‘SampleNum’ may be used uninitialized [-Wmaybe-uninitialized] 1681 | if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) { | ^ ncbisam.c:1618:27: note: ‘SampleNum’ was declared here 1618 | Int4 Start = 0, Stop, SampleNum; | ^~~~~~~~~ ncbisam.c:1750:36: warning: ‘KeyPage’ may be used uninitialized [-Wmaybe-uninitialized] 1750 | Key = SwapUint4(KeyPage[current]); | ^ ncbisam.c:1619:24: note: ‘KeyPage’ was declared here 1619 | Int4 NumElements, *KeyPage, *KeyPageStart; | ^~~~~~~ ../include/ncbimem.h:232:23: warning: ‘KeyPageStart’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1619:34: note: ‘KeyPageStart’ was declared here 1619 | Int4 NumElements, *KeyPage, *KeyPageStart; | ^~~~~~~~~~~~ ../include/ncbimem.h:232:23: warning: ‘KeyDataPageStart’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree ncbisam.c:1622:55: note: ‘KeyDataPageStart’ was declared here 1622 | NISAMKeyDataPtr KeyDataPage=NULL, KeyDataSamples, KeyDataPageStart; | ^~~~~~~~~~~~~~~~ ncbisam.c: In function ‘SISAMSearch’: ncbisam.c:2373:8: warning: ‘SampleNum’ may be used uninitialized [-Wmaybe-uninitialized] 2373 | if ( (SampleNum < 0) || (SampleNum >= data->NumSamples)) { | ^ ncbisam.c:2280:29: note: ‘SampleNum’ was declared here 2280 | Int4 Diff, Start, Stop, SampleNum, Length, Pos; | ^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbisort.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbisort.h:62, from ../include/ncbisrti.h:60, from ncbisort.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbisort.c: In function ‘SORTFracCompare’: ncbisort.c:699:12: warning: type defaults to ‘int’ in declaration of ‘tmpa’ [-Wimplicit-int] 699 | register tmpa = UCHAR(*a), tmpb = UCHAR(*b); | ^~~~ ncbisort.c:699:30: warning: type defaults to ‘int’ in declaration of ‘tmpb’ [-Wimplicit-int] 699 | register tmpa = UCHAR(*a), tmpb = UCHAR(*b); | ^~~~ ../include/ncbisrti.h: At top level: ../include/ncbisrti.h:213:13: warning: ‘inthandler’ declared ‘static’ but never defined [-Wunused-function] 213 | static void inthandler(int i); | ^~~~~~~~~~ ncbisort.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: ncbisort.c,v 6.9 2012/08/22 23:02:39 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/salign.h:10, from salign.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salign.c: In function ‘BandAlignTwoSeqLocsFunc’: salign.c:173:13: warning: variable ‘is_prot’ set but not used [-Wunused-but-set-variable] 173 | Boolean is_prot; | ^~~~~~~ salign.c: In function ‘SortBlastHits’: salign.c:391:15: warning: variable ‘totalvalmax’ set but not used [-Wunused-but-set-variable] 391 | totalvalmax = INT4_MAX, | ^~~~~~~~~~~ salign.c: In function ‘link_solution’: salign.c:1188:15: warning: unused variable ‘first’ [-Wunused-variable] 1188 | Boolean first = TRUE; | ^~~~~ salign.c: At top level: salign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: salign.c,v 6.11 2009/01/21 17:09:18 bollin Exp $"; | ^~~~~ salign.c: In function ‘SortBlastHits’: salign.c:411:35: warning: ‘salpdup’ may be used uninitialized [-Wmaybe-uninitialized] 411 | for (salptmp=salpdup; salptmp!=NULL; salptmp=salptmp->next) | ^ salign.c:380:15: note: ‘salpdup’ was declared here 380 | SeqAlignPtr salpdup, | ^~~~~~~ salign.c: In function ‘TranslateSeqLoc.constprop.0’: salign.c:660:10: warning: ‘slpp’ may be used uninitialized [-Wmaybe-uninitialized] 660 | return slpp; | ^~~~ salign.c:633:17: note: ‘slpp’ was declared here 633 | SeqLocPtr slpp; | ^~~~ In function ‘find_maxsolution’, inlined from ‘get_solutions’ at salign.c:1313:3, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1270:38: warning: ‘start1’ may be used uninitialized [-Wmaybe-uninitialized] 1270 | intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1229:22: note: ‘start1’ was declared here 1229 | Int4 start, start1, stop; | ^~~~~~ In function ‘find_maxsolution’, inlined from ‘get_solutions’ at salign.c:1313:3, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1270:38: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 1270 | intronlg = (float)(abs(stop - start1) - alignlen)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1229:30: note: ‘stop’ was declared here 1229 | Int4 start, start1, stop; | ^~~~ In function ‘get_solutions’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1348:38: warning: ‘start1’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1301:22: note: ‘start1’ was declared here 1301 | Int4 start, start1, stop; | ^~~~~~ In function ‘get_solutions’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1481:22: salign.c:1348:38: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | intronlg = (float)(abs(stop - start1) - alignlens)/(float)(j-1); | ~~~~~^~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1301:30: note: ‘stop’ was declared here 1301 | Int4 start, start1, stop; | ^~~~ In function ‘seqalign_reverse_sorting’, inlined from ‘BlastBandAlignTwoSeqLocs.isra.0’ at salign.c:1489:25: salign.c:1433:17: warning: ‘tail’ may be used uninitialized [-Wmaybe-uninitialized] 1433 | tail->next = salptmp; | ~~~~~~~~~~~^~~~~~~~~ salign.c: In function ‘BlastBandAlignTwoSeqLocs.isra.0’: salign.c:1408:15: note: ‘tail’ was declared here 1408 | tail, | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF salptool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from salptool.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ salptool.c: In function ‘MergeTwoDspBySIM4’: salptool.c:285:17: warning: variable ‘has_overlap’ set but not used [-Wunused-but-set-variable] 285 | Boolean has_overlap; | ^~~~~~~~~~~ salptool.c:281:14: warning: variable ‘gap’ set but not used [-Wunused-but-set-variable] 281 | Int4 gap=0,gap_1, gap_2; | ^~~ salptool.c: In function ‘extend_dsp_ends’: salptool.c:1329:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1329 | else | ^~~~ salptool.c:1331:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1331 | if(extend_len > 0) | ^~ salptool.c:1346:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1346 | else | ^~~~ salptool.c:1348:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1348 | if(extend_len > 0) | ^~ salptool.c:1363:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1363 | else | ^~~~ salptool.c:1365:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1365 | if(extend_len > 0) | ^~ salptool.c:1380:21: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1380 | else | ^~~~ salptool.c:1382:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1382 | if(extend_len > 0) | ^~ In file included from ../include/sqnutils.h:51, from salptool.c:12: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from salptool.c:14: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ salptool.c:1518:24: warning: ‘OrderBestHits’ defined but not used [-Wunused-function] 1518 | static int LIBCALLBACK OrderBestHits(Pointer ptr1, Pointer ptr2) | ^~~~~~~~~~~~~ salptool.c:1468:13: warning: ‘showtextalign_fromalign’ defined but not used [-Wunused-function] 1468 | static void showtextalign_fromalign (SeqAlignPtr salp, CharPtr path, FILE *fp) | ^~~~~~~~~~~~~~~~~~~~~~~ salptool.c:1453:13: warning: ‘getlengthforid’ defined but not used [-Wunused-function] 1453 | static Int4 getlengthforid (SeqIdPtr sip) | ^~~~~~~~~~~~~~ salptool.c:1267:16: warning: ‘need_recompute’ defined but not used [-Wunused-function] 1267 | static Boolean need_recompute(SeqAlignPtr align, Int4 m_len, Int4 s_len) | ^~~~~~~~~~~~~~ salptool.c:838:13: warning: ‘SeqLocTrimPolyATail’ defined but not used [-Wunused-function] 838 | static void SeqLocTrimPolyATail(SeqLocPtr loc_2, BioseqPtr bsp_2) { | ^~~~~~~~~~~~~~~~~~~ salptool.c:46:13: warning: ‘SeqAnnotWrite’ defined but not used [-Wunused-function] 46 | static void SeqAnnotWrite(SeqAlignPtr align) | ^~~~~~~~~~~~~ salptool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: salptool.c,v 6.57 2008/07/07 18:52:31 bollin Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from urkutil.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkutil.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkpcc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkpcc.h:54, from urkpcc.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkpcc.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkpcc.c,v 6.13 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkptpf.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objres.h:73, from urkptpf.c:65: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkptpf.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkptpf.c,v 6.33 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkepi.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkepi.h:54, from urkepi.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkepi.c: In function ‘PredictEpiI0’: urkepi.c:214:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 214 | epip->epiarray[*seq] += 1; | ^~~~ urkepi.c:239:59: warning: array subscript has type ‘char’ [-Wchar-subscripts] 239 | episcore = DownArrayScore (episcore, epip->epiarray[*seq]); | ^~~~ urkepi.c:240:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 240 | epip->epiarray[*seq] += 1; | ^~~~ urkepi.c:241:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 241 | episcore = UpArrayScore (episcore, epip->epiarray[*seq]); | ^~~~ urkepi.c:263:59: warning: array subscript has type ‘char’ [-Wchar-subscripts] 263 | episcore = DownArrayScore (episcore, epip->epiarray[*(seq-window)]); | ^~~~~~~~~~~~~ urkepi.c:264:22: warning: array subscript has type ‘char’ [-Wchar-subscripts] 264 | epip->epiarray[*(seq-window)] -= 1; | ^~~~~~~~~~~~~ urkepi.c:265:57: warning: array subscript has type ‘char’ [-Wchar-subscripts] 265 | episcore = UpArrayScore (episcore, epip->epiarray[*(seq-window)]); | ^~~~~~~~~~~~~ urkepi.c: In function ‘OptimizeEpiComp’: urkepi.c:605:18: warning: array subscript has type ‘char’ [-Wchar-subscripts] 605 | bin[seq[i]] += 1; | ~~~^~~ urkepi.c:621:18: warning: array subscript has type ‘char’ [-Wchar-subscripts] 621 | bin[seq[i]] += 1; | ~~~^~~ urkepi.c:651:19: warning: array subscript has type ‘char’ [-Wchar-subscripts] 651 | if (fbin[seq[i]] > expect) | ~~~^~~ urkepi.c:657:19: warning: array subscript has type ‘char’ [-Wchar-subscripts] 657 | if (fbin[seq[i]] > expect) | ~~~^~~ urkepi.c: In function ‘OptimizeEpiHP’: urkepi.c:782:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 782 | epip->epiarray[seq[j]] += 1; | ~~~^~~ urkepi.c:797:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 797 | epip->epiarray[seq[j]] += 1; | ~~~^~~ urkepi.c:837:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 837 | epip->epiarray[seq[n]] -= 1; | ~~~^~~ urkepi.c: In function ‘OptimizeEpiProbFunc’: urkepi.c:982:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 982 | epip->epiarray[seq[n]] += 1; | ~~~^~~ urkepi.c:994:31: warning: array subscript has type ‘char’ [-Wchar-subscripts] 994 | epip->epiarray[seq[n]] += 1; | ~~~^~~ urkepi.c: At top level: urkepi.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkepi.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ In function ‘OptimizeEpiProbFunc’, inlined from ‘FilterEpi’ at urkepi.c:1190:5: urkepi.c:1052:20: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized] 1052 | cfap->left = left; | ~~~~~~~~~~~^~~~~~ urkepi.c: In function ‘FilterEpi’: urkepi.c:936:50: note: ‘left’ was declared here 936 | Int4 i, n, j, k, start, stop, loop, fact, left, right; | ^~~~ In function ‘OptimizeEpiProbFunc’, inlined from ‘FilterEpi’ at urkepi.c:1190:5: urkepi.c:1053:21: warning: ‘right’ may be used uninitialized [-Wmaybe-uninitialized] 1053 | cfap->right = right; | ~~~~~~~~~~~~^~~~~~~ urkepi.c: In function ‘FilterEpi’: urkepi.c:936:56: note: ‘right’ was declared here 936 | Int4 i, n, j, k, start, stop, loop, fact, left, right; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkfltr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkfltr.h:51, from urkfltr.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkfltr.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkfltr.c,v 6.8 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkdust.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkdust.h:51, from urkdust.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkdust.c: In function ‘DustMe_h’: urkdust.c:196:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 196 | (dcvp->curlevel <= newlevel) && dcvp->curend == loop+1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ urkdust.c: In function ‘DustForGraph’: urkdust.c:776:17: warning: variable ‘drphead’ set but not used [-Wunused-but-set-variable] 776 | DustRegionPtr drphead; | ^~~~~~~ urkdust.c: At top level: urkdust.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkdust.c,v 6.10 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urksigu.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urksigu.h:57, from urksigu.c:59: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urksigu.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urksigu.c,v 6.5 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seg.c seg.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: seg.c,v 6.19 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ seg.c: In function ‘getprob’: seg.c:935:15: warning: ‘ans2’ may be used uninitialized [-Wmaybe-uninitialized] 935 | ans = ans1 + ans2 - totseq; | ~~~~~^~~~~~ seg.c:916:23: note: ‘ans2’ was declared here 916 | FloatHi ans, ans1, ans2, totseq; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkbias.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from urkbias.c:56: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkbias.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkbias.c,v 6.7 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urkcnsrt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urkcnsrt.h:60, from urkcnsrt.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urkcnsrt.c:1203:13: warning: ‘ScanFrame’ defined but not used [-Wunused-function] 1203 | static void ScanFrame (BioseqPtr bsp, SeqLocPtr slp, Int4 frame, | ^~~~~~~~~ urkcnsrt.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urkcnsrt.c,v 6.21 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ urkcnsrt.c: In function ‘Scan3Frames’: urkcnsrt.c:1385:19: warning: ‘length’ may be used uninitialized [-Wmaybe-uninitialized] 1385 | for (i = n; i < length; i++) | ~~^~~~~~~~ urkcnsrt.c:1312:34: note: ‘length’ was declared here 1312 | Int4 i, n, start, stop, length, chunk; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF urktree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/urktree.h:51, from urktree.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ urktree.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: urktree.c,v 6.6 2003/05/30 17:25:38 coulouri Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pseed3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pseed3.c:176: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pseed3.c: In function ‘SeedPruneHitsFromSeedReturn’: pseed3.c:230:17: warning: variable ‘curSegs’ set but not used [-Wunused-but-set-variable] 230 | DenseSegPtr curSegs, testSegs; /*Used to extract ids from curSeqAlign, testSeqAlign*/ | ^~~~~~~ pseed3.c: In function ‘seedEngineCore’: pseed3.c:507:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 507 | while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) { | ^~~~~~~ pseed3.c: In function ‘output_hits’: pseed3.c:1202:10: warning: variable ‘posBaseIndex’ set but not used [-Wunused-but-set-variable] 1202 | Int4 posBaseIndex; /*loop index for copying pos results arrays*/ | ^~~~~~~~~~~~ pseed3.c: In function ‘init_order’: pseed3.c:1483:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1483 | seedSearch->order[seedSearch->pchars[i]] = i; | ^ pseed3.c:1483:45: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1483 | seedSearch->order[seedSearch->pchars[i]] = i; | ~~~~~~~~~~~~~~~~~~^~~ pseed3.c:1487:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1487 | seedSearch->charMultiple[i] = 0; | ^ pseed3.c:1489:37: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1489 | if (seedSearch->standardProb[i] > seedepsilon) { | ^ pseed3.c:1490:29: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1490 | matrixRow = matrix[i]; | ^ pseed3.c:1493:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1493 | if (seedSearch->standardProb[j] > seedepsilon) | ^ pseed3.c:1494:49: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1494 | rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]); | ^ pseed3.c:1494:93: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1494 | rowSum += seedSearch->standardProb[j]*exp(-(seedSearch->paramLambda)*matrixRow[j]); | ^ pseed3.c:1496:35: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1496 | seedSearch->charMultiple[i] = rowSum; | ^ pseed3.c: At top level: pseed3.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pseed3.c,v 6.54 2008/10/31 18:51:07 madden Exp $"; | ^~~~~ pseed3.c: In function ‘seedParallelFill’: pseed3.c:712:68: warning: iteration 100 invokes undefined behavior [-Waggressive-loop-optimizations] 712 | returnData->seedSearch->name_space[i] = seedSearch->name_space[i]; | ~~~~~~~~~~~~~~~~~~~~~~^~~ pseed3.c:711:18: note: within this loop 711 | for( i = 0; i <= BUF_SIZE; i++) x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pattern1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from pattern1.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pattern1.c: In function ‘init_pattern’: pattern1.c:286:77: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | positionProbability = seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c:303:78: warning: array subscript has type ‘char’ [-Wchar-subscripts] 303 | positionProbability += seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c:317:78: warning: array subscript has type ‘char’ [-Wchar-subscripts] 317 | positionProbability -= seedSearch->standardProb[seedSearch->order[c]]; | ~~~~~~~~~~~~~~~~~^~~ pattern1.c: In function ‘find_hitsS_DNA’: pattern1.c:534:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 534 | if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { | ^~~ pattern1.c:547:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 547 | if (tmp = (prefixMatchedBitPattern & patternSearch->DNAwhichPrefixPosPtr[seq[i]])) { | ^~~ pattern1.c: At top level: pattern1.c:744:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 744 | static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch) | ^~~ pattern1.c: In function ‘and’: pattern1.c:750:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 750 | if (result[i] = (a[i] & b[i])) | ^~~~~~ pattern1.c: In function ‘align’: pattern1.c:1102:14: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 1102 | if (leftd >= 1) | ^ pattern1.c: In function ‘pat_output’: pattern1.c:1637:9: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 1637 | else | ^~~~ pattern1.c:1639:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 1639 | ValNodeCopyStr(info_vnp, 0, buffer); | ^~~~~~~~~~~~~~ pattern1.c: At top level: pattern1.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: pattern1.c,v 6.22 2006/08/04 21:11:17 papadopo Exp $"; | ^~~~~ pattern1.c: In function ‘align’: pattern1.c:1158:15: warning: ‘CDrow’ may be used uninitialized [-Wmaybe-uninitialized] 1158 | score = (CDrow-1)->CC; | ~~~~~~^~~~~~~~~~~~~~~ pattern1.c:1049:25: note: ‘CDrow’ was declared here 1049 | register dp_ptr CDrow; /*points to a row of CD*/ | ^~~~~ pattern1.c: In function ‘get_patLL’: pattern1.c:1393:19: warning: ‘pos’ may be used uninitialized [-Wmaybe-uninitialized] 1393 | for (j = 0; j < pos; j+= wordIndex) { | ~~^~~~~ pattern1.c:1363:10: note: ‘pos’ was declared here 1363 | Int4 pos; /*keeps track of how many intermediate hits*/ | ^~~ pattern1.c: In function ‘get_patL’: pattern1.c:1348:10: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 1348 | *end = wordIndex*BITS_PACKED_PER_WORD+j; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:1311:10: note: ‘j’ was declared here 1311 | Int4 j; /*index over bits in a word*/ | ^ In function ‘longpacking2’, inlined from ‘init_pattern’ at pattern1.c:357:7: pattern1.c:859:10: warning: ‘tj’ may be used uninitialized [-Wmaybe-uninitialized] 859 | if (placeIndex==numPlacesInPattern || inputPatternMasked[placeIndex] < 0 | ^ pattern1.c: In function ‘init_pattern’: pattern1.c:192:11: note: ‘tj’ was declared here 192 | Int4 tj; /*temporary copy of j*/ | ^~ pattern1.c: In function ‘align_of_pattern’: pattern1.c:1506:30: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 1506 | local_score += ALIGN_B(querySeq-1, dbSeq-1, hitArray1[wordIndex+1], hitArray2[wordIndex+1], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1507 | BAND_LOW, BAND_HIGH, matrix, gap_open, gap_extend, alignScript, data); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pattern1.c:1425:14: note: ‘data’ was declared here 1425 | data_dp *data; /*stores dynaic program info*/ | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF impatool.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from impatool.c:73: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ impatool.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: impatool.c,v 6.16 2006/06/30 18:44:40 camacho Exp $"; | ^~~~~ In file included from ../include/ncbi.h:59: impatool.c: In function ‘IMPALAPrintHelp’: ../include/ncbimem.h:232:23: warning: ‘ret_buffer’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define MemFree Nlm_MemFree impatool.c:288:17: note: ‘ret_buffer’ was declared here 288 | CharPtr ret_buffer; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF posit2.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from posit2.c:78: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ posit2.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: posit2.c,v 6.12 2006/09/18 20:54:27 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mbalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/mbalign.h:4, from mbalign.c:176: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mbalign.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: mbalign.c,v 6.43 2006/02/02 17:57:34 papadopo Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF vecscrn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vecscrn.h:74, from vecscrn.c:103: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ vecscrn.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: vecscrn.c,v 6.137 2005/12/27 14:46:44 madden Exp $"; | ^~~~~ vecscrn.c: In function ‘VSPrintOverviewFromSeqLocs’: vecscrn.c:1078:24: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1078 | while (tmp) | ^~~ vecscrn.c:993:75: note: ‘tmp’ was declared here 993 | SeqLocPtr seqloc1=NULL, seqloc2=NULL, seqloc3=NULL, seqloc4=NULL, tmp; | ^~~ vecscrn.c: In function ‘VSPrintListFromSeqLocs’: vecscrn.c:1188:24: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 1188 | while (tmp) | ^~~ vecscrn.c:1152:75: note: ‘tmp’ was declared here 1152 | SeqLocPtr seqloc1=NULL, seqloc2=NULL, seqloc3=NULL, seqloc4=NULL, tmp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF mblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from mblast.c:710: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mblast.c: In function ‘BioseqMegaBlastEngineCore’: mblast.c:961:19: warning: statement with no effect [-Wunused-value] 961 | stop_timer("BioseqBlastEngineCore: before do_the_blast_run()"); | ^ mblast.c:987:12: warning: statement with no effect [-Wunused-value] 987 | stop_timer("MegaBlastEngineCore: after do_the_blast_run()"); | ^ mblast.c:942:21: warning: variable ‘seqalign’ set but not used [-Wunused-but-set-variable] 942 | SeqAlignPtr seqalign, PNTR seqalignp; | ^~~~~~~~ mblast.c: In function ‘MegaBlastSetUpSearchInternalByLoc’: mblast.c:1167:16: warning: variable ‘avglen’ set but not used [-Wunused-but-set-variable] 1167 | Nlm_FloatHi avglen; | ^~~~~~ mblast.c: In function ‘MegaBlastPackAlignmentsByQuery’: mblast.c:1829:14: warning: variable ‘slp’ set but not used [-Wunused-but-set-variable] 1829 | SeqLocPtr slp; | ^~~ mblast.c: In function ‘MegaBlastWordFinder_disc_1b’: mblast.c:2372:32: warning: variable ‘mask’ set but not used [-Wunused-but-set-variable] 2372 | register Int4 s_off, ecode, mask, q_off, extra_code; | ^~~~ mblast.c: At top level: mblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: mblast.c,v 6.215 2006/09/21 13:42:37 madden Exp $"; | ^~~~~ mblast.c: In function ‘MegaBlastWordFinder_disc’: mblast.c:2250:53: warning: ‘ecode2’ may be used uninitialized [-Wmaybe-uninitialized] 2250 | (((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) { | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c:2024:17: note: ‘ecode2’ was declared here 2024 | Int4 ecode1, ecode2; | ^~~~~~ mblast.c:2117:51: warning: ‘ecode1’ may be used uninitialized [-Wmaybe-uninitialized] 2117 | (((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0) | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c:2024:9: note: ‘ecode1’ was declared here 2024 | Int4 ecode1, ecode2; | ^~~~~~ In function ‘MegaBlastWordFinder_disc_1b’, inlined from ‘MegaBlastWordFinder’ at mblast.c:2749:17: mblast.c:2620:54: warning: ‘ecode2’ may be used uninitialized [-Wmaybe-uninitialized] 2620 | (((PV_ARRAY_TYPE) 1)<<(ecode2&PV_ARRAY_MASK))) == 0))) { | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c: In function ‘MegaBlastWordFinder’: mblast.c:2373:17: note: ‘ecode2’ was declared here 2373 | Int4 ecode1, ecode2; | ^~~~~~ In function ‘MegaBlastWordFinder_disc_1b’, inlined from ‘MegaBlastWordFinder’ at mblast.c:2749:17: mblast.c:2475:52: warning: ‘ecode1’ may be used uninitialized [-Wmaybe-uninitialized] 2475 | (((PV_ARRAY_TYPE) 1)<<(ecode1&PV_ARRAY_MASK))) == 0) | ~~~~~~~^~~~~~~~~~~~~~~ mblast.c: In function ‘MegaBlastWordFinder’: mblast.c:2373:9: note: ‘ecode1’ was declared here 2373 | Int4 ecode1, ecode2; | ^~~~~~ mblast.c: In function ‘MegaBlastGapInfoToSeqAlign’: mblast.c:3575:11: warning: ‘seqalign’ may be used uninitialized [-Wmaybe-uninitialized] 3575 | return seqalign; | ^~~~~~~~ mblast.c:3504:16: note: ‘seqalign’ was declared here 3504 | SeqAlignPtr seqalign, seqalign_var, sap; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF rpsutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/rpsutil.h:128, from rpsutil.c:281: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rpsutil.c: In function ‘getAuxInformation’: rpsutil.c:399:30: warning: the comparison will always evaluate as ‘true’ for the address of ‘underlyingMatrixName’ will never be NULL [-Waddress] 399 | if (underlyingMatrixName != NULL) | ^~ rpsutil.c:382:10: note: ‘underlyingMatrixName’ declared here 382 | Char underlyingMatrixName[PATH_MAX]; /*name of matrix to read*/ | ^~~~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSBlastSearchLight’: rpsutil.c:1838:10: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1838 | Int2 status; | ^~~~~~ rpsutil.c: In function ‘SaveUntilChar’: rpsutil.c:2190:13: warning: comparison between pointer and zero character constant [-Wpointer-compare] 2190 | if (ptr != NULLB) | ^~ rpsutil.c:2190:9: note: did you mean to dereference the pointer? 2190 | if (ptr != NULLB) | ^ rpsutil.c: In function ‘RPSBgetCddHits’: rpsutil.c:2210:21: warning: variable ‘found_score’ set but not used [-Wunused-but-set-variable] 2210 | Boolean found_score = FALSE; | ^~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from rpsutil.c:282: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘getAuxInformation’: rpsutil.c:398:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 398 | fscanf(matrixAuxiliaryFile,"%s",underlyingMatrixName); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:404:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 404 | fscanf(matrixAuxiliaryFile,"%d\n", gap_open); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:405:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 405 | fscanf(matrixAuxiliaryFile,"%d\n", gap_extend); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf(matrixAuxiliaryFile, "%le", &Kungapped); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:407:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 407 | fscanf(matrixAuxiliaryFile, "%le", &Hungapped); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:408:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 408 | fscanf(matrixAuxiliaryFile, "%d", &maxLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:409:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 409 | fscanf(matrixAuxiliaryFile, "%d", &dbLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:410:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 410 | fscanf(matrixAuxiliaryFile, "%lf", &privateScalingFactor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:415:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 415 | fscanf(matrixAuxiliaryFile, "%d", &maxLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:416:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 416 | fscanf(matrixAuxiliaryFile, "%le", &(rpsinfo->karlinK[index])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c: At top level: rpsutil.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: rpsutil.c,v 6.76 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ rpsutil.c: In function ‘RPSAlignTraceBack’: rpsutil.c:1433:24: warning: ‘rev_subject_length’ may be used uninitialized [-Wmaybe-uninitialized] 1433 | seqalign = BlastGetGapAlgnTbck (search, 0, TRUE, FALSE, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1434 | subject, subject_length, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1435 | rev_subject, rev_subject_length); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rpsutil.c:1295:41: note: ‘rev_subject_length’ was declared here 1295 | Int4 index, index1, subject_length, rev_subject_length; | ^~~~~~~~~~~~~~~~~~ rpsutil.c:1444:32: warning: ‘posMatrix’ may be used uninitialized [-Wmaybe-uninitialized] 1444 | search->sbp->posMatrix = posMatrix; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ rpsutil.c:1296:18: note: ‘posMatrix’ was declared here 1296 | Int4Ptr PNTR posMatrix; | ^~~~~~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:451:28: warning: ‘.rps’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 451 | sprintf(rps_matrix, "%s.rps", rpsinfo->rdfp->full_filename); | ^~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:451:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:452:28: warning: ‘.loo’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 452 | sprintf(rps_lookup, "%s.loo", rpsinfo->rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:452:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSInitEx’: rpsutil.c:453:25: warning: ‘.aux’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 453 | sprintf(rps_aux, "%s.aux", rpsinfo->rdfp->full_filename); | ^~~~ In function ‘sprintf’, inlined from ‘RPSInitEx’ at rpsutil.c:453:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rpsutil.c: In function ‘RPSCalcEValue’: rpsutil.c:1269:30: warning: ‘posMatrix’ may be used uninitialized [-Wmaybe-uninitialized] 1269 | search->sbp->posMatrix = posMatrix; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ rpsutil.c:1188:16: note: ‘posMatrix’ was declared here 1188 | Int4Ptr PNTR posMatrix; | ^~~~~~~~~ In file included from ../include/ncbi.h:62: rpsutil.c: In function ‘RPSBgetCddHits’: ../include/ncbistr.h:284:25: warning: ‘dbname’ may be used uninitialized [-Wmaybe-uninitialized] 284 | #define Nlm_StrCmp strcmp rpsutil.c:2212:21: note: ‘dbname’ was declared here 2212 | CharPtr dbname; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF kappa.c kappa.c: In function ‘Kappa_SequenceGetProteinRange’: kappa.c:1399:7: warning: unused variable ‘i’ [-Wunused-variable] 1399 | int i; | ^ kappa.c: At top level: kappa.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: kappa.c,v 6.94 2013/11/04 15:42:10 boratyng Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF xmlblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/xmlblast.h:89, from xmlblast.c:171: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ xmlblast.c: In function ‘PSIXmlInit’: xmlblast.c:1239:13: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 1239 | Boolean retval = FALSE; | ^~~~~~ xmlblast.c: At top level: xmlblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: xmlblast.c,v 6.41 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ xmlblast.c: In function ‘BXMLGetSeqLineForStdSeg’: xmlblast.c:373:28: warning: ‘genetic_code2’ may be used uninitialized [-Wmaybe-uninitialized] 373 | CharPtr genetic_code1, genetic_code2; | ^~~~~~~~~~~~~ xmlblast.c: In function ‘BXMLSeqAlignToHits’: xmlblast.c:867:36: warning: ‘hspp’ may be used uninitialized [-Wmaybe-uninitialized] 867 | if((hspp->next = BXMLGetHspFromSeqAlign(sap2, is_aa, chain, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 868 | is_ooframe, mask_loc)) == NULL) | ~~~~~~~~~~~~~~~~~~~~~~ xmlblast.c:799:12: note: ‘hspp’ was declared here 799 | HspPtr hspp; | ^~~~ xmlblast.c: In function ‘SeqAlignToHits’: xmlblast.c:1646:24: warning: ‘hspp’ may be used uninitialized [-Wmaybe-uninitialized] 1646 | hspp->next = GetHspFromSeqAlign(sap2, ungapped, &hsp_count); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlblast.c:1618:11: note: ‘hspp’ was declared here 1618 | HspPtr hspp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF bxmlobj.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from bxmlobj.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ bxmlobj.c: In function ‘BlastOutputAsnRead’: bxmlobj.c:96:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 96 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘ParametersAsnRead’: bxmlobj.c:361:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 361 | AsnReadFunc func; | ^~~~ bxmlobj.c:360:12: warning: unused variable ‘isError’ [-Wunused-variable] 360 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: In function ‘IterationAsnRead’: bxmlobj.c:613:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 613 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘StatisticsAsnRead’: bxmlobj.c:829:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 829 | AsnReadFunc func; | ^~~~ bxmlobj.c:828:12: warning: unused variable ‘isError’ [-Wunused-variable] 828 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: In function ‘HitAsnRead’: bxmlobj.c:1039:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1039 | AsnReadFunc func; | ^~~~ bxmlobj.c: In function ‘HspAsnRead’: bxmlobj.c:1244:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1244 | AsnReadFunc func; | ^~~~ bxmlobj.c:1243:12: warning: unused variable ‘isError’ [-Wunused-variable] 1243 | Boolean isError = FALSE; | ^~~~~~~ bxmlobj.c: At top level: bxmlobj.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: bxmlobj.c,v 6.11 2006/09/18 15:20:39 bealer Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dotseq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from ../include/tofasta.h:47, from ../include/dotseq.h:63, from dotseq.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dotseq.c:96:36: warning: missing braces around initializer [-Wmissing-braces] 96 | static Int4 DOTblosum62[24][24] = { | ^ 97 | 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4, | { } 98 | -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4, | { } 99 | -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4, | { } 100 | -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4, | { } 101 | 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4, | { } 102 | -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4, | { } 103 | -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4, | { } 104 | 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4, | { } 105 | -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4, | { } 106 | -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4, | { } 107 | -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4, | { } 108 | -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4, | { } 109 | -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4, | { } 110 | -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4, | { } 111 | -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4, | { } 112 | 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4, | { } 113 | 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4, | { } 114 | -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4, | { } 115 | -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4, | { } 116 | 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4, | { } 117 | -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4, | { } 118 | -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4, | { } 119 | 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4, | { } 120 | -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1 | { 121 | }; | } dotseq.c: In function ‘DOT_BuildPLookup’: dotseq.c:887:31: warning: variable ‘found_ambig’ set but not used [-Wunused-but-set-variable] 887 | Boolean EXACTMATCH, found_ambig, saved_index = FALSE; | ^~~~~~~~~~~ dotseq.c:885:19: warning: unused variable ‘threshold’ [-Wunused-variable] 885 | Int4 threshold=13; /* one-hit heuristics T must be at least 13*/ | ^~~~~~~~~ dotseq.c:883:19: warning: unused variable ‘index’ [-Wunused-variable] 883 | Int4 index = 0; | ^~~~~ dotseq.c: In function ‘DOT_ComputeHits’: dotseq.c:1043:47: warning: variable ‘q_end’ set but not used [-Wunused-but-set-variable] 1043 | Uint1Ptr s, subject0, s_end, q_end; | ^~~~~ dotseq.c:1041:19: warning: unused variable ‘saved_index’ [-Wunused-variable] 1041 | Boolean saved_index = FALSE; | ^~~~~~~~~~~ dotseq.c:1039:19: warning: unused variable ‘threshold’ [-Wunused-variable] 1039 | Int4 threshold=13; | ^~~~~~~~~ dotseq.c: In function ‘DOT_SPI_FindBestAlnByDotPlot’: dotseq.c:2016:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 2016 | Uint1 strand; | ^~~~~~ dotseq.c:2015:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 2015 | Int4 start2; | ^~~~~~ dotseq.c:2014:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 2014 | Int4 start1; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from dotseq.c:87: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ dotseq.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: dotseq.c,v 6.14 2006/07/13 17:16:20 bollin Exp $"; | ^~~~~ In function ‘DOT_ScoreCount’, inlined from ‘DOT_BuildHitList’ at dotseq.c:1327:5: dotseq.c:1260:16: warning: ‘hitlist’ may be used uninitialized [-Wmaybe-uninitialized] 1260 | score=hitlist[0]->score; | ~~~~~~~^~~ dotseq.c: In function ‘DOT_BuildHitList’: dotseq.c:1309:19: note: ‘hitlist’ was declared here 1309 | DOTDiagPtr PNTR hitlist; | ^~~~~~~ In function ‘DOT_ScoreCount’, inlined from ‘DOT_BuildHitList’ at dotseq.c:1327:5: dotseq.c:1264:11: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 1264 | while (i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF spidey.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/spidey.h:102, from spidey.c:263: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ spidey.c: In function ‘SPI_PrintResult’: spidey.c:1740:21: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 1740 | Int4 offset; | ^~~~~~ spidey.c: In function ‘SPI_AlnSinglemRNAToPieces’: spidey.c:2854:19: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 2854 | if (spot->from == spot->to == 0) | ~~~~~~~~~~~^~~~~~~~~~~ spidey.c: In function ‘SPI_FillInLastmRNAHoles’: spidey.c:6299:21: warning: variable ‘internal’ set but not used [-Wunused-but-set-variable] 6299 | Boolean internal; | ^~~~~~~~ spidey.c: In function ‘SPI_FindBestAlnByDotPlot’: spidey.c:6445:20: warning: variable ‘strand’ set but not used [-Wunused-but-set-variable] 6445 | Uint1 strand; | ^~~~~~ spidey.c:6444:20: warning: variable ‘start2’ set but not used [-Wunused-but-set-variable] 6444 | Int4 start2; | ^~~~~~ spidey.c:6443:20: warning: variable ‘start1’ set but not used [-Wunused-but-set-variable] 6443 | Int4 start1; | ^~~~~~ spidey.c: In function ‘SPI_ConnectAlnPieces’: spidey.c:7814:30: warning: variable ‘tmparray’ set but not used [-Wunused-but-set-variable] 7814 | SPI_FragPtr PNTR tmparray; | ^~~~~~~~ spidey.c:7800:25: warning: variable ‘sfpprev’ set but not used [-Wunused-but-set-variable] 7800 | SPI_FragPtr sfpprev; | ^~~~~~~ spidey.c: In function ‘SPI_AdjustSplicesInPieces’: spidey.c:8448:23: warning: variable ‘minus’ set but not used [-Wunused-but-set-variable] 8448 | Boolean minus; | ^~~~~ spidey.c: In function ‘SPI_CheckMrnaOrder’: spidey.c:10296:35: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10296 | if ((ival->strand == Seq_strand_plus == ival2->strand spidey.c:10300:38: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10300 | || (ival->strand == Seq_strand_minus == ival2->strand spidey.c:10313:35: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10313 | if ((ival->strand == Seq_strand_plus == ival2->strand spidey.c:10315:38: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] 10315 | || (ival->strand == Seq_strand_plus == ival2->strand In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/spidey.h:103: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ spidey.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: spidey.c,v 6.74 2016/09/02 14:57:38 ucko Exp $"; | ^~~~~ spidey.c: In function ‘SPI_GetProteinFrommRNA’: spidey.c:9765:14: warning: ‘c1start’ may be used uninitialized [-Wmaybe-uninitialized] 9765 | tmp += c1start; | ^~ spidey.c:9727:18: note: ‘c1start’ was declared here 9727 | Int4 c1start; | ^~~~~~~ spidey.c:9771:14: warning: ‘c2start’ may be used uninitialized [-Wmaybe-uninitialized] 9771 | tmp += c2start; | ^~ spidey.c:9728:18: note: ‘c2start’ was declared here 9728 | Int4 c2start; | ^~~~~~~ spidey.c:9777:14: warning: ‘c3start’ may be used uninitialized [-Wmaybe-uninitialized] 9777 | tmp += c3start; | ^~ spidey.c:9729:18: note: ‘c3start’ was declared here 9729 | Int4 c3start; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF motif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/motif.h:45, from motif.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ motif.c: In function ‘MOT_FindPolyA’: motif.c:86:18: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 86 | Uint1 buf[MOT_WINSIZE]; | ^~~ motif.c: In function ‘MOT_FindKozak’: motif.c:216:18: warning: variable ‘buf’ set but not used [-Wunused-but-set-variable] 216 | Uint1 buf[MOT_WINSIZE]; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from ../include/motif.h:48: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ motif.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: motif.c,v 6.7 2007/05/07 13:30:54 kans Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blfmtutl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from blfmtutl.c:175: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blfmtutl.c: In function ‘CBStatisticsGetReference’: blfmtutl.c:593:11: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 593 | } else | ^~~~ blfmtutl.c:595:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 595 | add_string_to_bufferEx("Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,", &ret_buffer, &ret_buffer_length, TRUE); | ^~~~~~~~~~~~~~~~~~~~~~ blfmtutl.c: In function ‘BlastPrintTabularResults’: blfmtutl.c:1281:16: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1281 | for (index=1; ssp->next; index++) | ^~~ blfmtutl.c:1283:20: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1283 | num_gap_opens = index / 2; | ^~~~~~~~~~~~~ blfmtutl.c: At top level: blfmtutl.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: blfmtutl.c,v 1.44 2012/10/10 14:05:50 fongah2 Exp $"; | ^~~~~ blfmtutl.c: In function ‘BlastPrintTabularResults’: blfmtutl.c:1076:11: warning: ‘query_id’ may be used uninitialized [-Wmaybe-uninitialized] 1076 | if (SeqIdComp(query_id, old_query_id) != SIC_YES) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blfmtutl.c:1039:13: note: ‘query_id’ was declared here 1039 | SeqIdPtr query_id, old_query_id = NULL, subject_id, old_subject_id = NULL; | ^~~~~~~~ blfmtutl.c:1117:13: warning: ‘alignments_count’ may be used uninitialized [-Wmaybe-uninitialized] 1117 | if (--alignments_count < 0) | ^ blfmtutl.c:1048:9: note: ‘alignments_count’ was declared here 1048 | Int4 alignments_count; | ^~~~~~~~~~~~~~~~ blfmtutl.c:1350:21: warning: ‘q_start’ may be used uninitialized [-Wmaybe-uninitialized] 1350 | q_start += q_shift; | ~~~~~~~~^~~~~~~~~~ blfmtutl.c:1035:9: note: ‘q_start’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~~~ blfmtutl.c:1351:19: warning: ‘q_end’ may be used uninitialized [-Wmaybe-uninitialized] 1351 | q_end += q_shift; | ~~~~~~^~~~~~~~~~ blfmtutl.c:1035:18: note: ‘q_end’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~ blfmtutl.c:1352:21: warning: ‘s_start’ may be used uninitialized [-Wmaybe-uninitialized] 1352 | s_start += s_shift; | ~~~~~~~~^~~~~~~~~~ blfmtutl.c:1035:25: note: ‘s_start’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~~~ blfmtutl.c:1353:19: warning: ‘s_end’ may be used uninitialized [-Wmaybe-uninitialized] 1353 | s_end += s_shift; | ~~~~~~^~~~~~~~~~ blfmtutl.c:1035:34: note: ‘s_end’ was declared here 1035 | Int4 q_start, q_end, s_start, s_end; | ^~~~~ blfmtutl.c: In function ‘BlastSetUserErrorString’: blfmtutl.c:1448:21: warning: ‘title’ may be used uninitialized [-Wmaybe-uninitialized] 1448 | else if (title) | ^ blfmtutl.c:1413:33: note: ‘title’ was declared here 1413 | CharPtr buf_start, ptr, title; | ^~~~~ rm -f libncbitool.a ar cru libncbitool.a csim.o db_slist.o dust.o blast_dust.o falign.o g_any.o sim2.o sim3.o sim4.o simutil.o slist.o sec.o tfuns.o toasn3.o toporg.o pobutil.o stsutil.o suggadj.o suggest.o suggslp.o blast.o blastutl.o blastool.o blastconcat.o splutil.o gapxdrop.o bandalg0.o bandalg1.o bandalg2.o bandalg3.o bandalg4.o bandalg5.o bandalgn.o blastkar.o actutils.o posit.o lookup.o readdb.o ncbisam.o ncbisort.o salign.o salptool.o urkutil.o urkpcc.o urkptpf.o urkepi.o urkfltr.o urkdust.o urksigu.o seg.o urkbias.o urkcnsrt.o urktree.o pseed3.o pattern1.o impatool.o posit2.o mbalign.o vecscrn.o mblast.o rpsutil.o kappa.o xmlblast.o bxmlobj.o dotseq.o spidey.o motif.o blfmtutl.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbitool.a ../lib ranlib ../lib/libncbitool.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF matrix_frequency_data.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF compo_mode_condition.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF composition_adjustment.c In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:780:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:475:26: warning: ‘RowProb’ may be used uninitialized [-Wmaybe-uninitialized] 475 | probs[eBchar] = probs[eDchar] + probs[eNchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:772:12: note: ‘RowProb’ declared here 772 | double RowProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:780:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:475:42: warning: ‘RowProb’ may be used uninitialized [-Wmaybe-uninitialized] 475 | probs[eBchar] = probs[eDchar] + probs[eNchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:772:12: note: ‘RowProb’ declared here 772 | double RowProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:780:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:476:26: warning: ‘RowProb’ may be used uninitialized [-Wmaybe-uninitialized] 476 | probs[eZchar] = probs[eEchar] + probs[eQchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:772:12: note: ‘RowProb’ declared here 772 | double RowProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:780:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:476:42: warning: ‘RowProb’ may be used uninitialized [-Wmaybe-uninitialized] 476 | probs[eZchar] = probs[eEchar] + probs[eQchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:772:12: note: ‘RowProb’ declared here 772 | double RowProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:783:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:475:26: warning: ‘ColProb’ may be used uninitialized [-Wmaybe-uninitialized] 475 | probs[eBchar] = probs[eDchar] + probs[eNchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:773:12: note: ‘ColProb’ declared here 773 | double ColProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:783:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:475:42: warning: ‘ColProb’ may be used uninitialized [-Wmaybe-uninitialized] 475 | probs[eBchar] = probs[eDchar] + probs[eNchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:773:12: note: ‘ColProb’ declared here 773 | double ColProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:783:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:476:26: warning: ‘ColProb’ may be used uninitialized [-Wmaybe-uninitialized] 476 | probs[eZchar] = probs[eEchar] + probs[eQchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:773:12: note: ‘ColProb’ declared here 773 | double ColProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ In function ‘s_SetPairAmbigProbsToSum’, inlined from ‘s_ScoresStdAlphabet’ at composition_adjustment.c:783:5, inlined from ‘Blast_CompositionMatrixAdj’ at composition_adjustment.c:1405:9: composition_adjustment.c:476:42: warning: ‘ColProb’ may be used uninitialized [-Wmaybe-uninitialized] 476 | probs[eZchar] = probs[eEchar] + probs[eQchar]; | ~~~~~^~~~~~~~ composition_adjustment.c: In function ‘Blast_CompositionMatrixAdj’: composition_adjustment.c:773:12: note: ‘ColProb’ declared here 773 | double ColProb[COMPO_LARGEST_ALPHABET]; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF nlm_linear_algebra.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF optimize_target_freq.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF compo_heap.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF smith_waterman.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF redo_alignment.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF unified_pvalues.c rm -f libblastcompadj.a ar cru libblastcompadj.a matrix_frequency_data.o compo_mode_condition.o composition_adjustment.o nlm_linear_algebra.o optimize_target_freq.o compo_heap.o smith_waterman.o redo_alignment.o unified_pvalues.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblastcompadj.a ../lib ranlib ../lib/libblastcompadj.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gdfontg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontg.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gdfontmb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontmb.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gdfontt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontt.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pictogif.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from pictogif.c:50: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gdfontl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfontl.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gdfonts.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/gifgen.h:115, from gdfonts.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -DWIN_GIF -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbidrwg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ncbidrwg.c:43: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ncbidrwg.c: In function ‘Nlm_ClearRgn’: ncbidrwg.c:6081:16: warning: variable ‘ntool’ set but not used [-Wunused-but-set-variable] 6081 | Nlm_RgnTool ntool; | ^~~~~ ncbidrwg.c: In function ‘Nlm_DiffRgn’: ncbidrwg.c:6273:16: warning: variable ‘ntool3’ set but not used [-Wunused-but-set-variable] 6273 | Nlm_RgnTool ntool3; | ^~~~~~ ncbidrwg.c:6272:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6272 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6271:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6271 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_XorRgn’: ncbidrwg.c:6324:16: warning: variable ‘ntool3’ set but not used [-Wunused-but-set-variable] 6324 | Nlm_RgnTool ntool3; | ^~~~~~ ncbidrwg.c:6323:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6323 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6322:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6322 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_EqualRgn’: ncbidrwg.c:6353:16: warning: variable ‘ntool2’ set but not used [-Wunused-but-set-variable] 6353 | Nlm_RgnTool ntool2; | ^~~~~~ ncbidrwg.c:6352:16: warning: variable ‘ntool1’ set but not used [-Wunused-but-set-variable] 6352 | Nlm_RgnTool ntool1; | ^~~~~~ ncbidrwg.c: In function ‘Nlm_EmptyRgn’: ncbidrwg.c:6381:17: warning: variable ‘ntool’ set but not used [-Wunused-but-set-variable] 6381 | Nlm_RgnTool ntool; | ^~~~~ ncbidrwg.c: In function ‘Nlm_CopyPixmap’: ncbidrwg.c:7040:25: warning: variable ‘height’ set but not used [-Wunused-but-set-variable] 7040 | Nlm_Int2 height; | ^~~~~~ ncbidrwg.c:7039:25: warning: variable ‘width’ set but not used [-Wunused-but-set-variable] 7039 | Nlm_Int2 width; | ^~~~~ ncbidrwg.c: In function ‘s_DoQuadrant’: ncbidrwg.c:5618:22: warning: ‘rr.left’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~ ncbidrwg.c:5614:12: note: ‘rr.left’ was declared here 5614 | Nlm_RecT rr; | ^~ ncbidrwg.c:5619:22: warning: ‘rr.top’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~ ncbidrwg.c:5614:12: note: ‘rr.top’ was declared here 5614 | Nlm_RecT rr; | ^~ ncbidrwg.c:5618:10: warning: ‘rr.right’ may be used uninitialized [-Wmaybe-uninitialized] 5618 | rx = rr.right - rr.left; | ~~^~~~~~ ncbidrwg.c:5614:12: note: ‘rr.right’ was declared here 5614 | Nlm_RecT rr; | ^~ ncbidrwg.c:5619:10: warning: ‘rr.bottom’ may be used uninitialized [-Wmaybe-uninitialized] 5619 | ry = rr.bottom - rr.top; | ~~^~~~~~~ ncbidrwg.c:5614:12: note: ‘rr.bottom’ was declared here 5614 | Nlm_RecT rr; | ^~ ncbidrwg.c: In function ‘Nlm_SelectFont.part.0’: ncbidrwg.c:2879:8: warning: ‘fdata.print’ may be used uninitialized [-Wmaybe-uninitialized] 2879 | if (fdata.print != NULL && Nlm_nowPrinting) { | ^ ncbidrwg.c:2875:17: note: ‘fdata.print’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ ncbidrwg.c:2906:8: warning: ‘fdata.fontspec.size’ may be used uninitialized [-Wmaybe-uninitialized] 2906 | if (fdata.fontspec.size >= 16) { | ^ ncbidrwg.c:2875:17: note: ‘fdata.fontspec.size’ was declared here 2875 | Nlm_FontData fdata; | ^~~~~ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_ResetDrawingTools’ at ncbidrwg.c:854:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_ResetDrawingTools’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Black’ at ncbidrwg.c:1056:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Black’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Red’ at ncbidrwg.c:1077:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Red’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Green’ at ncbidrwg.c:1098:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Green’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Blue’ at ncbidrwg.c:1119:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Blue’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Cyan’ at ncbidrwg.c:1140:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Cyan’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Magenta’ at ncbidrwg.c:1161:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Magenta’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Yellow’ at ncbidrwg.c:1182:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Yellow’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_White’ at ncbidrwg.c:1203:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_White’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_Gray’ at ncbidrwg.c:1210:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_Gray’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_LtGray’ at ncbidrwg.c:1216:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_LtGray’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ In function ‘Nlm_SelectColor’, inlined from ‘Nlm_DkGray’ at ncbidrwg.c:1222:3: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c: In function ‘Nlm_DkGray’: ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ ncbidrwg.c: In function ‘Nlm_SelectColor’: ncbidrwg.c:1319:19: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1319 | Nlm_curGIFColor = (int)Nlm_GetColorRGB ( red, green, blue ); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ ncbidrwg.c: In function ‘Nlm_GetColorRGB’: ncbidrwg.c:1373:10: warning: ‘i’ may be used uninitialized [-Wmaybe-uninitialized] 1373 | return (Nlm_Uint4)i; | ^~~~~~~~~~~~ ncbidrwg.c:1360:7: note: ‘i’ was declared here 1360 | int i; | ^ rm -f libvibgif.a ar cru libvibgif.a gdfontg.o gdfontmb.o gdfontt.o pictogif.o gdfontl.o gdfonts.o ncbidrwg.o drawing.o mapping.o picture.o ncbimain.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibgif.a ../lib ranlib ../lib/libvibgif.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF algorend.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/viewer3d.h:125, from algorend.c:584: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ algorend.c: In function ‘ColorFromSS’: algorend.c:893:10: warning: unused variable ‘rsult’ [-Wunused-variable] 893 | Int2 rsult = 0; | ^~~~~ algorend.c: In function ‘Cn3D_RenWire’: algorend.c:1400:10: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1400 | PMLD pmldThis = NULL; | ^~~~~~~~ algorend.c:1399:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1399 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ algorend.c:1398:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1398 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘Cn3D_ColSeqCons’: algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1795 | pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i); | ^ algorend.c: In function ‘RenderObject’: algorend.c:3135:25: warning: variable ‘fZTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3135:19: warning: variable ‘fYTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3135:13: warning: variable ‘fXTo’ set but not used [-Wunused-but-set-variable] 3135 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3134:29: warning: variable ‘fZFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3134:21: warning: variable ‘fYFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3134:13: warning: variable ‘fXFrom’ set but not used [-Wunused-but-set-variable] 3134 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c: In function ‘RenderLabel’: algorend.c:3393:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 3393 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘RenderBond’: algorend.c:3554:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3554 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderHalfWormBond’: algorend.c:3673:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3673 | PMSD pmsdParent; | ^~~~~~~~~~ algorend.c:3671:24: warning: variable ‘pmad2’ set but not used [-Wunused-but-set-variable] 3671 | PMAD pmad0, pmad1, pmad2, pmad3; | ^~~~~ algorend.c: In function ‘RenderAnAtom’: algorend.c:3758:10: warning: unused variable ‘pmadFrom’ [-Wunused-variable] 3758 | PMAD pmadFrom = NULL; | ^~~~~~~~ algorend.c:3757:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3757 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderAllAtom’: algorend.c:3829:9: warning: variable ‘iMenu’ set but not used [-Wunused-but-set-variable] 3829 | int iMenu; | ^~~~~ algorend.c:3815:11: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 3815 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c:3811:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 3811 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderGraph’: algorend.c:4498:10: warning: unused variable ‘bReservedThis’ [-Wunused-variable] 4498 | Byte bReservedThis = 0; | ^~~~~~~~~~~~~ algorend.c: In function ‘LabelChainTermini’: algorend.c:4772:14: warning: unused variable ‘pmbdThis’ [-Wunused-variable] 4772 | PMBD pmbdThis = NULL; | ^~~~~~~~ algorend.c:4771:15: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 4771 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderMolecule’: algorend.c:4871:11: warning: variable ‘pdnmmThis’ set but not used [-Wunused-but-set-variable] 4871 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘fnARLoop’: algorend.c:5556:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 5556 | Int2 iTest; | ^~~~~ algorend.c: In function ‘AlgorithmicRendering’: algorend.c:5684:10: warning: unused variable ‘i’ [-Wunused-variable] 5684 | Int2 i = 0; | ^ algorend.c:5683:10: warning: unused variable ‘Cn3d_LayerNow_sofar’ [-Wunused-variable] 5683 | Int2 Cn3d_LayerNow_sofar = 0; | ^~~~~~~~~~~~~~~~~~~ algorend.c: In function ‘Do3DOrigin’: algorend.c:5756:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 5756 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c:5751:13: warning: variable ‘fTo’ set but not used [-Wunused-but-set-variable] 5751 | FloatLo fTo[3]; | ^~~ algorend.c:5750:13: warning: variable ‘fFrom’ set but not used [-Wunused-but-set-variable] 5750 | FloatLo fFrom[3]; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from algorend.c:598: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ algorend.c:2265:13: warning: ‘LabelGroupOnOffProc’ defined but not used [-Wunused-function] 2265 | static void LabelGroupOnOffProc(GrouP g) | ^~~~~~~~~~~~~~~~~~~ algorend.c:717:16: warning: ‘Cn3d_CopyToNode’ defined but not used [-Wunused-variable] 717 | static Boolean Cn3d_CopyToNode = FALSE; | ^~~~~~~~~~~~~~~ In file included from ../include/viewer3d.h:129: algorend.c: In function ‘RenderLabel’: ../include/pictur3d.h:235:27: warning: ‘iX’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:10: note: ‘iX’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ ../include/pictur3d.h:235:27: warning: ‘iY’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:14: note: ‘iY’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ ../include/pictur3d.h:235:27: warning: ‘iZ’ may be used uninitialized [-Wmaybe-uninitialized] 235 | #define AddText3D Nlm_AddText3D algorend.c:3389:18: note: ‘iZ’ was declared here 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3442:41: warning: ‘fXCen’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3391:13: note: ‘fXCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3443:41: warning: ‘fYCen’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3391:20: note: ‘fYCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3444:41: warning: ‘fZCen’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3391:27: note: ‘fZCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3442:41: warning: ‘fXTo’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3390:13: note: ‘fXTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3443:41: warning: ‘fYTo’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3390:19: note: ‘fYTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3444:41: warning: ‘fZTo’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3390:25: note: ‘fZTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3442:22: warning: ‘fXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:13: note: ‘fXFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3443:22: warning: ‘fYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:21: note: ‘fYFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3444:22: warning: ‘fZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~~~ algorend.c:3388:29: note: ‘fZFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c: In function ‘MasterChangeRenderProc.isra.0’: algorend.c:1295:29: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 1295 | pars->PBBRender = k; | ~~~~~~~~~~~~~~~~^~~ algorend.c:1138:16: note: ‘k’ was declared here 1138 | Int2 i, j, k; | ^ algorend.c: In function ‘RenderObject’: ../include/pictur3d.h:234:27: warning: ‘iXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:10: note: ‘iXFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:18: note: ‘iYFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3136:26: note: ‘iZFrom’ was declared here 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:234:27: warning: ‘iXTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:10: note: ‘iXTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:234:27: warning: ‘iYTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:16: note: ‘iYTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:234:27: warning: ‘iZTo’ may be used uninitialized [-Wmaybe-uninitialized] 234 | #define AddCylinder3D Nlm_AddCylinder3D algorend.c:3137:22: note: ‘iZTo’ was declared here 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c: In function ‘Do3DOrigin’: ../include/pictur3d.h:232:27: warning: ‘iXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:10: note: ‘iXFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:18: note: ‘iYFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5752:26: note: ‘iZFrom’ was declared here 5752 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ ../include/pictur3d.h:232:27: warning: ‘iXTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:10: note: ‘iXTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:232:27: warning: ‘iYTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:16: note: ‘iYTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ ../include/pictur3d.h:232:27: warning: ‘iZTo’ may be used uninitialized [-Wmaybe-uninitialized] 232 | #define AddLine3D Nlm_AddLine3D algorend.c:5753:22: note: ‘iZTo’ was declared here 5753 | Int4 iXTo, iYTo, iZTo; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dmsel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsel.c:60: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dopen.c:394: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dopen.c: In function ‘Cn3D_OpenStart’: cn3dopen.c:722:10: warning: unused variable ‘iBioseq’ [-Wunused-variable] 722 | Int4 iBioseq = 0; | ^~~~~~~ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:1000:19: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1000 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dopen.c:989:25: warning: unused variable ‘pbsasThis’ [-Wunused-variable] 989 | BiostrucAlignSeqPtr pbsasThis = NULL; | ^~~~~~~~~ cn3dopen.c: In function ‘Cn3D_NetOpenBiostruc’: cn3dopen.c:1310:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 1310 | ButtoN b; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dopen.c:412: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from cn3dopen.c:413: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ cn3dopen.c:431:15: warning: ‘Cn3D_bOpenBrowse’ defined but not used [-Wunused-variable] 431 | static ButtoN Cn3D_bOpenBrowse; | ^~~~~~~~~~~~~~~~ cn3dopen.c:430:15: warning: ‘Cn3D_wOpen’ defined but not used [-Wunused-variable] 430 | static WindoW Cn3D_wOpen; | ^~~~~~~~~~ In function ‘Cn3D_ShredCBlast’, inlined from ‘MMDB_ReadMime’ at cn3dopen.c:1058:23: cn3dopen.c:527:8: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 527 | if (salp) { | ^ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:513:15: note: ‘salp’ was declared here 513 | SeqAlign *salp; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dsave.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dsave.c:157: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportAsnNow’: cn3dsave.c:375:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 375 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dsave.c:372:24: warning: variable ‘pbsfThis’ set but not used [-Wunused-but-set-variable] 372 | BiostrucFeaturePtr pbsfThis; | ^~~~~~~~ cn3dsave.c:366:10: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 366 | PMSD pmsdSlave = NULL, pmsdMaster = NULL; | ^~~~~~~~~ cn3dsave.c:362:27: warning: variable ‘FirstSlave’ set but not used [-Wunused-but-set-variable] 362 | Boolean iCn3d = TRUE, FirstSlave = FALSE; | ^~~~~~~~~~ cn3dsave.c:357:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 357 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveBiostruc’: cn3dsave.c:524:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 524 | ButtoN b; | ^ cn3dsave.c:523:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 523 | GrouP gMS; | ^~~ cn3dsave.c:518:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 518 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportDictNow’: cn3dsave.c:598:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 598 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c:596:10: warning: unused variable ‘iCount’ [-Wunused-variable] 596 | Int4 iCount = 0; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveDictionary’: cn3dsave.c:629:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 629 | ButtoN b; | ^ cn3dsave.c:624:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 624 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_SaveSub’: cn3dsave.c:688:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 688 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dsave.c:171: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dsave.c:184:15: warning: ‘Cn3D_bFeatOn’ defined but not used [-Wunused-variable] 184 | static ButtoN Cn3D_bFeatOn; | ^~~~~~~~~~~~ In file included from cn3dsave.c:165: ../include/asnmime.h:119:21: warning: ‘amp’ defined but not used [-Wunused-variable] 119 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnmime.h:118:19: warning: ‘at’ defined but not used [-Wunused-variable] 118 | static AsnTypePtr at = atx; | ^~ ../include/asnmime.h:117:23: warning: ‘avn’ defined but not used [-Wunused-variable] 117 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/asnmime.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnmime.h12"; | ^~~~~~~~~~~ cn3dsave.c: In function ‘Cn3D_GetSubSet’: cn3dsave.c:289:24: warning: ‘isep’ may be used uninitialized [-Wmaybe-uninitialized] 289 | isep->next = SeqEntryNew(); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ cn3dsave.c:261:28: note: ‘isep’ was declared here 261 | SeqEntry *sep = NULL, *isep; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dxprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dxprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportPDB’: cn3dxprt.c:209:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 209 | ButtoN b; | ^ cn3dxprt.c:208:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 208 | GrouP gMS; | ^~~ cn3dxprt.c:203:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 203 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportKin’: cn3dxprt.c:381:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 381 | ButtoN b; | ^ cn3dxprt.c:380:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 380 | GrouP gMS; | ^~~ cn3dxprt.c:375:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 375 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportSub’: cn3dxprt.c:513:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 513 | IteM i; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dwin.c:647: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces] 733 | { | ^ 734 | 255, 255, 255, /* default 0 */ | { } 735 | 255, 20, 147, /* hotpink 1 */ | { } 736 | 255, 0, 255, /* magenta 2 */ | { } 737 | 155, 48, 255, /* purple 3 */ | { } 738 | 0, 0, 255, /* blue 4 */ | { } 739 | 30, 144, 255, /* sky 5 */ | { } 740 | 0, 255, 255, /* cyan 6 */ | { } 741 | 0, 255, 127, /* sea 7 */ | { } 742 | 0, 255, 0, /* green 8 */ | { } 743 | 255, 255, 0, /* yellow 9 */ | { } 744 | 255, 165, 0, /* gold 10 */ | { } 745 | 255, 69, 0, /* orange 11 */ | { } 746 | 255, 0, 0, /* red 12 */ | { } 747 | 255, 114, 86, /* pink 13 */ | { } 748 | 255, 174, 185, /* pinktint 14 */ | { } 749 | 255, 255, 255, /* white 15 */ | { } 750 | 0, 0, 0, /* black 16 */ | { } 751 | 176, 226, 255, /* bluetint 17 */ | { } 752 | 154, 255, 154, /* greentint 18 */ | { } 753 | 255, 236, 139, /* yellowtint 19 */ | { } 754 | 125, 125, 125, /* gray 20 */ | { } 755 | 139, 87, 66, /* brown 21 */ | { } 756 | 255, 0, 0, /* perm colors 22: red */ | { } 757 | 0, 255, 0, /* perm colors 23: green */ | { } 758 | 255, 0, 255, /* perm colors 24: magenta */ | { } 759 | 30, 144, 255, /* perm colors 25: sky */ | { } 760 | 155, 48, 255, /* perm colors 26: purple */ | { } 761 | 0, 255, 0, /* SS colors 27: helix, green */ | { } 762 | 255, 165, 0, /* SS colors 28: strand, gold */ | { } 763 | 255, 69, 0, /* SS colors 29: turn, orange */ | { } 764 | 0, 255, 255, /* SS colors 30: coil, cyan */ | { } 765 | 255, 255, 0, /* highlight colors 31: yellow */ | { } 766 | 0, 0, 0, /* background colors 32: black */ | { } 767 | 160, 82, 45, /* sienna 33 */ | { } 768 | 240, 230, 140, /* khaki 34 */ | { } 769 | 171, 130, 255, /* light purple 35 */ | { } 770 | 255, 200, 0, /* orange yellow 36 */ | { } 771 | 117, 128, 160, /* 37 */ | { } 772 | 5, 53, 239, /* 38 */ | { } 773 | 27, 62, 255, /* 39 */ | { } 774 | 84, 110, 203, /* 40 */ | { } 775 | 216, 77, 84, /* 41 */ | { } 776 | 125, 128, 135, /* 42 */ | { } 777 | 237, 29, 61, /* 43 */ | { } 778 | 184, 118, 120, /* 44 */ | { } 779 | 155, 9, 0, /* 45 */ | { } 780 | 155, 119, 107, /* 46 */ | { } 781 | 80, 110, 196, /* 47 */ | { } 782 | 122, 127, 157, /* 48 */ | { } 783 | 50, 85, 241, /* 49 */ | { } 784 | 201, 93, 91, /* 50 */ | { } 785 | 254, 0, 5, /* 51 */ | { } 786 | 155, 137, 133, /* 52 */ | { } 787 | 3, 53, 246 /* 53 */ | { 788 | }; | } cn3dwin.c: In function ‘Viewer3DGroups’: cn3dwin.c:1728:10: warning: unused variable ‘groups’ [-Wunused-variable] 1728 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Viewer3DViewer’: cn3dwin.c:1784:10: warning: unused variable ‘groups’ [-Wunused-variable] 1784 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_AlignEdit’: cn3dwin.c:1936:10: warning: unused variable ‘iCount’ [-Wunused-variable] 1936 | Int2 iCount = 0; | ^~~~~~ cn3dwin.c:1935:10: warning: variable ‘pmmdThis’ set but not used [-Wunused-but-set-variable] 1935 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dwin.c:1933:17: warning: unused variable ‘salp’ [-Wunused-variable] 1933 | SeqAlignPtr salp = NULL; | ^~~~ cn3dwin.c:1931:29: warning: variable ‘pmsdSlave’ set but not used [-Wunused-but-set-variable] 1931 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dwin.c:1930:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 1930 | PDNMS pdnmsSlave = NULL; | ^~~~~~~~~~ cn3dwin.c: In function ‘Cn3D_Menus’: cn3dwin.c:2131:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2131 | (Nlm_VoidPtr) i, NULL); | ^ In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from cn3dwin.c:665: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dwin.c:1626:13: warning: ‘HLmolecule_MA’ defined but not used [-Wunused-function] 1626 | static void HLmolecule_MA(MAPtr ma, | ^~~~~~~~~~~~~ cn3dwin.c:1428:13: warning: ‘HLatom_MA’ defined but not used [-Wunused-function] 1428 | static void HLatom_MA(MAPtr ma, | ^~~~~~~~~ cn3dwin.c:929:13: warning: ‘Cn3D_MoveCB’ defined but not used [-Wunused-function] 929 | static void Cn3D_MoveCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:922:13: warning: ‘Cn3D_ZoomCB’ defined but not used [-Wunused-function] 922 | static void Cn3D_ZoomCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:688:13: warning: ‘Cn3D_iModelCtrl’ defined but not used [-Wunused-variable] 688 | static IteM Cn3D_iModelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:682:13: warning: ‘Cn3D_iLabelCtrl’ defined but not used [-Wunused-variable] 682 | static IteM Cn3D_iLabelCtrl = NULL; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dentr.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dmsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsg.c:254: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmsg.c: In function ‘SeqStrucMediaMsgFunc’: cn3dmsg.c:593:19: warning: variable ‘omudp’ set but not used [-Wunused-but-set-variable] 593 | OMUserDataPtr omudp = NULL; | ^~~~~ In file included from ../include/sqnutils.h:51, from cn3dmsg.c:267: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmsg.c:271: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dmatn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmatn.c:173: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmatn.c: In function ‘FindMM’: cn3dmatn.c:217:29: warning: unused variable ‘pdnmsThisSlave’ [-Wunused-variable] 217 | PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL; | ^~~~~~~~~~~~~~ cn3dmatn.c: In function ‘DoMediaHL’: cn3dmatn.c:249:10: warning: variable ‘MainAtom’ set but not used [-Wunused-but-set-variable] 249 | Byte MainAtom = 0; | ^~~~~~~~ cn3dmatn.c:247:10: warning: unused variable ‘paldThis’ [-Wunused-variable] 247 | PALD paldThis = NULL; | ^~~~~~~~ cn3dmatn.c:246:11: warning: unused variable ‘pvnalThis’ [-Wunused-variable] 246 | PVNAL pvnalThis = NULL; | ^~~~~~~~~ cn3dmatn.c:245:10: warning: unused variable ‘pmadThis’ [-Wunused-variable] 245 | PMAD pmadThis = NULL; | ^~~~~~~~ cn3dmatn.c:244:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 244 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ cn3dmatn.c: In function ‘Cn3DCheckAndDoHighlight’: cn3dmatn.c:372:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 372 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmatn.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dmodl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dmodl.c:302: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckNoSingleHighlight’: cn3dmodl.c:353:11: warning: unused variable ‘pdnmgThis’ [-Wunused-variable] 353 | PDNMG pdnmgThis = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckHighlighted’: cn3dmodl.c:364:29: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 364 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ReSetVisibleStatus’: cn3dmodl.c:508:10: warning: unused variable ‘pmgd’ [-Wunused-variable] 508 | PMGD pmgd = NULL; | ^~~~ cn3dmodl.c:507:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 507 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:506:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 506 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘fnAlignList’: cn3dmodl.c:996:25: warning: unused variable ‘itemtype’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:996:11: warning: unused variable ‘entityID’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:995:14: warning: unused variable ‘sipThis’ [-Wunused-variable] 995 | SeqIdPtr sipThis = NULL; | ^~~~~~~ cn3dmodl.c:993:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 993 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SynchronizeModVisibleStatus’: cn3dmodl.c:1065:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 1065 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:1064:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 1064 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SetResidueVisibilities’: cn3dmodl.c:1201:11: warning: unused variable ‘pvnmoThis’ [-Wunused-variable] 1201 | PVNMO pvnmoThis = NULL; | ^~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmodl.c:319: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dmodl.c:323: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:413:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 413 | sprintf(MolName, "%4s %2s %2d", | ^~ cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767] 413 | sprintf(MolName, "%4s %2s %2d", | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:413:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 32 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:410:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 410 | sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName, | ^~ In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:410:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 24 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dshim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dshim.c:131: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dmesh.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmesh.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:103:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 103 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmesh.c: In function ‘Cn3D_OpenMesh’: cn3dmesh.c:151:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 151 | ButtoN b; | ^ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | &(Mesh.NumTri)); | ~~~~~~~~~~~~~~~ cn3dmesh.c:119:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | &(Mesh.Vertices[i].Vertex[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 | &(Mesh.Vertices[i].Vertex[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 | &(Mesh.Vertices[i].Vertex[2]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 123 | &(Mesh.Vertices[i].Normal[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 124 | &(Mesh.Vertices[i].Normal[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | &(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:129:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 | &Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:133:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 | &Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 | &Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 | &Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 | &lDummy); | ~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF cn3dstyl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dstyl.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dstyl.c: In function ‘GetThisSpecialAlgorRenderSet’: cn3dstyl.c:459:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 459 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘GetSpecialAlgorRenderSet’: cn3dstyl.c:641:10: warning: unused variable ‘parsThis’ [-Wunused-variable] 641 | PARS parsThis = NULL; | ^~~~~~~~ cn3dstyl.c:640:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 640 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ChangeSpecialLabelsProc’: cn3dstyl.c:866:44: warning: unused variable ‘PDBOn’ [-Wunused-variable] 866 | Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn = | ^~~~~ cn3dstyl.c: In function ‘lFeatureEditedAction’: cn3dstyl.c:1136:10: warning: unused variable ‘val’ [-Wunused-variable] 1136 | Int4 val = 0; | ^~~ cn3dstyl.c: In function ‘bFeatureMoveAction’: cn3dstyl.c:1153:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1153 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘bFeatureEditAction’: cn3dstyl.c:1176:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1176 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ModelControls’: cn3dstyl.c:1364:19: warning: variable ‘ppt13’ set but not used [-Wunused-but-set-variable] 1364 | PrompT ppt12, ppt13, ppt14; | ^~~~~ cn3dstyl.c:1362:36: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:12: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c: In function ‘GetBiostrucFeatureLocationForHihglightedResidues’: cn3dstyl.c:1728:30: warning: variable ‘SingleInterval’ set but not used [-Wunused-but-set-variable] 1728 | Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound = | ^~~~~~~~~~~~~~ cn3dstyl.c:1725:20: warning: variable ‘iMolCurrent’ set but not used [-Wunused-but-set-variable] 1725 | Int2 iMol = 0, iMolCurrent = 0; | ^~~~~~~~~~~ cn3dstyl.c: In function ‘MakeBiostrucFeatureSetForUserDefinedFeature’: cn3dstyl.c:2122:60: warning: unused variable ‘bsfsp_tail’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c:2122:41: warning: unused variable ‘bsfsp_head’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c: In function ‘GetUserDefinedFeature’: cn3dstyl.c:2196:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 2196 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘Cn3DIndexUserDefinedFeature’: cn3dstyl.c:2551:23: warning: variable ‘sfpThis’ set but not used [-Wunused-but-set-variable] 2551 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c:2549:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 2549 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dstyl.c:2548:11: warning: unused variable ‘pdnmmHead’ [-Wunused-variable] 2548 | PDNMM pdnmmHead = NULL; | ^~~~~~~~~ cn3dstyl.c:2547:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 2547 | PMSD pmsdThis = NULL; | ^~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dstyl.c:89: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:456:30: warning: ‘GetThisSpecialAlgorRenderSet’ defined but not used [-Wunused-function] 456 | static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:149:15: warning: ‘bResetFeatureTitle’ defined but not used [-Wunused-variable] 149 | static ButtoN bResetFeatureTitle; | ^~~~~~~~~~~~~~~~~~ cn3dstyl.c:144:14: warning: ‘Cn3D_pupModelStyleItem’ defined but not used [-Wunused-variable] 144 | static PopuP Cn3D_pupModelStyleItem; | ^~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c: In function ‘CopyLocation’: cn3dstyl.c:496:27: warning: ‘rsipNewHead’ may be used uninitialized [-Wmaybe-uninitialized] 496 | rspNew->data.ptrvalue = (VoidPtr) rsipNewHead; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:478:61: note: ‘rsipNewHead’ was declared here 478 | ResidueIntervalPntrPtr rsipNew = NULL, rsipPrev = NULL, rsipNewHead, | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqcons.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from seqcons.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from seqcons.c:115: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from seqcons.c:116: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ seqcons.c:263:19: warning: ‘CSC_Blosum62Fields’ defined but not used [-Wunused-const-variable=] 263 | static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] = | ^~~~~~~~~~~~~~~~~~ seqcons.c: In function ‘CSC_Algorithm_ByBlosum62’: seqcons.c:398:12: warning: ‘maxScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:30: note: ‘maxScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ seqcons.c:398:12: warning: ‘minScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:40: note: ‘minScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ rm -f libncbicn3d.a ar cru libncbicn3d.a algorend.o cn3dmsel.o cn3dopen.o cn3dsave.o cn3dxprt.o cn3dwin.o cn3dentr.o cn3dmsg.o cn3dmatn.o cn3dmodl.o cn3dshim.o cn3dmesh.o cn3dstyl.o seqcons.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicn3d.a ../lib ranlib ../lib/libncbicn3d.a mv algorend.o algorend.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL algorend.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/shim3d.h:153, from algorend.c:582: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ algorend.c: In function ‘Cn3D_SetOGLFont’: algorend.c:791:24: warning: unused variable ‘currentUnderlined’ [-Wunused-variable] 791 | currentUnderlined = FALSE; | ^~~~~~~~~~~~~~~~~ algorend.c:790:45: warning: unused variable ‘currentItalic’ [-Wunused-variable] 790 | static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE, | ^~~~~~~~~~~~~ algorend.c:790:24: warning: unused variable ‘currentBold’ [-Wunused-variable] 790 | static Nlm_Boolean currentBold = FALSE, currentItalic = FALSE, | ^~~~~~~~~~~ algorend.c:789:40: warning: unused variable ‘currentSize’ [-Wunused-variable] 789 | static Nlm_Int2 currentIndex = -1, currentSize = -1; | ^~~~~~~~~~~ algorend.c:789:21: warning: unused variable ‘currentIndex’ [-Wunused-variable] 789 | static Nlm_Int2 currentIndex = -1, currentSize = -1; | ^~~~~~~~~~~~ algorend.c: In function ‘ColorFromSS’: algorend.c:893:10: warning: unused variable ‘rsult’ [-Wunused-variable] 893 | Int2 rsult = 0; | ^~~~~ algorend.c: In function ‘Cn3D_RenWire’: algorend.c:1400:10: warning: unused variable ‘pmldThis’ [-Wunused-variable] 1400 | PMLD pmldThis = NULL; | ^~~~~~~~ algorend.c:1399:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1399 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ algorend.c:1398:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1398 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c: In function ‘Cn3D_ColSeqCons’: algorend.c:1795:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1795 | pars->ConsColAlg = (Nlm_Int2) GetObjectExtra(i); | ^ algorend.c: In function ‘MasterChangeLabelsProc’: algorend.c:2075:44: warning: unused variable ‘TopOn’ [-Wunused-variable] 2075 | Boolean NumOn, NameOn, PDBOn, WhiteOn, TopOn; | ^~~~~ algorend.c:2073:13: warning: unused variable ‘k’ [-Wunused-variable] 2073 | Int2 i, k, nameval; | ^ algorend.c: In function ‘ResetLabelCtrls’: algorend.c:2272:25: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2272 | Int2 i, val, style, size, termStyle; | ^~~~ algorend.c: In function ‘LabelControls’: algorend.c:2434:19: warning: variable ‘ppt11’ set but not used [-Wunused-but-set-variable] 2434 | PrompT ppt10, ppt11; | ^~~~~ algorend.c:2431:36: warning: unused variable ‘ppt7’ [-Wunused-variable] 2431 | PrompT ppt1, ppt2, ppt3, ppt4, ppt7, ppt8, ppt9; | ^~~~ algorend.c: In function ‘Cn3D_SetQualityFromAppParams’: algorend.c:2649:9: warning: unused variable ‘i’ [-Wunused-variable] 2649 | int i; | ^ algorend.c: In function ‘OGL_Quality’: algorend.c:2769:23: warning: unused variable ‘q’ [-Wunused-variable] 2769 | Nlm_PrompT bp, p, q; | ^ algorend.c:2769:20: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 2769 | Nlm_PrompT bp, p, q; | ^ algorend.c:2769:16: warning: variable ‘bp’ set but not used [-Wunused-but-set-variable] 2769 | Nlm_PrompT bp, p, q; | ^~ algorend.c: In function ‘RenderControls’: algorend.c:2893:12: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 2893 | PrompT ppt5; | ^~~~ algorend.c: In function ‘RenderObject’: algorend.c:3138:10: warning: unused variable ‘iCylRadius’ [-Wunused-variable] 3138 | Int4 iCylRadius; | ^~~~~~~~~~ algorend.c:3137:22: warning: unused variable ‘iZTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3137:16: warning: unused variable ‘iYTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3137:10: warning: unused variable ‘iXTo’ [-Wunused-variable] 3137 | Int4 iXTo, iYTo, iZTo; | ^~~~ algorend.c:3136:26: warning: unused variable ‘iZFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3136:18: warning: unused variable ‘iYFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3136:10: warning: unused variable ‘iXFrom’ [-Wunused-variable] 3136 | Int4 iXFrom, iYFrom, iZFrom; | ^~~~~~ algorend.c:3133:10: warning: unused variable ‘i’ [-Wunused-variable] 3133 | Int4 i = 0; | ^ algorend.c: In function ‘RenderLabel’: algorend.c:3394:10: warning: variable ‘paldPrim’ set but not used [-Wunused-but-set-variable] 3394 | PALD paldPrim = NULL; | ^~~~~~~~ algorend.c:3393:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 3393 | PMSD pmsdThis = NULL; | ^~~~~~~~ algorend.c:3389:18: warning: unused variable ‘iZ’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3389:14: warning: unused variable ‘iY’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c:3389:10: warning: unused variable ‘iX’ [-Wunused-variable] 3389 | Int4 iX, iY, iZ; | ^~ algorend.c: In function ‘RenderBond’: algorend.c:3554:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3554 | PMSD pmsdParent = NULL; | ^~~~~~~~~~ algorend.c: In function ‘RenderHalfWormBond’: algorend.c:3673:10: warning: variable ‘pmsdParent’ set but not used [-Wunused-but-set-variable] 3673 | PMSD pmsdParent; | ^~~~~~~~~~ algorend.c:3671:24: warning: variable ‘pmad2’ set but not used [-Wunused-but-set-variable] 3671 | PMAD pmad0, pmad1, pmad2, pmad3; | ^~~~~ algorend.c: In function ‘RenderAnAtom’: algorend.c:3758:10: warning: unused variable ‘pmadFrom’ [-Wunused-variable] 3758 | PMAD pmadFrom = NULL; | ^~~~~~~~ algorend.c: In function ‘RenderAllAtom’: algorend.c:3829:9: warning: variable ‘iMenu’ set but not used [-Wunused-but-set-variable] 3829 | int iMenu; | ^~~~~ algorend.c:3815:11: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 3815 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c:3811:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 3811 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderGraph’: algorend.c:4498:10: warning: unused variable ‘bReservedThis’ [-Wunused-variable] 4498 | Byte bReservedThis = 0; | ^~~~~~~~~~~~~ algorend.c: In function ‘LabelChainTermini’: algorend.c:4772:14: warning: unused variable ‘pmbdThis’ [-Wunused-variable] 4772 | PMBD pmbdThis = NULL; | ^~~~~~~~ algorend.c:4771:15: warning: unused variable ‘pvnmbThis’ [-Wunused-variable] 4771 | PVNMB pvnmbThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘RenderMolecule’: algorend.c:4871:11: warning: variable ‘pdnmmThis’ set but not used [-Wunused-but-set-variable] 4871 | PDNMM pdnmmThis = NULL; | ^~~~~~~~~ algorend.c: In function ‘fnARLoop’: algorend.c:5556:10: warning: variable ‘iTest’ set but not used [-Wunused-but-set-variable] 5556 | Int2 iTest; | ^~~~~ algorend.c: In function ‘AlgorithmicRendering’: algorend.c:5684:10: warning: unused variable ‘i’ [-Wunused-variable] 5684 | Int2 i = 0; | ^ algorend.c:5683:10: warning: unused variable ‘Cn3d_LayerNow_sofar’ [-Wunused-variable] 5683 | Int2 Cn3d_LayerNow_sofar = 0; | ^~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from algorend.c:598: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ algorend.c:2265:13: warning: ‘LabelGroupOnOffProc’ defined but not used [-Wunused-function] 2265 | static void LabelGroupOnOffProc(GrouP g) | ^~~~~~~~~~~~~~~~~~~ algorend.c:717:16: warning: ‘Cn3d_CopyToNode’ defined but not used [-Wunused-variable] 717 | static Boolean Cn3d_CopyToNode = FALSE; | ^~~~~~~~~~~~~~~ algorend.c: In function ‘MasterChangeRenderProc’: algorend.c:1295:29: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 1295 | pars->PBBRender = k; | ~~~~~~~~~~~~~~~~^~~ algorend.c:1138:16: note: ‘k’ was declared here 1138 | Int2 i, j, k; | ^ algorend.c: In function ‘RenderLabel’: algorend.c:3442:41: warning: ‘fXCen’ may be used uninitialized [-Wmaybe-uninitialized] 3442 | fXt = (fXCen - fXFrom) + (fXCen - fXTo); | ~~~~~~~^~~~~~~ algorend.c:3391:13: note: ‘fXCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3443:41: warning: ‘fYCen’ may be used uninitialized [-Wmaybe-uninitialized] 3443 | fYt = (fYCen - fYFrom) + (fYCen - fYTo); | ~~~~~~~^~~~~~~ algorend.c:3391:20: note: ‘fYCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3444:41: warning: ‘fZCen’ may be used uninitialized [-Wmaybe-uninitialized] 3444 | fZt = (fZCen - fZFrom) + (fZCen - fZTo); | ~~~~~~~^~~~~~~ algorend.c:3391:27: note: ‘fZCen’ was declared here 3391 | FloatLo fXCen, fYCen, fZCen; | ^~~~~ algorend.c:3437:30: warning: ‘fXTo’ may be used uninitialized [-Wmaybe-uninitialized] 3437 | fXCen = fXTo + (fXTo - fXFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:13: note: ‘fXTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3438:30: warning: ‘fYTo’ may be used uninitialized [-Wmaybe-uninitialized] 3438 | fYCen = fYTo + (fYTo - fYFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:19: note: ‘fYTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3439:30: warning: ‘fZTo’ may be used uninitialized [-Wmaybe-uninitialized] 3439 | fZCen = fZTo + (fZTo - fZFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3390:25: note: ‘fZTo’ was declared here 3390 | FloatLo fXTo, fYTo, fZTo; | ^~~~ algorend.c:3437:30: warning: ‘fXFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3437 | fXCen = fXTo + (fXTo - fXFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:13: note: ‘fXFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3438:30: warning: ‘fYFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3438 | fYCen = fYTo + (fYTo - fYFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:21: note: ‘fYFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ algorend.c:3439:30: warning: ‘fZFrom’ may be used uninitialized [-Wmaybe-uninitialized] 3439 | fZCen = fZTo + (fZTo - fZFrom) / 2.0; | ~~~~~~^~~~~~~~~ algorend.c:3388:29: note: ‘fZFrom’ was declared here 3388 | FloatLo fXFrom, fYFrom, fZFrom; | ^~~~~~ mv algorend.o algorend.glo mv algorend.tmp algorend.o mv cn3dmsel.o cn3dmsel.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsel.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsel.c:60: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv cn3dmsel.o cn3dmsel.glo mv cn3dmsel.tmp cn3dmsel.o mv cn3dopen.o cn3dopen.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dopen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dopen.c:394: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dopen.c: In function ‘Cn3D_OpenStart’: cn3dopen.c:722:10: warning: unused variable ‘iBioseq’ [-Wunused-variable] 722 | Int4 iBioseq = 0; | ^~~~~~~ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:1000:19: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 1000 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dopen.c:989:25: warning: unused variable ‘pbsasThis’ [-Wunused-variable] 989 | BiostrucAlignSeqPtr pbsasThis = NULL; | ^~~~~~~~~ cn3dopen.c: In function ‘Cn3D_NetOpenBiostruc’: cn3dopen.c:1310:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 1310 | ButtoN b; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dopen.c:412: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from cn3dopen.c:413: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ cn3dopen.c:431:15: warning: ‘Cn3D_bOpenBrowse’ defined but not used [-Wunused-variable] 431 | static ButtoN Cn3D_bOpenBrowse; | ^~~~~~~~~~~~~~~~ cn3dopen.c:430:15: warning: ‘Cn3D_wOpen’ defined but not used [-Wunused-variable] 430 | static WindoW Cn3D_wOpen; | ^~~~~~~~~~ In function ‘Cn3D_ShredCBlast’, inlined from ‘MMDB_ReadMime’ at cn3dopen.c:1058:23: cn3dopen.c:527:8: warning: ‘salp’ may be used uninitialized [-Wmaybe-uninitialized] 527 | if (salp) { | ^ cn3dopen.c: In function ‘MMDB_ReadMime’: cn3dopen.c:513:15: note: ‘salp’ was declared here 513 | SeqAlign *salp; | ^~~~ mv cn3dopen.o cn3dopen.glo mv cn3dopen.tmp cn3dopen.o mv cn3dsave.o cn3dsave.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dsave.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dsave.c:157: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dsave.c: In function ‘Cn3D_AddMatrix’: cn3dsave.c:206:41: warning: unused variable ‘bsfsp_new’ [-Wunused-variable] 206 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_new = NULL; | ^~~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportAsnNow’: cn3dsave.c:375:11: warning: unused variable ‘pdnmlThis’ [-Wunused-variable] 375 | PDNML pdnmlThis = NULL; | ^~~~~~~~~ cn3dsave.c:372:24: warning: variable ‘pbsfThis’ set but not used [-Wunused-but-set-variable] 372 | BiostrucFeaturePtr pbsfThis; | ^~~~~~~~ cn3dsave.c:366:10: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 366 | PMSD pmsdSlave = NULL, pmsdMaster = NULL; | ^~~~~~~~~ cn3dsave.c:362:27: warning: variable ‘FirstSlave’ set but not used [-Wunused-but-set-variable] 362 | Boolean iCn3d = TRUE, FirstSlave = FALSE; | ^~~~~~~~~~ cn3dsave.c:357:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 357 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveBiostruc’: cn3dsave.c:524:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 524 | ButtoN b; | ^ cn3dsave.c:523:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 523 | GrouP gMS; | ^~~ cn3dsave.c:518:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 518 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_ExportDictNow’: cn3dsave.c:598:13: warning: unused variable ‘pcSave’ [-Wunused-variable] 598 | CharPtr pcSave = NULL; | ^~~~~~ cn3dsave.c:596:10: warning: unused variable ‘iCount’ [-Wunused-variable] 596 | Int4 iCount = 0; | ^~~~~~ cn3dsave.c: In function ‘Cn3D_SaveDictionary’: cn3dsave.c:629:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 629 | ButtoN b; | ^ cn3dsave.c:624:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 624 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dsave.c: In function ‘Cn3D_SaveSub’: cn3dsave.c:688:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 688 | IteM i; | ^ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dsave.c:171: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dsave.c:184:15: warning: ‘Cn3D_bFeatOn’ defined but not used [-Wunused-variable] 184 | static ButtoN Cn3D_bFeatOn; | ^~~~~~~~~~~~ In file included from cn3dsave.c:165: ../include/asnmime.h:119:21: warning: ‘amp’ defined but not used [-Wunused-variable] 119 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnmime.h:118:19: warning: ‘at’ defined but not used [-Wunused-variable] 118 | static AsnTypePtr at = atx; | ^~ ../include/asnmime.h:117:23: warning: ‘avn’ defined but not used [-Wunused-variable] 117 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/asnmime.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnmime.h12"; | ^~~~~~~~~~~ cn3dsave.c: In function ‘Cn3D_GetSubSet’: cn3dsave.c:289:24: warning: ‘isep’ may be used uninitialized [-Wmaybe-uninitialized] 289 | isep->next = SeqEntryNew(); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ cn3dsave.c:261:28: note: ‘isep’ was declared here 261 | SeqEntry *sep = NULL, *isep; | ^~~~ mv cn3dsave.o cn3dsave.glo mv cn3dsave.tmp cn3dsave.o mv cn3dxprt.o cn3dxprt.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dxprt.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dxprt.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportPDB’: cn3dxprt.c:209:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 209 | ButtoN b; | ^ cn3dxprt.c:208:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 208 | GrouP gMS; | ^~~ cn3dxprt.c:203:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 203 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportKin’: cn3dxprt.c:381:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 381 | ButtoN b; | ^ cn3dxprt.c:380:11: warning: variable ‘gMS’ set but not used [-Wunused-but-set-variable] 380 | GrouP gMS; | ^~~ cn3dxprt.c:375:10: warning: variable ‘pmsdThis’ set but not used [-Wunused-but-set-variable] 375 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dxprt.c: In function ‘Cn3D_ExportSub’: cn3dxprt.c:513:10: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 513 | IteM i; | ^ mv cn3dxprt.o cn3dxprt.glo mv cn3dxprt.tmp cn3dxprt.o mv cn3dwin.o cn3dwin.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dwin.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dwin.c:647: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dwin.c:733:1: warning: missing braces around initializer [-Wmissing-braces] 733 | { | ^ 734 | 255, 255, 255, /* default 0 */ | { } 735 | 255, 20, 147, /* hotpink 1 */ | { } 736 | 255, 0, 255, /* magenta 2 */ | { } 737 | 155, 48, 255, /* purple 3 */ | { } 738 | 0, 0, 255, /* blue 4 */ | { } 739 | 30, 144, 255, /* sky 5 */ | { } 740 | 0, 255, 255, /* cyan 6 */ | { } 741 | 0, 255, 127, /* sea 7 */ | { } 742 | 0, 255, 0, /* green 8 */ | { } 743 | 255, 255, 0, /* yellow 9 */ | { } 744 | 255, 165, 0, /* gold 10 */ | { } 745 | 255, 69, 0, /* orange 11 */ | { } 746 | 255, 0, 0, /* red 12 */ | { } 747 | 255, 114, 86, /* pink 13 */ | { } 748 | 255, 174, 185, /* pinktint 14 */ | { } 749 | 255, 255, 255, /* white 15 */ | { } 750 | 0, 0, 0, /* black 16 */ | { } 751 | 176, 226, 255, /* bluetint 17 */ | { } 752 | 154, 255, 154, /* greentint 18 */ | { } 753 | 255, 236, 139, /* yellowtint 19 */ | { } 754 | 125, 125, 125, /* gray 20 */ | { } 755 | 139, 87, 66, /* brown 21 */ | { } 756 | 255, 0, 0, /* perm colors 22: red */ | { } 757 | 0, 255, 0, /* perm colors 23: green */ | { } 758 | 255, 0, 255, /* perm colors 24: magenta */ | { } 759 | 30, 144, 255, /* perm colors 25: sky */ | { } 760 | 155, 48, 255, /* perm colors 26: purple */ | { } 761 | 0, 255, 0, /* SS colors 27: helix, green */ | { } 762 | 255, 165, 0, /* SS colors 28: strand, gold */ | { } 763 | 255, 69, 0, /* SS colors 29: turn, orange */ | { } 764 | 0, 255, 255, /* SS colors 30: coil, cyan */ | { } 765 | 255, 255, 0, /* highlight colors 31: yellow */ | { } 766 | 0, 0, 0, /* background colors 32: black */ | { } 767 | 160, 82, 45, /* sienna 33 */ | { } 768 | 240, 230, 140, /* khaki 34 */ | { } 769 | 171, 130, 255, /* light purple 35 */ | { } 770 | 255, 200, 0, /* orange yellow 36 */ | { } 771 | 117, 128, 160, /* 37 */ | { } 772 | 5, 53, 239, /* 38 */ | { } 773 | 27, 62, 255, /* 39 */ | { } 774 | 84, 110, 203, /* 40 */ | { } 775 | 216, 77, 84, /* 41 */ | { } 776 | 125, 128, 135, /* 42 */ | { } 777 | 237, 29, 61, /* 43 */ | { } 778 | 184, 118, 120, /* 44 */ | { } 779 | 155, 9, 0, /* 45 */ | { } 780 | 155, 119, 107, /* 46 */ | { } 781 | 80, 110, 196, /* 47 */ | { } 782 | 122, 127, 157, /* 48 */ | { } 783 | 50, 85, 241, /* 49 */ | { } 784 | 201, 93, 91, /* 50 */ | { } 785 | 254, 0, 5, /* 51 */ | { } 786 | 155, 137, 133, /* 52 */ | { } 787 | 3, 53, 246 /* 53 */ | { 788 | }; | } cn3dwin.c: In function ‘Cn3D_Default_HLColor’: cn3dwin.c:982:27: warning: variable ‘colorB’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c:982:19: warning: variable ‘colorG’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c:982:11: warning: variable ‘colorR’ set but not used [-Wunused-but-set-variable] 982 | Uint1 colorR, colorG, colorB; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_RedrawEx’: cn3dwin.c:1251:19: warning: unused variable ‘iColor’ [-Wunused-variable] 1251 | DDV_ColorCell iColor; | ^~~~~~ cn3dwin.c: In function ‘fnPreCHLresidue’: cn3dwin.c:1543:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 1543 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dwin.c: In function ‘Viewer3DGroups’: cn3dwin.c:1728:10: warning: unused variable ‘groups’ [-Wunused-variable] 1728 | Int2 groups = 0; | ^~~~~~ cn3dwin.c: In function ‘Cn3D_AlignEdit’: cn3dwin.c:1936:10: warning: unused variable ‘iCount’ [-Wunused-variable] 1936 | Int2 iCount = 0; | ^~~~~~ cn3dwin.c:1935:10: warning: variable ‘pmmdThis’ set but not used [-Wunused-but-set-variable] 1935 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dwin.c:1933:17: warning: unused variable ‘salp’ [-Wunused-variable] 1933 | SeqAlignPtr salp = NULL; | ^~~~ cn3dwin.c:1931:29: warning: variable ‘pmsdSlave’ set but not used [-Wunused-but-set-variable] 1931 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dwin.c:1930:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 1930 | PDNMS pdnmsSlave = NULL; | ^~~~~~~~~~ cn3dwin.c: In function ‘Cn3D_Menus’: cn3dwin.c:2131:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2131 | (Nlm_VoidPtr) i, NULL); | ^ cn3dwin.c: In function ‘Cn3DWin’: cn3dwin.c:2364:5: warning: implicit declaration of function ‘Nlm_SetOGLContext’; did you mean ‘Nlm_InitAppContext’? [-Wimplicit-function-declaration] 2364 | Nlm_SetOGLContext(NULL, NULL, NULL, NULL); | ^~~~~~~~~~~~~~~~~ | Nlm_InitAppContext In file included from ../include/sqnutils.h:51, from ../include/udviewer.h:219, from cn3dwin.c:665: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/udviewer.h:228: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dwin.c:1626:13: warning: ‘HLmolecule_MA’ defined but not used [-Wunused-function] 1626 | static void HLmolecule_MA(MAPtr ma, | ^~~~~~~~~~~~~ cn3dwin.c:1428:13: warning: ‘HLatom_MA’ defined but not used [-Wunused-function] 1428 | static void HLatom_MA(MAPtr ma, | ^~~~~~~~~ cn3dwin.c:1349:25: warning: ‘DoHighlightSeg’ defined but not used [-Wunused-function] 1349 | static void LIBCALLBACK DoHighlightSeg(PFB pfbThis, | ^~~~~~~~~~~~~~ cn3dwin.c:979:13: warning: ‘Cn3D_Default_HLColor’ defined but not used [-Wunused-function] 979 | static void Cn3D_Default_HLColor(IteM i) | ^~~~~~~~~~~~~~~~~~~~ cn3dwin.c:953:13: warning: ‘Cn3D_BgColor’ defined but not used [-Wunused-function] 953 | static void Cn3D_BgColor(IteM i) | ^~~~~~~~~~~~ cn3dwin.c:936:13: warning: ‘Cn3D_Default_BgColor’ defined but not used [-Wunused-function] 936 | static void Cn3D_Default_BgColor(IteM i) | ^~~~~~~~~~~~~~~~~~~~ cn3dwin.c:929:13: warning: ‘Cn3D_MoveCB’ defined but not used [-Wunused-function] 929 | static void Cn3D_MoveCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:922:13: warning: ‘Cn3D_ZoomCB’ defined but not used [-Wunused-function] 922 | static void Cn3D_ZoomCB(IteM i) | ^~~~~~~~~~~ cn3dwin.c:719:14: warning: ‘Cn3D_gViewCtrl’ defined but not used [-Wunused-variable] 719 | static GrouP Cn3D_gViewCtrl; | ^~~~~~~~~~~~~~ cn3dwin.c:713:14: warning: ‘Cn3D_gViewer’ defined but not used [-Wunused-variable] 713 | static GrouP Cn3D_gViewer; | ^~~~~~~~~~~~ cn3dwin.c:688:13: warning: ‘Cn3D_iModelCtrl’ defined but not used [-Wunused-variable] 688 | static IteM Cn3D_iModelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:682:13: warning: ‘Cn3D_iLabelCtrl’ defined but not used [-Wunused-variable] 682 | static IteM Cn3D_iLabelCtrl = NULL; | ^~~~~~~~~~~~~~~ cn3dwin.c:676:14: warning: ‘Cn3D_Vy’ defined but not used [-Wunused-variable] 676 | static Uint2 Cn3D_Vy, Cn3D_Rx; | ^~~~~~~ mv cn3dwin.o cn3dwin.glo mv cn3dwin.tmp cn3dwin.o mv cn3dentr.o cn3dentr.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dentr.c:81: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mv cn3dentr.o cn3dentr.glo mv cn3dentr.tmp cn3dentr.o mv cn3dmsg.o cn3dmsg.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmsg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmsg.c:254: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmsg.c: In function ‘SeqStrucMediaMsgFunc’: cn3dmsg.c:593:19: warning: variable ‘omudp’ set but not used [-Wunused-but-set-variable] 593 | OMUserDataPtr omudp = NULL; | ^~~~~ In file included from ../include/sqnutils.h:51, from cn3dmsg.c:267: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmsg.c:271: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv cn3dmsg.o cn3dmsg.glo mv cn3dmsg.tmp cn3dmsg.o mv cn3dmatn.o cn3dmatn.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmatn.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmatn.c:173: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmatn.c: In function ‘FindMM’: cn3dmatn.c:217:29: warning: unused variable ‘pdnmsThisSlave’ [-Wunused-variable] 217 | PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL; | ^~~~~~~~~~~~~~ cn3dmatn.c: In function ‘DoMediaHL’: cn3dmatn.c:249:10: warning: variable ‘MainAtom’ set but not used [-Wunused-but-set-variable] 249 | Byte MainAtom = 0; | ^~~~~~~~ cn3dmatn.c:247:10: warning: unused variable ‘paldThis’ [-Wunused-variable] 247 | PALD paldThis = NULL; | ^~~~~~~~ cn3dmatn.c:246:11: warning: unused variable ‘pvnalThis’ [-Wunused-variable] 246 | PVNAL pvnalThis = NULL; | ^~~~~~~~~ cn3dmatn.c:245:10: warning: unused variable ‘pmadThis’ [-Wunused-variable] 245 | PMAD pmadThis = NULL; | ^~~~~~~~ cn3dmatn.c:244:11: warning: unused variable ‘pvnmaThis’ [-Wunused-variable] 244 | PVNMA pvnmaThis = NULL; | ^~~~~~~~~ cn3dmatn.c: In function ‘Cn3DCheckAndDoHighlight’: cn3dmatn.c:372:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 372 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmatn.c:371:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 371 | PMMD pmmdThis = NULL; | ^~~~~~~~ mv cn3dmatn.o cn3dmatn.glo mv cn3dmatn.tmp cn3dmatn.o mv cn3dmodl.o cn3dmodl.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmodl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dmodl.c:302: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckNoSingleHighlight’: cn3dmodl.c:353:11: warning: unused variable ‘pdnmgThis’ [-Wunused-variable] 353 | PDNMG pdnmgThis = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3DCheckHighlighted’: cn3dmodl.c:364:29: warning: unused variable ‘pmsdSlave’ [-Wunused-variable] 364 | PMSD pmsdMaster = NULL, pmsdSlave = NULL; | ^~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ReSetVisibleStatus’: cn3dmodl.c:508:10: warning: unused variable ‘pmgd’ [-Wunused-variable] 508 | PMGD pmgd = NULL; | ^~~~ cn3dmodl.c:507:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 507 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:506:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 506 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘fnAlignList’: cn3dmodl.c:996:25: warning: unused variable ‘itemtype’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:996:11: warning: unused variable ‘entityID’ [-Wunused-variable] 996 | Uint2 entityID = 0, itemtype = 0; | ^~~~~~~~ cn3dmodl.c:995:14: warning: unused variable ‘sipThis’ [-Wunused-variable] 995 | SeqIdPtr sipThis = NULL; | ^~~~~~~ cn3dmodl.c:993:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 993 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SynchronizeModVisibleStatus’: cn3dmodl.c:1065:11: warning: unused variable ‘pdnmg’ [-Wunused-variable] 1065 | PDNMG pdnmg = NULL; | ^~~~~ cn3dmodl.c:1064:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 1064 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dmodl.c: In function ‘SetResidueVisibilities’: cn3dmodl.c:1201:11: warning: unused variable ‘pvnmoThis’ [-Wunused-variable] 1201 | PVNMO pvnmoThis = NULL; | ^~~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dmodl.c:319: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from cn3dmodl.c:323: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:413:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 413 | sprintf(MolName, "%4s %2s %2d", | ^~ cn3dmodl.c:413:30: note: directive argument in the range [-32768, 32767] 413 | sprintf(MolName, "%4s %2s %2d", | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:413:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 32 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cn3dmodl.c: In function ‘Cn3D_ListDomainProc’: cn3dmodl.c:410:34: warning: ‘ ’ directive writing 2 bytes into a region of size between 1 and 16 [-Wformat-overflow=] 410 | sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName, | ^~ In function ‘sprintf’, inlined from ‘Cn3D_ListDomainProc’ at cn3dmodl.c:410:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 24 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mv cn3dmodl.o cn3dmodl.glo mv cn3dmodl.tmp cn3dmodl.o mv cn3dshim.o cn3dshim.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dshim.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/cn3dmain.h:182, from cn3dshim.c:131: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dshim.c: In function ‘Cn3D_Size’: cn3dshim.c:413:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 413 | PMSD pmsdThis; | ^~~~~~~~ cn3dshim.c:412:11: warning: unused variable ‘pdnmsSlave’ [-Wunused-variable] 412 | PDNMS pdnmsSlave; | ^~~~~~~~~~ cn3dshim.c: In function ‘Cn3D_SizeCB’: cn3dshim.c:399:36: warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations] 399 | BoundBox->x[i + 1]) BoundBox->x[i + 1] = | ~~~~~~~~~~~^~~~~~~ cn3dshim.c:395:31: note: within this loop 395 | for (i = 0; i < 6; i += 2) { /* check to see if the atom lies outside the bound box */ | ~~^~~ cn3dshim.c:391:36: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 391 | BoundBox->x[i] = pflvDataThis[i / (int) 2]; | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dshim.c:390:31: note: within this loop 390 | for (i = 0; i < 6; i++) { | ~~^~~ mv cn3dshim.o cn3dshim.glo mv cn3dshim.tmp cn3dshim.o mv cn3dmesh.o cn3dmesh.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dmesh.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from cn3dmesh.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:103:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 103 | PMSD pmsdThis = NULL; | ^~~~~~~~ cn3dmesh.c: In function ‘Cn3D_OpenMesh’: cn3dmesh.c:151:12: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 151 | ButtoN b; | ^ cn3dmesh.c: In function ‘Cn3D_MeshAcceptProc’: cn3dmesh.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(hFile, "%d %d %d", &(Mesh.NumVert), &(Mesh.NumEdge), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | &(Mesh.NumTri)); | ~~~~~~~~~~~~~~~ cn3dmesh.c:119:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fscanf(hFile, "%lf %lf %lf %lf %lf %lf %f %f %f %d %d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | &(Mesh.Vertices[i].Vertex[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 121 | &(Mesh.Vertices[i].Vertex[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 | &(Mesh.Vertices[i].Vertex[2]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 123 | &(Mesh.Vertices[i].Normal[0]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 124 | &(Mesh.Vertices[i].Normal[1]), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | &(Mesh.Vertices[i].Normal[2]), &fDummy, &fDummy, &fDummy, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:129:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fscanf(hFile, "%d %d %d %d %d", &Mesh.Edges[i].Vertex[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 | &Mesh.Edges[i].Vertex[1], &lDummy, &lDummy, &lDummy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dmesh.c:133:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fscanf(hFile, "%d %d %d %d %d %d %d %d %d", &Mesh.Tri[i].Edge[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 | &Mesh.Tri[i].Edge[1], &Mesh.Tri[i].Edge[2], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 | &Mesh.Tri[i].Vertex[0], &Mesh.Tri[i].Vertex[1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 | &Mesh.Tri[i].Vertex[2], &lDummy, &Mesh.Tri[i].Atom, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 137 | &lDummy); | ~~~~~~~~ mv cn3dmesh.o cn3dmesh.glo mv cn3dmesh.tmp cn3dmesh.o mv cn3dstyl.o cn3dstyl.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL cn3dstyl.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dstyl.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dstyl.c: In function ‘GetThisSpecialAlgorRenderSet’: cn3dstyl.c:459:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 459 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘GetSpecialAlgorRenderSet’: cn3dstyl.c:641:10: warning: unused variable ‘parsThis’ [-Wunused-variable] 641 | PARS parsThis = NULL; | ^~~~~~~~ cn3dstyl.c:640:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 640 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ChangeSpecialLabelsProc’: cn3dstyl.c:867:16: warning: unused variable ‘TopOn’ [-Wunused-variable] 867 | FALSE, TopOn = FALSE; | ^~~~~ cn3dstyl.c:866:44: warning: unused variable ‘PDBOn’ [-Wunused-variable] 866 | Boolean NumOn = FALSE, NameOn = FALSE, PDBOn = FALSE, WhiteOn = | ^~~~~ cn3dstyl.c:864:17: warning: unused variable ‘k’ [-Wunused-variable] 864 | Int2 i = 0, k = 0, nameval = 0; | ^ cn3dstyl.c: In function ‘ModelSetLabelCtrls’: cn3dstyl.c:1059:37: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 1059 | Int2 i = 0, val = 0, style = 0, size = 0; | ^~~~ cn3dstyl.c: In function ‘lFeatureEditedAction’: cn3dstyl.c:1136:10: warning: unused variable ‘val’ [-Wunused-variable] 1136 | Int4 val = 0; | ^~~ cn3dstyl.c: In function ‘bFeatureMoveAction’: cn3dstyl.c:1153:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1153 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘bFeatureEditAction’: cn3dstyl.c:1176:23: warning: unused variable ‘sfpThis’ [-Wunused-variable] 1176 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c: In function ‘ModelControls’: cn3dstyl.c:1364:19: warning: variable ‘ppt13’ set but not used [-Wunused-but-set-variable] 1364 | PrompT ppt12, ppt13, ppt14; | ^~~~~ cn3dstyl.c:1363:9: warning: unused variable ‘ppt11’ [-Wunused-variable] 1363 | ppt11; | ^~~~~ cn3dstyl.c:1362:60: warning: unused variable ‘ppt9’ [-Wunused-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:36: warning: variable ‘ppt5’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c:1362:12: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 1362 | PrompT ppt1, ppt2, ppt3, ppt4, ppt5, ppt6, ppt7, ppt8, ppt9, ppt10, | ^~~~ cn3dstyl.c: In function ‘GetBiostrucFeatureLocationForHihglightedResidues’: cn3dstyl.c:1728:30: warning: variable ‘SingleInterval’ set but not used [-Wunused-but-set-variable] 1728 | Boolean Started = FALSE, SingleInterval, UserDefinedFeatureFound = | ^~~~~~~~~~~~~~ cn3dstyl.c:1725:20: warning: variable ‘iMolCurrent’ set but not used [-Wunused-but-set-variable] 1725 | Int2 iMol = 0, iMolCurrent = 0; | ^~~~~~~~~~~ cn3dstyl.c: In function ‘MakeBiostrucFeatureSetForUserDefinedFeature’: cn3dstyl.c:2122:60: warning: unused variable ‘bsfsp_tail’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c:2122:41: warning: unused variable ‘bsfsp_head’ [-Wunused-variable] 2122 | BiostrucFeatureSetPtr bsfsp = NULL, bsfsp_head = NULL, bsfsp_tail = | ^~~~~~~~~~ cn3dstyl.c: In function ‘GetUserDefinedFeature’: cn3dstyl.c:2196:27: warning: unused variable ‘sfipThis’ [-Wunused-variable] 2196 | SpecialFeatureInfoPtr sfipThis = NULL; | ^~~~~~~~ cn3dstyl.c: In function ‘Cn3DIndexUserDefinedFeature’: cn3dstyl.c:2551:23: warning: variable ‘sfpThis’ set but not used [-Wunused-but-set-variable] 2551 | SpecialFeaturePtr sfpThis = NULL; | ^~~~~~~ cn3dstyl.c:2549:10: warning: unused variable ‘pmmdThis’ [-Wunused-variable] 2549 | PMMD pmmdThis = NULL; | ^~~~~~~~ cn3dstyl.c:2548:11: warning: unused variable ‘pdnmmHead’ [-Wunused-variable] 2548 | PDNMM pdnmmHead = NULL; | ^~~~~~~~~ cn3dstyl.c:2547:10: warning: unused variable ‘pmsdThis’ [-Wunused-variable] 2547 | PMSD pmsdThis = NULL; | ^~~~~~~~ In file included from ../include/cn3dopen.h:111, from cn3dstyl.c:89: ../include/objmime.h: At top level: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:456:30: warning: ‘GetThisSpecialAlgorRenderSet’ defined but not used [-Wunused-function] 456 | static SpecialFeatureInfoPtr GetThisSpecialAlgorRenderSet(Int2 id) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:149:15: warning: ‘bResetFeatureTitle’ defined but not used [-Wunused-variable] 149 | static ButtoN bResetFeatureTitle; | ^~~~~~~~~~~~~~~~~~ cn3dstyl.c:144:14: warning: ‘Cn3D_pupModelStyleItem’ defined but not used [-Wunused-variable] 144 | static PopuP Cn3D_pupModelStyleItem; | ^~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c: In function ‘CopyLocation’: cn3dstyl.c:496:27: warning: ‘rsipNewHead’ may be used uninitialized [-Wmaybe-uninitialized] 496 | rspNew->data.ptrvalue = (VoidPtr) rsipNewHead; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cn3dstyl.c:478:61: note: ‘rsipNewHead’ was declared here 478 | ResidueIntervalPntrPtr rsipNew = NULL, rsipPrev = NULL, rsipNewHead, | ^~~~~~~~~~~ mv cn3dstyl.o cn3dstyl.glo mv cn3dstyl.tmp cn3dstyl.o mv seqcons.o seqcons.tmp x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF -D_OPENGL seqcons.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from seqcons.c:112: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from seqcons.c:115: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from seqcons.c:116: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ seqcons.c:263:19: warning: ‘CSC_Blosum62Fields’ defined but not used [-Wunused-const-variable=] 263 | static const char CSC_Blosum62Fields[CSC_BLOSUMSIZE] = | ^~~~~~~~~~~~~~~~~~ seqcons.c: In function ‘CSC_Algorithm_ByBlosum62’: seqcons.c:398:12: warning: ‘maxScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:30: note: ‘maxScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ seqcons.c:398:12: warning: ‘minScore’ may be used uninitialized [-Wmaybe-uninitialized] 398 | if (minScore == maxScore) | ^ seqcons.c:340:40: note: ‘minScore’ was declared here 340 | int c, pr1, pr2, offset, maxScore, minScore, nRows, i = 0, sum, nGaps; | ^~~~~~~~ mv seqcons.o seqcons.glo mv seqcons.tmp seqcons.o rm -f libncbicn3dOGL.a ar cru libncbicn3dOGL.a algorend.glo cn3dmsel.glo cn3dopen.glo cn3dsave.glo cn3dxprt.glo cn3dwin.glo cn3dentr.glo cn3dmsg.glo cn3dmatn.glo cn3dmodl.glo cn3dshim.glo cn3dmesh.glo cn3dstyl.glo seqcons.glo ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbicn3dOGL.a ../lib ranlib ../lib/libncbicn3dOGL.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF aa_ungapped.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_diagnostics.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_engine.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_extend.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_filter.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_gapalign.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_hits.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_itree.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_lookup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_message.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_options.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_seg.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_seqsrc.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_sw.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_setup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_stat.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_traceback.c blast_traceback.c: In function ‘BLAST_ComputeTraceback_MT’: blast_traceback.c:1500: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 1500 | #pragma omp parallel for default(none) num_threads(actual_num_threads) schedule(guided) if (actual_num_threads > 1) \ | blast_traceback.c:1524: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1524 | #pragma omp critical(retval) | blast_traceback.c:1530: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 1530 | #pragma omp flush(has_been_interrupted) | blast_traceback.c:1561: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1561 | #pragma omp critical(tback_gen_code) | blast_traceback.c:1591: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1591 | #pragma omp critical(retval) | blast_traceback.c:1631: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1631 | #pragma omp critical(tback_gen_code) | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_util.c blast_util.c: In function ‘BlastProgram2Number’: blast_util.c:306:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 306 | else if (strcasecmp("mapper", program) == 0) | ^~ blast_util.c:309:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 309 | return 0; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gapinfo.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF greedy_align.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF link_hsps.c link_hsps.c: In function ‘s_FwdCompareHSPs’: link_hsps.c:133:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 133 | else if (h1->context > h2->context) | ^~ link_hsps.c:136:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 136 | if (h1->query.offset < h2->query.offset) | ^~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF lookup_wrap.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF na_ungapped.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_math.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF ncbi_std.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF pattern.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF phi_extend.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF phi_lookup.c phi_lookup.c: In function ‘SPHIPatternSearchBlkNew’: phi_lookup.c:634:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 634 | localPattern[posIndex-1] = 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~ phi_lookup.c:411:11: note: at offset [-2147483648, -1] into destination object ‘localPattern’ of size 330 411 | Uint1 localPattern[PHI_MAX_PATTERN_LENGTH]; /*local variable to hold for each position whether | ^~~~~~~~~~~~ phi_lookup.c:634:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 634 | localPattern[posIndex-1] = 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~ phi_lookup.c:411:11: note: at offset -1 into destination object ‘localPattern’ of size 330 411 | Uint1 localPattern[PHI_MAX_PATTERN_LENGTH]; /*local variable to hold for each position whether | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF lookup_util.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_encoding.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_psi.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_psi_priv.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_kappa.c blast_kappa.c: In function ‘Blast_RedoAlignmentCore_MT’: blast_kappa.c:3407: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3407 | #pragma omp parallel \ | blast_kappa.c:3426: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 3426 | #pragma omp for schedule(static) | blast_kappa.c:3428: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3428 | #pragma omp flush(interrupt) | blast_kappa.c:3489: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3489 | #pragma omp critical(intrpt) | blast_kappa.c:3491: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3491 | #pragma omp flush(interrupt) | blast_kappa.c:3504: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3504 | #pragma omp critical(intrpt) | blast_kappa.c:3506: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3506 | #pragma omp flush(interrupt) | blast_kappa.c:3722: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 3722 | #pragma omp critical(intrpt) | blast_kappa.c:3724: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 3724 | #pragma omp flush(interrupt) | blast_kappa.c:3730: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 3730 | #pragma omp barrier | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF matrix_freq_ratios.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_hspstream.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_parameters.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_posit.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF phi_gapalign.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_program.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_query_info.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_tune.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_aalookup.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_nalookup.c blast_nalookup.c: In function ‘s_NaHashLookupScanSubjectForWordCounts’: blast_nalookup.c:1850: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 1850 | #pragma omp parallel for if (num_threads > 1) num_threads(num_threads) \ | blast_nalookup.c:1858: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 1858 | #pragma omp critical (get_sequence_for_word_counts) | x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_aascan.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_nascan.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_dynarray.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF split_query.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF gencode_singleton.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF index_ungapped.c In function ‘ir_fp_entry_destroy’, inlined from ‘ir_fp_entry_destroy’ at index_ungapped.c:45:22, inlined from ‘ir_fp_entry_create’ at index_ungapped.c:67:35, inlined from ‘ir_locate’ at index_ungapped.c:136:28: index_ungapped.c:48:16: warning: ‘result_38->entries’ may be used uninitialized [-Wmaybe-uninitialized] 48 | free( e->entries ); | ~^~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF hspfilter_collector.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_hspstream_mt_utils.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_traceback_mt_priv.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF boost_erf.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF jumper.c rm -f libblast.a ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblast.a ../lib ranlib ../lib/libblast.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_tabular.h:42, from ../include/algo/blast/api/blast_api.h:47, from blast_api.c:38: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:149:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fscanf(auxfile, "%s", buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:151:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fscanf(auxfile, "%d", &info->aux_info.gap_open_penalty); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:152:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fscanf(auxfile, "%d", &info->aux_info.gap_extend_penalty); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:153:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | fscanf(auxfile, "%le", &info->aux_info.ungapped_k); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:154:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 154 | fscanf(auxfile, "%le", &info->aux_info.ungapped_h); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:155:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(auxfile, "%d", &info->aux_info.max_db_seq_length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:156:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(auxfile, "%d", &info->aux_info.db_length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:157:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(auxfile, "%lf", &info->aux_info.scale_factor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:161:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 161 | fscanf(auxfile, "%d", &seq_size); /* not used */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c:162:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fscanf(auxfile, "%le", &info->aux_info.karlin_k[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:502:39: warning: ‘%s’ directive writing up to 2 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 502 | sprintf(buf_full, "%s%s%s%s", buf_path, | ^~ 503 | alphabet_type, DIRDELIMSTR, matrix_name); | ~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:502:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4099) into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:484:35: warning: ‘data’ directive writing 4 bytes into a region of size between 0 and 4095 [-Wformat-overflow=] 484 | sprintf(buf_path_2, "%s%sdata%s", buf_path, DIRDELIMSTR, DIRDELIMSTR); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:484:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 4102 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastFindMatrixPath’: blast_api.c:470:35: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 470 | sprintf(buf_path_2, "%s%s", buf_path, DIRDELIMSTR); | ^ In function ‘sprintf’, inlined from ‘s_BlastFindMatrixPath’ at blast_api.c:470:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 4097 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:104:25: warning: ‘.loo’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 104 | sprintf(filename, "%s.loo", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:104:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:123:25: warning: ‘.rps’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 123 | sprintf(filename, "%s.rps", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:123:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ blast_api.c: In function ‘s_BlastRPSInfoInit’: blast_api.c:144:25: warning: ‘.aux’ directive writing 4 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 144 | sprintf(filename, "%s.aux", (char *)pathname); | ^~~~ In function ‘sprintf’, inlined from ‘s_BlastRPSInfoInit’ at blast_api.c:144:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_input.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from blast_input.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_input.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast_input.c,v 1.32 2008/06/09 17:28:41 madden Exp $"; | ^~~~~ blast_input.c: In function ‘BLAST_GetQuerySeqLoc’: blast_input.c:98:21: warning: ‘%ld’ directive writing between 1 and 7 bytes into a region of size 4 [-Wformat-overflow=] 98 | sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES)); | ^~~ blast_input.c:98:20: note: directive argument in the range [-131080, 131080] 98 | sprintf(prefix, "%ld", (long) (*ctr/MAX_NUM_QUERIES)); | ^~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘BLAST_GetQuerySeqLoc’ at blast_input.c:98:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 8 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_format.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_format.h:45, from blast_format.c:38: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_format.c: In function ‘s_MBXmlInit’: blast_format.c:255:13: warning: variable ‘retval’ set but not used [-Wunused-but-set-variable] 255 | Boolean retval = FALSE; | ^~~~~~ blast_format.c: In function ‘s_LoadMatrix’: blast_format.c:673:27: warning: array subscript has type ‘char’ [-Wchar-subscripts] 673 | ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j]; | ~~~~~~^~~ blast_format.c:673:38: warning: array subscript has type ‘char’ [-Wchar-subscripts] 673 | ss[pchars[i]][pchars[j]] = pack_matrix->scores[(i*dim)+j]; | ~~~~~~^~~ blast_format.c: At top level: blast_format.c:35:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 35 | static char const rcsid[] = "$Id: blast_format.c,v 1.120 2012/10/10 14:07:01 fongah2 Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_mtlock.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/ncbithr.h:87, from blast_mtlock.c:39: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_mtlock.c:35:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 35 | static char const rcsid[] = | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_options_api.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_prelim.c blast_prelim.c: In function ‘Blast_PrelimSearchThreadRun’: blast_prelim.c:100:9: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 100 | Int2 status = 0; | ^~~~~~ blast_prelim.c: At top level: blast_prelim.c:34:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 34 | static char const rcsid[] = "$Id: blast_prelim.c,v 1.8 2006/05/24 21:17:50 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_returns.c blast_returns.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_returns.c,v 1.39 2010/06/10 13:44:46 madden Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_seq.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from blast_seq.c:34: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_seq.c: In function ‘s_SeqLocFillSequenceBuffer’: blast_seq.c:529:10: warning: variable ‘seq_code’ set but not used [-Wunused-but-set-variable] 529 | Uint1 seq_code, strand; | ^~~~~~~~ blast_seq.c: At top level: blast_seq.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: blast_seq.c,v 1.89 2008/06/09 17:29:14 madden Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_seqalign.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from ../include/algo/blast/api/blast_seqalign.h:42, from blast_seqalign.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_seqalign.c: In function ‘s_HSPListToSeqAlignUngapped’: blast_seqalign.c:343:26: warning: variable ‘hspset_cnt_old’ set but not used [-Wunused-but-set-variable] 343 | Int4 hsp_cnt, index2, hspset_cnt_old; | ^~~~~~~~~~~~~~ blast_seqalign.c: At top level: blast_seqalign.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_seqalign.c,v 1.64 2010/02/12 20:54:54 maning Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_tabular.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/algo/blast/api/blast_tabular.h:42, from blast_tabular.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ blast_tabular.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: blast_tabular.c,v 1.41 2009/06/01 14:33:38 maning Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF repeats_filter.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from ../include/algo/blast/api/repeats_filter.h:41, from repeats_filter.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ repeats_filter.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqsrc_multiseq.c seqsrc_multiseq.c:33:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 33 | static char const rcsid[] = "$Id: seqsrc_multiseq.c,v 1.28 2011/05/26 20:59:45 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF seqsrc_readdb.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/readdb.h:757, from ../include/algo/blast/api/seqsrc_readdb.h:38, from seqsrc_readdb.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ seqsrc_readdb.c: In function ‘s_ReaddbGetNextChunk’: seqsrc_readdb.c:375:11: warning: variable ‘real_readdb_entries’ set but not used [-Wunused-but-set-variable] 375 | Uint4 real_readdb_entries; | ^~~~~~~~~~~~~~~~~~~ seqsrc_readdb.c: At top level: seqsrc_readdb.c:32:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 32 | static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.60 2011/05/26 20:59:45 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF twoseq_api.c twoseq_api.c: In function ‘s_TwoSeqBasicFillOptions’: twoseq_api.c:100:10: warning: unused variable ‘status’ [-Wunused-variable] 100 | Int2 status = 0; | ^~~~~~ In file included from ../include/sqnutils.h:51, from ../include/algo/blast/api/twoseq_api.h:41, from twoseq_api.c:45: ../include/objentgene.h: At top level: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF dust_filter.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objloc.h:88, from ../include/algo/blast/api/dust_filter.h:41, from dust_filter.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dust_filter.c: In function ‘s_GetFilteringLocations’: dust_filter.c:171:32: warning: unused variable ‘filter_slp_rev’ [-Wunused-variable] 171 | BlastSeqLoc* filter_slp_rev = NULL; | ^~~~~~~~~~~~~~ dust_filter.c: At top level: dust_filter.c:2:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 2 | static char const rcsid[] = "$Id: dust_filter.c,v 1.12 2007/12/19 22:05:56 camacho Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF blast_message_api.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from blast_message_api.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -D_PNG -I../include -DWIN_MOTIF hspfilter_queue.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbistd.h:61, from ../include/ncbithr.h:87, from hspfilter_queue.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ hspfilter_queue.c: In function ‘s_BlastHSPQueueInit’: hspfilter_queue.c:65:24: warning: unused variable ‘q_data’ [-Wunused-variable] 65 | BlastHSPQueueData * q_data = data; | ^~~~~~ hspfilter_queue.c: In function ‘s_BlastHSPQueueNew’: hspfilter_queue.c:157:24: warning: assignment to ‘BlastHSPWriterInitFn’ {aka ‘int (*)(void *, void *)’} from incompatible pointer type ‘int (*)(void *, BlastHSPResults *)’ [-Wincompatible-pointer-types] 157 | writer->InitFnPtr = &s_BlastHSPQueueInit; | ^ hspfilter_queue.c:158:24: warning: assignment to ‘BlastHSPWriterFinalFn’ {aka ‘int (*)(void *, void *)’} from incompatible pointer type ‘int (*)(void *, BlastHSPResults *)’ [-Wincompatible-pointer-types] 158 | writer->FinalFnPtr = &s_BlastHSPQueueFinal; | ^ hspfilter_queue.c: In function ‘BlastHSPQueueInfoNew’: hspfilter_queue.c:189:26: warning: assignment to ‘BlastHSPWriterNewFn’ {aka ‘BlastHSPWriter * (*)(void *, BlastQueryInfo *, BLAST_SequenceBlk *)’} from incompatible pointer type ‘BlastHSPWriter * (*)(void *, BlastQueryInfo *)’ [-Wincompatible-pointer-types] 189 | writer_info->NewFnPtr = &s_BlastHSPQueueNew; | ^ hspfilter_queue.c: At top level: hspfilter_queue.c:36:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 36 | static char const rcsid[] = | ^~~~~ rm -f libblastapi.a ar cru libblastapi.a blast_api.o blast_input.o blast_format.o blast_mtlock.o blast_options_api.o blast_prelim.o blast_returns.o blast_seq.o blast_seqalign.o blast_tabular.o repeats_filter.o seqsrc_multiseq.o seqsrc_readdb.o twoseq_api.o dust_filter.o blast_message_api.o hspfilter_queue.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libblastapi.a ../lib ranlib ../lib/libblastapi.a x86_64-linux-gnu-gcc -o asntool -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -DWIN_MOTIF -L../shlib asntool.c asncode.c ../lib/libncbi.a -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asntool.c:64: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from asnbuild.h:70, from asncode.c:52: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asncode.c: In function ‘AsnCodeGenEnumDefines’: asncode.c:736:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Nlm_Int8’ {aka ‘long int’} [-Wformat=] 736 | sprintf (iter->buf, "%s %d\n", AsnCodeCleanName (avtp->name, lclbuf, | ~^ | | | int | %ld 737 | CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength), avtp->intvalue); | ~~~~~~~~~~~~~~ | | | Nlm_Int8 {aka long int} asncode.c: In function ‘AsnCode_SETOF_base_or_user’: asncode.c:1518:20: warning: variable ‘real_type’ set but not used [-Wunused-but-set-variable] 1518 | Int2 real_type; | ^~~~~~~~~ asncode.c:1517:20: warning: variable ‘valslot’ set but not used [-Wunused-but-set-variable] 1517 | CharPtr valslot; | ^~~~~~~ asncode.c: In function ‘userobj_and_basetype_SETOF’: asncode.c:2472:20: warning: variable ‘valslot’ set but not used [-Wunused-but-set-variable] 2472 | CharPtr valslot; | ^~~~~~~ asncode.c: In function ‘AsnCodeIsReallyChoice’: asncode.c:3201:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 3201 | if (now_atp) | ^ asncode.c: At top level: asncode.c:3533:38: warning: argument 2 of type ‘char[100]’ with mismatched bound [-Warray-parameter=] 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ~~~~~^~~~~~~~~~~~ asncode.c:269:58: note: previously declared as ‘char *’ 269 | CharPtr AsnCodeCleanName PROTO ((CharPtr name, char PNTR buf, int wash_or_buf, int maxlen)); | ~~~~~~~~~~^~~ ../include/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’ 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ asncode.c: In function ‘AsnCodeFunctionWriteFuncChoiceStart’: asncode.c:3623:20: warning: variable ‘obj_use’ set but not used [-Wunused-but-set-variable] 3623 | CharPtr obj_use = which_node->obj_name; | ^~~~~~~ asncode.c: In function ‘AsnCodeIter’: asncode.c:4238:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 4238 | if (iter->atp != NULL) | ^ asncode.c: In function ‘AsnCode’: asncode.c:4317:48: warning: variable ‘objnamety’ set but not used [-Wunused-but-set-variable] 4317 | CharPtr objnameuc = NULL, objnamemc = NULL, objnamety = NULL; | ^~~~~~~~~ asncode.c: At top level: asncode.c:291:17: warning: ‘defbyte’ defined but not used [-Wunused-variable] 291 | static CharPtr defbyte = "ASNCODE_BYTEVAL_SLOT"; | ^~~~~~~ asncode.c:290:17: warning: ‘defbool’ defined but not used [-Wunused-variable] 290 | static CharPtr defbool = "ASNCODE_BOOLVAL_SLOT"; | ^~~~~~~ asncode.c:289:17: warning: ‘defreal’ defined but not used [-Wunused-variable] 289 | static CharPtr defreal = "ASNCODE_REALVAL_SLOT"; | ^~~~~~~ asncode.c:288:17: warning: ‘defbigint’ defined but not used [-Wunused-variable] 288 | static CharPtr defbigint = "ASNCODE_BIGINTVAL_SLOT"; | ^~~~~~~~~ asncode.c:286:17: warning: ‘defptr’ defined but not used [-Wunused-variable] 286 | static CharPtr defptr = "ASNCODE_PTRVAL_SLOT"; | ^~~~~~ asncode.c: In function ‘AsnCodePush’: asncode.c:4054:25: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4054 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4055 | CLEAN_FOR_SLOT, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4054:25: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ asncode.c:4068:25: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4068 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4069 | CLEAN_FOR_OBJ_NAME, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4068:25: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ asncode.c:4080:22: warning: ‘AsnCodeCleanName’ accessing 100 bytes in a region of size 60 [-Wstringop-overflow=] 4080 | StringSave (AsnCodeCleanName (atp->name, buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4081 | CLEAN_FOR_ASN_TYPE, iter -> acip -> maxDefineLength)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ asncode.c:4080:22: note: referencing argument 2 of type ‘char[100]’ asncode.c:3533:1: note: in a call to function ‘AsnCodeCleanName’ 3533 | AsnCodeCleanName (CharPtr name, char buf[BUF_LEN], int wash_or_buf, int maxlen) | ^~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘ErrMsgRoot_fopen’ at ncbierr.c:955:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 4096 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ cp -p asntool ../bin make[3]: Leaving directory '/<>/build' /usr/bin/make -C build -f makedemo.unx LCL=lnx CC="x86_64-linux-gnu-gcc" LDFLAGS1="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS NCBI_LINKINGLIBDIR="../shlib" \ CFLAGS1="-c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3" VIBLIBS= VIBFLAG= LIB50=-lpcre make[3]: Entering directory '/<>/build' ./ln-if-absent ../demo/*.* . ./ln-if-absent ../regexp/test/*.* . ./ln-if-absent ../regexp/demo/*.* . ./ln-if-absent ../internal/*.* . set: No match. make[3]: [makedemo.unx:160: copy] Error 1 (ignored) chmod -R ug+rw,o+r . echo Waiting...go Waiting...go x86_64-linux-gnu-gcc -o testcore -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib testcore.c -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from testcore.c:42: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ testcore.c:337:13: warning: ‘TestStrings’ defined but not used [-Wunused-function] 337 | static void TestStrings (void) | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -o makeset -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib makeset.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/all.h:9, from makeset.c:9: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ../include/all.h:7293: warning: "RNA_QUAL" redefined 7293 | #define RNA_QUAL &at[2254] | ../include/all.h:5823: note: this is the location of the previous definition 5823 | #define RNA_QUAL &at[1025] | makeset.c: In function ‘Nlm_Main’: makeset.c:35:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 35 | if (! AsnLoad()) | ^~ makeset.c:38:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 38 | if (! GetArgs("MakeSet 1.0", NUMARGS, myargs)) | ^~ makeset.c:27:33: warning: unused variable ‘uid’ [-Wunused-variable] 27 | Int4 seekptr, tempseek, uid; | ^~~ makeset.c:27:23: warning: unused variable ‘tempseek’ [-Wunused-variable] 27 | Int4 seekptr, tempseek, uid; | ^~~~~~~~ makeset.c:27:14: warning: unused variable ‘seekptr’ [-Wunused-variable] 27 | Int4 seekptr, tempseek, uid; | ^~~~~~~ x86_64-linux-gnu-gcc -o getmesh -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib getmesh.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/allpub.h:9, from getmesh.c:8: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o indexpub -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib indexpub.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/allpub.h:9, from indexpub.c:7: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ indexpub.c: In function ‘Nlm_Main’: indexpub.c:26:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 26 | if (! AsnLoad()) | ^~ indexpub.c:29:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 29 | if (! GetArgs("IndexPub 1.0", NUMARGS, myargs)) | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘fprintf’, inlined from ‘Nlm_Main’ at indexpub.c:60:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: ‘seekptr’ may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ indexpub.c: In function ‘Nlm_Main’: indexpub.c:21:14: note: ‘seekptr’ was declared here 21 | Int4 seekptr, tempseek, uid; | ^~~~~~~ x86_64-linux-gnu-gcc -o getpub -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib getpub.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/allpub.h:9, from getpub.c:7: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ getpub.c: In function ‘Nlm_Main’: getpub.c:30:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 30 | if (! AsnLoad()) | ^~ getpub.c:33:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | if (! GetArgs("GetPub 1.0", NUMARGS, myargs)) | ^~ x86_64-linux-gnu-gcc -o testobj -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib testobj.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmedli.h:80, from testobj.c:8: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o seqtest -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib seqtest.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from seqtest.c:8: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o dosimple -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib dosimple.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/simple.h:63, from dosimple.c:7: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o asn2ff -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib asn2ff.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from asn2ff.c:7: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2ff.c: In function ‘Nlm_Main’: asn2ff.c:129:17: warning: unused variable ‘good’ [-Wunused-variable] 129 | Boolean good = FALSE; | ^~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from asn2ff.c:9: ../include/asnprt.h: At top level: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ asn2ff.c: In function ‘Nlm_Main’: asn2ff.c:351:28: warning: ‘atp1’ may be used uninitialized [-Wmaybe-uninitialized] 351 | if (atp == atp1) { | ^ asn2ff.c:121:32: note: ‘atp1’ was declared here 121 | AsnTypePtr atp = NULL, atp1, atp2; | ^~~~ asn2ff.c:404:28: warning: ‘atp2’ may be used uninitialized [-Wmaybe-uninitialized] 404 | if (atp == atp2) { /* top level Seq-entry */ | ^ asn2ff.c:121:38: note: ‘atp2’ was declared here 121 | AsnTypePtr atp = NULL, atp1, atp2; | ^~~~ x86_64-linux-gnu-gcc -o checksub -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib checksub.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from checksub.c:8: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ checksub.c: In function ‘Nlm_Main’: checksub.c:24:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 24 | if (! SubmitAsnLoad()) | ^~ checksub.c:27:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 27 | atp = AsnFind("Seq-submit"); | ^~~ x86_64-linux-gnu-gcc -o asndhuff -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib asndhuff.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/casn.h:96, from asndhuff.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asndhuff.c: In function ‘do_medline’: asndhuff.c:182:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 182 | for (count=0; entry=CASN_NextMedlineEntry(casnh); ++count) | ^~~~~ asndhuff.c: In function ‘do_sequence’: asndhuff.c:221:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 221 | for (count=0; entry=CASN_NextSeqEntry(casnh); ++count) | ^~~~~ asndhuff.c:200:17: warning: unused variable ‘val’ [-Wunused-variable] 200 | DataVal val; | ^~~ x86_64-linux-gnu-gcc -o entrcmd -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib entrcmd.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from entrcmd.c:113: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ entrcmd.c: In function ‘PrintDSPMwww’: entrcmd.c:373:21: warning: unused variable ‘lsp’ [-Wunused-variable] 373 | LocalLinkSetPtr lsp; | ^~~ entrcmd.c: In function ‘PrintDSPNwww’: entrcmd.c:465:21: warning: unused variable ‘lsp’ [-Wunused-variable] 465 | LocalLinkSetPtr lsp; | ^~~ entrcmd.c: In function ‘PrintDSPPwww’: entrcmd.c:569:21: warning: unused variable ‘lsp’ [-Wunused-variable] 569 | LocalLinkSetPtr lsp; | ^~~ entrcmd.c: In function ‘TermProcessing’: entrcmd.c:1297:13: warning: variable ‘inclusive’ set but not used [-Wunused-but-set-variable] 1297 | Boolean inclusive; | ^~~~~~~~~ entrcmd.c:1296:13: warning: variable ‘endWithTerm’ set but not used [-Wunused-but-set-variable] 1296 | Boolean endWithTerm = FALSE; | ^~~~~~~~~~~ entrcmd.c:1295:13: warning: variable ‘beginWithTerm’ set but not used [-Wunused-but-set-variable] 1295 | Boolean beginWithTerm = FALSE; | ^~~~~~~~~~~~~ entrcmd.c: At top level: entrcmd.c:284:16: warning: ‘IsGenBank’ defined but not used [-Wunused-function] 284 | static Boolean IsGenBank (SeqEntryPtr sep) | ^~~~~~~~~ entrcmd.c: In function ‘RunProgram’: entrcmd.c:1154:13: warning: ‘lsp’ may be used uninitialized [-Wmaybe-uninitialized] 1154 | if (lsp != NULL && !parseOnly) | ^ entrcmd.c:1026:48: note: ‘lsp’ was declared here 1026 | RunProgram(CharPtr programStr, LocalLinkSetPtr lsp, DocType db, Boolean parseOnly) | ~~~~~~~~~~~~~~~~^~~ In file included from ../include/ncbi.h:65: entrcmd.c: In function ‘Nlm_Main’: ../include/ncbifile.h:121:20: warning: ‘neighborFile’ may be used uninitialized [-Wmaybe-uninitialized] 121 | #define FileLength Nlm_FileLength entrcmd.c:1919:13: note: ‘neighborFile’ was declared here 1919 | CharPtr neighborFile; | ^~~~~~~~~~~~ In function ‘ParseImportedFiles’, inlined from ‘Nlm_Main’ at entrcmd.c:2098:28: entrcmd.c:1548:17: warning: ‘db’ may be used uninitialized [-Wmaybe-uninitialized] 1548 | slp->db = db; | ~~~~~~~~^~~~ entrcmd.c: In function ‘Nlm_Main’: entrcmd.c:1476:13: note: ‘db’ was declared here 1476 | DocType db; | ^~ entrcmd.c:2187:16: warning: ‘lsp’ may be used uninitialized [-Wmaybe-uninitialized] 2187 | if (lsp != NULL) | ^ entrcmd.c:203:21: note: ‘lsp’ was declared here 203 | LocalLinkSetPtr lsp; | ^~~ entrcmd.c:2235:9: warning: ‘lsp’ may be used uninitialized [-Wmaybe-uninitialized] 2235 | RunProgram(programStr, lsp, db, FALSE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ entrcmd.c:203:21: note: ‘lsp’ was declared here 203 | LocalLinkSetPtr lsp; | ^~~ x86_64-linux-gnu-gcc -o errhdr -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib errhdr.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from errhdr.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ errhdr.c: In function ‘main’: errhdr.c:44:25: warning: ‘__strncat_chk’ specified bound 32 equals destination size [-Wstringop-truncation] 44 | strncat(mod,argv[i],sizeof mod); | ^ In file included from /usr/include/string.h:548, from ../include/ncbilcl.h:156: In function ‘strncat’, inlined from ‘main’ at errhdr.c:44:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__strncat_chk’ specified bound 32 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncat’, inlined from ‘main’ at errhdr.c:44:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:138:10: warning: ‘__builtin___strncat_chk’ specified bound 32 equals destination size [-Wstringop-overflow=] 138 | return __builtin___strncat_chk (__dest, __src, __len, | ^ x86_64-linux-gnu-gcc -o cdscan -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib cdscan.c -lncbiacc -lncbicdr -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cdscan.c:83: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cdscan.c:576:13: warning: ‘SeqEntryToFeat’ defined but not used [-Wunused-function] 576 | static void SeqEntryToFeat (SeqEntryPtr sep, FILE *fp) | ^~~~~~~~~~~~~~ cdscan.c:392:13: warning: ‘GenBankPubs’ defined but not used [-Wunused-function] 392 | static void GenBankPubs (SeqEntryPtr sep, FILE * fp) | ^~~~~~~~~~~ cdscan.c:133:13: warning: ‘root’ defined but not used [-Wunused-variable] 133 | static Char root [PATH_MAX]; | ^~~~ x86_64-linux-gnu-gcc -o findspl -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib findspl.c -lncbiacc -lncbicdr -lncbiobj -lncbi \ -lconnssl -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from findspl.c:62: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o ncbisort -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib sortcmd.c -lncbitool -lblastcompadj \ -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ncbisort.h:62, from sortcmd.c:64: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o fa2htgs -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib fa2htgs.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from ../include/subutil.h:50, from fa2htgs.c:30: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In function ‘MakeAssemblyFragments’, inlined from ‘Nlm_Main’ at fa2htgs.c:1241:10: fa2htgs.c:474:6: warning: ‘dsp’ may be used uninitialized [-Wmaybe-uninitialized] 474 | if (dsp != NULL && dsp->choice == 2) { | ^ fa2htgs.c: In function ‘Nlm_Main’: fa2htgs.c:448:16: note: ‘dsp’ was declared here 448 | DeltaSeqPtr dsp; | ^~~ x86_64-linux-gnu-gcc -o testval -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib testval.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from testval.c:9: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ testval.c: In function ‘Nlm_Main’: testval.c:186:28: warning: ‘atp2’ may be used uninitialized [-Wmaybe-uninitialized] 186 | if (atp == atp2) /* top level Seq-entry */ | ^ testval.c:38:25: note: ‘atp2’ was declared here 38 | AsnTypePtr atp, atp2; | ^~~~ testval.c:183:31: warning: ‘atp’ may be used uninitialized [-Wmaybe-uninitialized] 183 | while ((atp = AsnReadId(aip, amp, atp)) != NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~ testval.c:38:20: note: ‘atp’ was declared here 38 | AsnTypePtr atp, atp2; | ^~~ x86_64-linux-gnu-gcc -o vecscreen -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib vecscreen.c -lncbitool \ -lblastcompadj -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from vecscreen.c:57: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/sqnutils.h:51, from vecscreen.c:68: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -o gil2bin -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib gil2bin.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from gil2bin.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gil2bin.c: In function ‘Nlm_Main’: gil2bin.c:90:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 90 | else | ^~~~ gil2bin.c:93:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 93 | return 0; | ^~~~~~ x86_64-linux-gnu-gcc -o asn2xml -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib asn2xml.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from asn2xml.c:21: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o debruijn -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib debruijn.c -lblast -lblastcompadj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from debruijn.c:38: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ debruijn.c: In function ‘Nlm_Main’: debruijn.c:72:12: warning: pointer targets in assignment from ‘Nlm_CharPtr’ {aka ‘char *’} to ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} differ in signedness [-Wpointer-sign] 72 | alphabet = myargs[1].strvalue; | ^ debruijn.c:80:14: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign] 80 | k = strlen(alphabet); | ^~~~~~~~ | | | Nlm_Uint1 * {aka unsigned char *} In file included from ../include/ncbilcl.h:156: /usr/include/string.h:407:35: note: expected ‘const char *’ but argument is of type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} 407 | extern size_t strlen (const char *__s) | ~~~~~~~~~~~~^~~ debruijn.c:89:10: warning: pointer targets in assignment from ‘char *’ to ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} differ in signedness [-Wpointer-sign] 89 | output = (char *) malloc(outputsize + 1); | ^ debruijn.c:106:8: warning: pointer targets in passing argument 1 of ‘puts’ differ in signedness [-Wpointer-sign] 106 | puts(output); | ^~~~~~ | | | Nlm_Uint1 * {aka unsigned char *} In file included from ../include/ncbilcl.h:154: /usr/include/stdio.h:724:30: note: expected ‘const char *’ but argument is of type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} 724 | extern int puts (const char *__s); | ~~~~~~~~~~~~^~~ debruijn.c:109:1: warning: control reaches end of non-void function [-Wreturn-type] 109 | } | ^ debruijn.c: At top level: debruijn.c:29:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 29 | static char const rcsid[] = "$Id: debruijn.c,v 1.4 2004/02/09 21:24:59 ucko Exp $"; | ^~~~~ x86_64-linux-gnu-gcc -o asn2idx -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib asn2idx.c -lncbitool -lblastcompadj -lncbiobj \ -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2idx.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o sortbyquote -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib sortbyquote.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from sortbyquote.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o subfuse -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib subfuse.c -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from subfuse.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o test_regexp -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib pcretest.c -lpcre x86_64-linux-gnu-gcc -o demo_regexp -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib pcredemo.c -lpcre x86_64-linux-gnu-gcc -o demo_regexp_grep -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib pcregrep.c -lpcre pcregrep.c: In function ‘main’: pcregrep.c:515:64: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 515 | if (pattern_count == 1) s[0] = 0; else sprintf(s, " number %d", j); | ^~ pcregrep.c:515:55: note: directive argument in the range [0, 2147483646] 515 | if (pattern_count == 1) s[0] = 0; else sprintf(s, " number %d", j); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from pcregrep.c:9: In function ‘sprintf’, inlined from ‘main’ at pcregrep.c:515:44: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 10 and 19 bytes into a destination of size 16 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/build' /usr/bin/make -C build -f makenet.unx LCL=lnx CC="x86_64-linux-gnu-gcc" LDFLAGS1="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib" RAN="ranlib" OTHERLIBS="-lm" VIBLIBS="-lXm -lXmu -lXt -lX11 " VIBFLAG="-DWIN_MOTIF" GNUTLS_INCLUDE=-DHAVE_LIBGNUTLS NCBI_LINKINGLIBDIR="../shlib" \ CFLAGS1="-c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3" THREAD_OBJ="ncbithr.o" \ THREAD_OTHERLIBS="-lpthread" \ NETENTREZVERSION="2.02c2ASN1SPEC6" BLIB31=libvibnet.a \ OGLLIBS= VIBLIBS= VIB="Psequin sbtedit udv ddv taxblast idfetch asn2gb tbl2asn gene2xml entrez2 gbseqget asn2all asn2asn asn2fsa asn2xml asndisc asnmacro asnval cleanasn insdseqget nps2gps spidey trna2sap trna2tbl Cn3D" make[3]: Entering directory '/<>/build' ./ln-if-absent ../connect/test/*.c . ./ln-if-absent ../network/entrez/client/*.h ../include ./ln-if-absent ../network/entrez/client/*.c . ./ln-if-absent ../network/medarch/client/*.h ../include ./ln-if-absent ../network/medarch/client/*.c . ./ln-if-absent ../network/taxonomy/client/*.h ../include set: No match. make[3]: [makenet.unx:480: copy] Error 1 (ignored) ./ln-if-absent ../network/taxonomy/client/*.c . set: No match. make[3]: [makenet.unx:481: copy] Error 1 (ignored) ./ln-if-absent ../network/taxon1/common/*.h ../include ./ln-if-absent ../network/taxon1/common/*.c . ./ln-if-absent ../network/taxon1/taxon2/*.h ../include ./ln-if-absent ../network/taxon1/taxon2/*.c . ./ln-if-absent ../network/id0arch/client/*.h ../include set: No match. make[3]: [makenet.unx:486: copy] Error 1 (ignored) ./ln-if-absent ../network/id0arch/client/*.c . set: No match. make[3]: [makenet.unx:487: copy] Error 1 (ignored) ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id1arch/*.c . ./ln-if-absent ../network/id2arch/*.h ../include ./ln-if-absent ../network/id2arch/*.c . ./ln-if-absent ../network/spell/client/*.h ../include ./ln-if-absent ../network/spell/client/*.c . ./ln-if-absent ../network/suggest/client/*.h ../include ./ln-if-absent ../network/suggest/client/*.c . ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/blast3/client/*.c . ./ln-if-absent ../tools/taxblast.h ../include ./ln-if-absent ../tools/taxblast.c . ./ln-if-absent /*.c . set: No match. make[3]: [makenet.unx:500: copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.c . set: No match. make[3]: [makenet.unx:501: copy] Error 1 (ignored) ./ln-if-absent ../internal/misc/*.h ../include set: No match. make[3]: [makenet.unx:502: copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.c . set: No match. make[3]: [makenet.unx:503: copy] Error 1 (ignored) ./ln-if-absent ../internal/ssparse/*.h ../include set: No match. make[3]: [makenet.unx:504: copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.c . set: No match. make[3]: [makenet.unx:505: copy] Error 1 (ignored) ./ln-if-absent ../internal/libparsn/*.h ../include set: No match. make[3]: [makenet.unx:506: copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.c . set: No match. make[3]: [makenet.unx:507: copy] Error 1 (ignored) ./ln-if-absent ../internal/smart/smartnet/*.h ../include set: No match. make[3]: [makenet.unx:508: copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.c . set: No match. make[3]: [makenet.unx:509: copy] Error 1 (ignored) ./ln-if-absent ../internal/www/*.h ../include set: No match. make[3]: [makenet.unx:510: copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.c . set: No match. make[3]: [makenet.unx:511: copy] Error 1 (ignored) ./ln-if-absent ../internal/query/*.h ../include set: No match. make[3]: [makenet.unx:512: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.c . set: No match. make[3]: [makenet.unx:513: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/ctlib/*.h ../include set: No match. make[3]: [makenet.unx:514: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.c . set: No match. make[3]: [makenet.unx:515: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/oslib/*.h ../include set: No match. make[3]: [makenet.unx:516: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.c . set: No match. make[3]: [makenet.unx:517: copy] Error 1 (ignored) ./ln-if-absent ../network/sybutils/idloadlib/*.h ../include set: No match. make[3]: [makenet.unx:518: copy] Error 1 (ignored) ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/nsclilib/*.c . ./ln-if-absent ../network/vibnet/*.c . ./ln-if-absent ../network/vibnet/*.h ../include ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../network/wwwblast/Src/*.c . ./ln-if-absent ../cdromlib/accentr.c . ./ln-if-absent ../cdromlib/accutils.c . ./ln-if-absent ../sequin/*.* . ./ln-if-absent ../demo/entrez.c . ./ln-if-absent ../demo/seqget.c . ./ln-if-absent ../demo/entrcmd.c . ./ln-if-absent ../demo/batch.c . ./ln-if-absent ../demo/qbatch.c . ./ln-if-absent ../demo/elecpcr.c . ./ln-if-absent ../demo/asn2fast.c . ./ln-if-absent ../demo/asn2asn.c . ./ln-if-absent ../demo/cleanasn.c . ./ln-if-absent ../demo/cspeedtest.c . ./ln-if-absent ../demo/sqn2agp.c . ./ln-if-absent ../demo/sugint.c . ./ln-if-absent ../demo/fetchent.c . ./ln-if-absent ../demo/udvmain.c . ./ln-if-absent ../demo/rtestval.c . ./ln-if-absent ../demo/aceread_tst.c . ./ln-if-absent ../demo/asn2ff.c . ./ln-if-absent ../demo/asn2gb.c . ./ln-if-absent ../demo/asn2fsa.c . ./ln-if-absent ../demo/asn2all.c . ./ln-if-absent ../demo/gene2xml.c . ./ln-if-absent ../demo/asnval.c . ./ln-if-absent ../demo/asndisc.c . ./ln-if-absent ../demo/asnbarval.c . ./ln-if-absent ../demo/aceread_tst.c . ./ln-if-absent ../demo/asnmacro.c . ./ln-if-absent ../demo/asnstrip.c . ./ln-if-absent ../demo/tbl2asn.c . ./ln-if-absent ../demo/raw2delt.c . ./ln-if-absent ../demo/flint.c . ./ln-if-absent ../demo/xlint.c . ./ln-if-absent ../demo/diffshift.c . ./ln-if-absent ../demo/gbseqget.c . ./ln-if-absent ../demo/insdseqget.c . ./ln-if-absent ../demo/nps2gps.c . ./ln-if-absent ../demo/testent2.c . ./ln-if-absent ../demo/trna2sap.c . ./ln-if-absent ../demo/trna2tbl.c . ./ln-if-absent ../demo/entrez2.c . ./ln-if-absent ../demo/condense.c . ./ln-if-absent ../demo/spideymain.c . ./ln-if-absent ../demo/dotmain.c . ./ln-if-absent ../demo/ingenmain.c . ./ln-if-absent ../demo/bl2seq.c . ./ln-if-absent ../demo/blastall.c . ./ln-if-absent ../demo/blast_driver.c . ./ln-if-absent ../demo/src_chk.c . ./ln-if-absent ../demo/tbl_chk.c . ./ln-if-absent ../demo/export_cmt.c . ./ln-if-absent ../internal/parser/flat2asn.c . make[3]: [makenet.unx:577: copy] Error 1 (ignored) ./ln-if-absent ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c ../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c ../demo/cnsrt.c ../demo/cnsgn.c ../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c ../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c . ./ln-if-absent ../network/entrez/server/*.* . set: No match. make[3]: [makenet.unx:579: copy] Error 1 (ignored) ./ln-if-absent ../network/suggest/server/*.* . chmod -R ug+rw,o+r . echo Waiting...go Waiting...go x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_lib_.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from ni_lib_.c:76: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_debug.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ni_debug.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_service.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ni_service.c:125: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ni_service.c: In function ‘s_GenericGetService’: ni_service.c:201:19: warning: unused variable ‘c’ [-Wunused-variable] 201 | CONNECTOR c; | ^ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ni_error.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from ../include/ni_error.h:76, from ni_error.c:72: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rm -f libnetcli.a ar cru libnetcli.a ni_lib_.o ni_debug.o ni_service.o ni_error.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetcli.a ../lib ranlib ../lib/libnetcli.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from netentr.c:161: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netentr.c: In function ‘s_NetEntTLEvalCount’: netentr.c:798:5: warning: "/*" within comment [-Wcomment] 798 | /*MsgSetReadTimeout(Entrez_ni, 60);*/ | netentr.c: In function ‘s_NetDocSumListGet’: netentr.c:856:18: warning: variable ‘amp’ set but not used [-Wunused-but-set-variable] 856 | AsnModulePtr amp; | ^~~ netentr.c: In function ‘s_NetTermListByTerm’: netentr.c:1212:9: warning: variable ‘terms_to_read’ set but not used [-Wunused-but-set-variable] 1212 | int terms_to_read; | ^~~~~~~~~~~~~ netentr.c:1200:14: warning: unused variable ‘asnout’ [-Wunused-variable] 1200 | AsnIoPtr asnout = Entrez_asnout; | ^~~~~~ netentr.c: In function ‘s_NetTermListByPage’: netentr.c:1343:14: warning: unused variable ‘asnout’ [-Wunused-variable] 1343 | AsnIoPtr asnout = Entrez_asnout; | ^~~~~~ netentr.c: In function ‘NetEntTLEval’: netentr.c:675:12: warning: ‘lsp’ may be used uninitialized [-Wmaybe-uninitialized] 675 | return lsp; | ^~~ netentr.c:660:16: note: ‘lsp’ was declared here 660 | LinkSetPtr lsp; | ^~~ In function ‘s_NetEntTLEvalCount’, inlined from ‘NetEntTLEvalCount’ at netentr.c:829:18: netentr.c:800:8: warning: ‘atp’ may be used uninitialized [-Wmaybe-uninitialized] 800 | if (atp == ENTREZ_BACK_eval_count) | ^ netentr.c: In function ‘NetEntTLEvalCount’: netentr.c:782:16: note: ‘atp’ was declared here 782 | AsnTypePtr atp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netlib.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from netlib.c:82: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netlib.c: In function ‘BoolExprAsnWrite’: netlib.c:307:16: warning: unused variable ‘n’ [-Wunused-variable] 307 | static int n = 0; | ^ netlib.c: At top level: netlib.c:96:16: warning: ‘loaded’ defined but not used [-Wunused-variable] 96 | static Boolean loaded = FALSE; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objneten.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/asnneten.h:9, from objneten.c:86: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objneten.c: In function ‘NetEntAsnLoad’: objneten.c:106:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 106 | if (loaded) | ^~ objneten.c:108:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 108 | loaded = TRUE; | ^~~~~~ objneten.c: In function ‘EntrezNeighborTextAsnRead’: objneten.c:2938:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2938 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘ChildLinkAsnRead’: objneten.c:3148:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3148 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘EntrezHierarchyAsnRead’: objneten.c:3442:15: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3442 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘EntrezBlastreqAsnRead’: objneten.c:3705:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3705 | AsnReadFunc func; | ^~~~ objneten.c:3704:12: warning: unused variable ‘isError’ [-Wunused-variable] 3704 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘EntrezExtraInfoAsnRead’: objneten.c:3911:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3911 | AsnReadFunc func; | ^~~~ objneten.c:3910:12: warning: unused variable ‘isError’ [-Wunused-variable] 3910 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘ClusterArticlesAsnRead’: objneten.c:4262:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4262 | AsnReadFunc func; | ^~~~ objneten.c:4261:12: warning: unused variable ‘isError’ [-Wunused-variable] 4261 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘ClusterRespAsnRead’: objneten.c:4455:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4455 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘DateConstraintsAsnRead’: objneten.c:4622:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4622 | AsnReadFunc func; | ^~~~ objneten.c: In function ‘DateVectorAsnRead’: objneten.c:4785:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4785 | AsnReadFunc func; | ^~~~ objneten.c:4784:12: warning: unused variable ‘isError’ [-Wunused-variable] 4784 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘GetByFidAsnRead’: objneten.c:4963:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4963 | AsnReadFunc func; | ^~~~ objneten.c:4962:12: warning: unused variable ‘isError’ [-Wunused-variable] 4962 | Boolean isError = FALSE; | ^~~~~~~ objneten.c: In function ‘GetFeatIdsAsnRead’: objneten.c:5133:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 5133 | AsnReadFunc func; | ^~~~ objneten.c:5132:12: warning: unused variable ‘isError’ [-Wunused-variable] 5132 | Boolean isError = FALSE; | ^~~~~~~ rm -f libnetentr.a ar cru libnetentr.a netentr.o netlib.o objneten.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetentr.a ../lib ranlib ../lib/libnetentr.a ./ln-if-absent accentr.c Naccentr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NETENT_ Naccentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from Naccentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ Naccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces] 357 | Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = { | ^ 358 | 8, 6, 3, 3, | { } 359 | 8, 6, 3, 3, | { } 360 | 8, 6, 3, 3, | { } 361 | 8, 6, 3, 3, | { } 362 | 9, 7, 4, 3, | { } 363 | 9, 8, 5, 3, | { } 364 | 10, 9, 5, 3, | { } 365 | 10, 10, 5, 3, | { } 366 | 11, 10, 5, 3, | { } 367 | 11, 11, 5, 3, | { } 368 | 12, 11, 5, 3, | { } 369 | 12, 11, 5, 3, | { } 370 | 12, 11, 5, 3 | { 371 | }; | } Naccentr.c: In function ‘EntrezDocSumListGet’: Naccentr.c:1409:14: warning: variable ‘actual’ set but not used [-Wunused-but-set-variable] 1409 | Int2 actual; | ^~~~~~ Naccentr.c: In function ‘EntrezGIForSeqIdFunc’: Naccentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ Naccentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ Naccentr.c: In function ‘EntrezMedlineEntryGet’: Naccentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at Naccentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Naccentr.c: In function ‘EntrezSeqEntryGet’: Naccentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at Naccentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbiNacc.a ar cru libncbiNacc.a Naccentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiNacc.a ../lib ranlib ../lib/libncbiNacc.a ./ln-if-absent accentr.c Caccentr.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -D_NET_AND_CD_ Caccentr.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/accentr.h:125, from Caccentr.c:297: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ Caccentr.c:357:93: warning: missing braces around initializer [-Wmissing-braces] 357 | Uint1 AdaptiveDocSumMatrix[MAX_CHUNK_IN_ADAPTIVE_MATRIX+1][MAX_SECS_IN_ADAPTIVE_MATRIX+1] = { | ^ 358 | 8, 6, 3, 3, | { } 359 | 8, 6, 3, 3, | { } 360 | 8, 6, 3, 3, | { } 361 | 8, 6, 3, 3, | { } 362 | 9, 7, 4, 3, | { } 363 | 9, 8, 5, 3, | { } 364 | 10, 9, 5, 3, | { } 365 | 10, 10, 5, 3, | { } 366 | 11, 10, 5, 3, | { } 367 | 11, 11, 5, 3, | { } 368 | 12, 11, 5, 3, | { } 369 | 12, 11, 5, 3, | { } 370 | 12, 11, 5, 3 | { 371 | }; | } Caccentr.c: In function ‘EntrezDocSumListGet’: Caccentr.c:1409:14: warning: variable ‘actual’ set but not used [-Wunused-but-set-variable] 1409 | Int2 actual; | ^~~~~~ Caccentr.c: In function ‘EntrezGIForSeqIdFunc’: Caccentr.c:3283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3283 | if (! gi) return OM_MSG_RET_OK; | ^~ Caccentr.c:3285:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3285 | sip2 = ValNodeNew(NULL); | ^~~~ Caccentr.c: In function ‘EntrezMedlineEntryGet’: Caccentr.c:1978:58: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 10 [-Wformat-overflow=] 1978 | sprintf(errorString, "(EntrezMedlineEntryGet: %ld)",(long)uid); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EntrezMedlineEntryGet’ at Caccentr.c:1978:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 27 and 37 bytes into a destination of size 35 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Caccentr.c: In function ‘EntrezSeqEntryGet’: Caccentr.c:2383:55: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2383 | sprintf(errorString, "(EntrezSeqEntryGet: %ld)",(long)uid); | ^ In function ‘sprintf’, inlined from ‘EntrezSeqEntryGet’ at Caccentr.c:2383:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 23 and 33 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libncbiCacc.a ar cru libncbiCacc.a Caccentr.o accutils.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiCacc.a ../lib ranlib ../lib/libncbiCacc.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netcnfg.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from netcnfg.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netcnfg.c: In function ‘ShowNetConfigForm’: netcnfg.c:319:23: warning: variable ‘ppt1’ set but not used [-Wunused-but-set-variable] 319 | PrompT ppt0, ppt1; | ^~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" trmlst.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from trmlst.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ trmlst.c: In function ‘FetchFromTermList’: trmlst.c:1048:16: warning: variable ‘numRead’ set but not used [-Wunused-but-set-variable] 1048 | Int2 numRead; | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" docsum.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from docsum.c:252: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ docsum.c: In function ‘ImportDocSumForm’: docsum.c:2298:21: warning: unused variable ‘sephead’ [-Wunused-variable] 2298 | SeqEntryPtr sephead = NULL; | ^~~~~~~ docsum.c:2296:21: warning: unused variable ‘is_na’ [-Wunused-variable] 2296 | Boolean is_na = TRUE; | ^~~~~ docsum.c:2290:21: warning: unused variable ‘choice’ [-Wunused-variable] 2290 | Uint1 choice = 0; | ^~~~~~ docsum.c: In function ‘SaveDocsumProject’: docsum.c:3042:16: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 3042 | SummFormPtr sfp; | ^~~ docsum.c: In function ‘LaunchStructureViewer’: docsum.c:4192:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4192 | system (cmmd); | ^~~~~~~~~~~~~ docsum.c: At top level: docsum.c:439:15: warning: ‘checkmark’ defined but not used [-Wunused-variable] 439 | static Uint1 checkmark [] = { | ^~~~~~~~~ docsum.c: In function ‘SetDefaultFailureMessage’: docsum.c:687:48: warning: ‘ in ’ directive writing 4 bytes into a region of size between 3 and 42 [-Wformat-overflow=] 687 | sprintf (tmp, "%sProblem with sequence %s in %s database", prefix, buf, dbname); | ^~~~ docsum.c:687:21: note: assuming directive output of 3 bytes 687 | sprintf (tmp, "%sProblem with sequence %s in %s database", prefix, buf, dbname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SetDefaultFailureMessage’ at docsum.c:687:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 36 or more bytes (assuming 78) into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ docsum.c: In function ‘FetchLocalBioseq’: docsum.c:1223:6: warning: ‘str’ may be used uninitialized [-Wmaybe-uninitialized] 1223 | if (str == NULL) return failed; | ^ docsum.c:1204:17: note: ‘str’ was declared here 1204 | CharPtr str; | ^~~ docsum.c: In function ‘LaunchStructureViewer.isra.0’: docsum.c:4191:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4091 [-Wformat-overflow=] 4191 | sprintf (cmmd, "Cn3D %s &", path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘LaunchStructureViewer.isra.0’ at docsum.c:4191:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 8 and 4103 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rm -f libvibnet.a ar cru libvibnet.a netcnfg.o trmlst.o docsum.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libvibnet.a ../lib ranlib ../lib/libvibnet.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objtax1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objtax1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objtax1.c: In function ‘Taxon1ReqFree’: objtax1.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objtax1.c: In function ‘Taxon1ReqAsnRead’: objtax1.c:92:12: warning: unused variable ‘isError’ [-Wunused-variable] 92 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1InfoAsnRead’: objtax1.c:502:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 502 | AsnReadFunc func; | ^~~~ objtax1.c:501:12: warning: unused variable ‘isError’ [-Wunused-variable] 501 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1ErrorAsnRead’: objtax1.c:1131:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1131 | AsnReadFunc func; | ^~~~ objtax1.c:1130:12: warning: unused variable ‘isError’ [-Wunused-variable] 1130 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1NameAsnRead’: objtax1.c:1296:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1296 | AsnReadFunc func; | ^~~~ objtax1.c:1295:12: warning: unused variable ‘isError’ [-Wunused-variable] 1295 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon1DataAsnRead’: objtax1.c:1482:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1482 | AsnReadFunc func; | ^~~~ objtax1.c:1481:12: warning: unused variable ‘isError’ [-Wunused-variable] 1481 | Boolean isError = FALSE; | ^~~~~~~ objtax1.c: In function ‘Taxon2DataAsnRead’: objtax1.c:1670:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1670 | AsnReadFunc func; | ^~~~ objtax1.c: In function ‘Taxon1ReqAsnRead’: objtax1.c:284:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 284 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax1.c:91:10: note: ‘choice’ was declared here 91 | Uint1 choice; | ^~~~~~ objtax1.c: In function ‘Taxon1RespAsnRead’: objtax1.c:920:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 920 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objtax1.c:695:10: note: ‘choice’ was declared here 695 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/utilpub.h:4, from taxutil.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ taxutil.c: In function ‘taxname_match’: taxutil.c:85:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if(err) | ^~ taxutil.c:88:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 88 | return -1; | ^~~~~~ taxutil.c:90:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 90 | if(err) | ^~ taxutil.c:93:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 93 | return -1; | ^~~~~~ taxutil.c:97:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 97 | if(err) | ^~ taxutil.c:100:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 100 | return -1; | ^~~~~~ taxutil.c:66:24: warning: unused variable ‘taxstr’ [-Wunused-variable] 66 | CharPtr taxstr = NULL; | ^~~~~~ taxutil.c: In function ‘get_lineage’: taxutil.c:140:42: warning: ‘onp’ may be used uninitialized [-Wmaybe-uninitialized] 140 | return Nlm_StringSave(onp->lineage); | ~~~^~~~~~~~~ taxutil.c:132:20: note: ‘onp’ was declared here 132 | OrgNamePtr onp; | ^~~ taxutil.c: In function ‘get_gcode’: taxutil.c:158:20: warning: ‘onp’ may be used uninitialized [-Wmaybe-uninitialized] 158 | if (onp) { | ^ taxutil.c:150:20: note: ‘onp’ was declared here 150 | OrgNamePtr onp; | ^~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o tc2dproc.o -DTAXSERVICE tc2proc.c tc2proc.c: In function ‘getIdByOrgRef’: tc2proc.c:407:17: warning: unused variable ‘om_flag’ [-Wunused-variable] 407 | Boolean om_flag= FALSE; | ^~~~~~~ tc2proc.c: In function ‘bldLineage’: tc2proc.c:1095:10: warning: unused variable ‘rank’ [-Wunused-variable] 1095 | Int2 rank= 0; | ^~~~ tc2proc.c: In function ‘storedTaxId’: tc2proc.c:2114:17: warning: unused variable ‘object_id’ [-Wunused-variable] 2114 | ObjectIdPtr object_id; | ^~~~~~~~~ tc2proc.c: In function ‘tax1e_needUpdate’: tc2proc.c:2181:13: warning: unused variable ‘hit_name’ [-Wunused-variable] 2181 | CharPtr hit_name; | ^~~~~~~~ tc2proc.c:2180:13: warning: unused variable ‘need_search_name’ [-Wunused-variable] 2180 | Boolean need_search_name= TRUE; | ^~~~~~~~~~~~~~~~ tc2proc.c:2179:9: warning: unused variable ‘is_species’ [-Wunused-variable] 2179 | int is_species; | ^~~~~~~~~~ tc2proc.c:2176:19: warning: unused variable ‘res’ [-Wunused-variable] 2176 | Taxon1DataPtr res; | ^~~ tc2proc.c: At top level: tc2proc.c:403:13: warning: ‘getIdByOrgRef’ defined but not used [-Wunused-function] 403 | static Int4 getIdByOrgRef(CharPtr sname, OrgNamePtr orNm) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -c -o txcdproc.o -DTAXSERVICE txcdproc.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from txcdproc.c:116: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" parttree.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/txclient.h:73, from parttree.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ parttree.c: In function ‘tax_ptree_addSubtree’: parttree.c:392:13: warning: unused variable ‘need_remove’ [-Wunused-variable] 392 | Boolean need_remove= FALSE; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxcs.c x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" taxblast.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from taxblast.c:161: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ taxblast.c: In function ‘TXBHtmlReportInternal’: taxblast.c:1359:37: warning: variable ‘linlines’ set but not used [-Wunused-but-set-variable] 1359 | Int2 numtaxa, numorgs, numhits, linlines, longname; | ^~~~~~~~ taxblast.c: In function ‘RDTaxLookupReset’: taxblast.c:2050:1: warning: control reaches end of non-void function [-Wreturn-type] 2050 | } | ^ taxblast.c: At top level: taxblast.c:1967:13: warning: ‘getTotalTaxIdCount’ defined but not used [-Wunused-function] 1967 | static Int4 getTotalTaxIdCount(TreeCursorPtr cursor) | ^~~~~~~~~~~~~~~~~~ taxblast.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: taxblast.c,v 6.31 2015/07/06 19:25:47 madden Exp $"; | ^~~~~ taxblast.c: In function ‘TXBGetTargetGi’: taxblast.c:504:12: warning: ‘gi’ may be used uninitialized [-Wmaybe-uninitialized] 504 | return gi; | ^~ taxblast.c:462:10: note: ‘gi’ was declared here 462 | Int4 gi; | ^~ In file included from ../include/ncbi.h:62: taxblast.c: In function ‘TXBHtmlReport’: ../include/ncbistr.h:281:25: warning: ‘strncpy’ specified bound 128 equals destination size [-Wstringop-truncation] 281 | #define Nlm_StrNCpy strncpy | ^~~~~~~ rm -f libncbitxc2.a ar cru libncbitxc2.a objtax1.o taxutil.o tc2dproc.o txcdproc.o parttree.o taxcs.o taxblast.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbitxc2.a ../lib ranlib ../lib/libncbitxc2.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1gen.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from id1gen.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ id1gen.c: In function ‘ID1serverRequestFree’: id1gen.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ id1gen.c: In function ‘ID1serverRequestAsnRead’: id1gen.c:90:12: warning: unused variable ‘isError’ [-Wunused-variable] 90 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1serverMaxcomplexAsnRead’: id1gen.c:348:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 348 | AsnReadFunc func; | ^~~~ id1gen.c:347:12: warning: unused variable ‘isError’ [-Wunused-variable] 347 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1SeqHistAsnRead’: id1gen.c:530:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 530 | AsnReadFunc func; | ^~~~ id1gen.c:529:12: warning: unused variable ‘isError’ [-Wunused-variable] 529 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1SeqEntryInfoAsnRead’: id1gen.c:979:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 979 | AsnReadFunc func; | ^~~~ id1gen.c:978:12: warning: unused variable ‘isError’ [-Wunused-variable] 978 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1blobInfoAsnRead’: id1gen.c:1147:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1147 | AsnReadFunc func; | ^~~~ id1gen.c:1146:12: warning: unused variable ‘isError’ [-Wunused-variable] 1146 | Boolean isError = FALSE; | ^~~~~~~ id1gen.c: In function ‘ID1serverDebugAsnRead’: id1gen.c:1368:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1368 | AsnReadFunc func; | ^~~~ id1gen.c: In function ‘ID1serverBackAsnRead’: id1gen.c:811:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 811 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ id1gen.c:697:10: note: ‘choice’ was declared here 697 | Uint1 choice; | ^~~~~~ id1gen.c: In function ‘ID1serverRequestAsnRead’: id1gen.c:186:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 186 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ id1gen.c:89:10: note: ‘choice’ was declared here 89 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" id1arch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from id1arch.c:31: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ id1arch.c: In function ‘ID1ArchSeqEntryGet’: id1arch.c:173:14: warning: unused variable ‘retval’ [-Wunused-variable] 173 | Int4 retval = 0; | ^~~~~~ id1arch.c: In function ‘ID1ArchGIGet’: id1arch.c:486:10: warning: unused variable ‘retval’ [-Wunused-variable] 486 | Int4 retval = 0; | ^~~~~~ id1arch.c: In function ‘SeqHistPrintTable’: id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 553 | sprintf(repl_date,"%0.2d/%0.2d/%0.4d", | ^~~~~~~~~~~~~~~~~~~ id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] id1arch.c:553:59: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] id1arch.c:563:47: warning: spurious trailing ‘%’ in format [-Wformat=] 563 | fprintf(fp,"%-20d%-20s%",old_gi,repl_date); | ^ id1arch.c:558:65: warning: ‘__sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 558 | sprintf(repl_date,"%-20s",shp->replace_date->str); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘SeqHistPrintTable’ at id1arch.c:558:41, inlined from ‘SeqHistPrintTable’ at id1arch.c:505:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 21 or more bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" accid1.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objmgr.h:51, from ../include/seqmgr.h:48, from accid1.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ accid1.c: In function ‘s_ID1BioseqFetchFunc’: accid1.c:262:33: warning: unused variable ‘retcode’ [-Wunused-variable] 262 | Int2 retcode=0; | ^~~~~~~ rm -f libncbiid1.a ar cru libncbiid1.a id1gen.o id1arch.o accid1.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbiid1.a ../lib ranlib ../lib/libncbiid1.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" objblst3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objblst3.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objblst3.c: In function ‘BlastSearchAsnRead’: objblst3.c:91:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 91 | AsnReadFunc func; | ^~~~ objblst3.c:90:12: warning: unused variable ‘isError’ [-Wunused-variable] 90 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastRequestFree’: objblst3.c:287:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 287 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastRequestAsnRead’: objblst3.c:337:12: warning: unused variable ‘isError’ [-Wunused-variable] 337 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff2_cutoff2Free’: objblst3.c:999:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 999 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1027:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1027 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘Cutoff2_cutoff2AsnRead’: objblst3.c:1422:12: warning: unused variable ‘isError’ [-Wunused-variable] 1422 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff_cutoffAsnRead’: objblst3.c:1788:12: warning: unused variable ‘isError’ [-Wunused-variable] 1788 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘Cutoff_cutoffFree’: objblst3.c:1871:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 1871 | Pointer pnt; | ^~~ objblst3.c: In function ‘BlastMatrixAsnRead’: objblst3.c:1936:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 1936 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastDbinfoAsnRead’: objblst3.c:2153:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2153 | AsnReadFunc func; | ^~~~ objblst3.c:2152:12: warning: unused variable ‘isError’ [-Wunused-variable] 2152 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastMaskAsnRead’: objblst3.c:2357:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2357 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastKABlkAsnRead’: objblst3.c:2517:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2517 | AsnReadFunc func; | ^~~~ objblst3.c:2516:12: warning: unused variable ‘isError’ [-Wunused-variable] 2516 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastErrorAsnRead’: objblst3.c:2697:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2697 | AsnReadFunc func; | ^~~~ objblst3.c:2696:12: warning: unused variable ‘isError’ [-Wunused-variable] 2696 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastPhialignAsnRead’: objblst3.c:2861:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 2861 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastDbinfoGetAsnRead’: objblst3.c:3022:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3022 | AsnReadFunc func; | ^~~~ objblst3.c:3021:12: warning: unused variable ‘isError’ [-Wunused-variable] 3021 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastSeqIdAsnRead’: objblst3.c:3187:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3187 | AsnReadFunc func; | ^~~~ objblst3.c:3186:12: warning: unused variable ‘isError’ [-Wunused-variable] 3186 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastSequenceAsnRead’: objblst3.c:3364:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3364 | AsnReadFunc func; | ^~~~ objblst3.c:3363:12: warning: unused variable ‘isError’ [-Wunused-variable] 3363 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastPartsAsnRead’: objblst3.c:3532:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3532 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastQueuedAsnRead’: objblst3.c:3694:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3694 | AsnReadFunc func; | ^~~~ objblst3.c:3693:12: warning: unused variable ‘isError’ [-Wunused-variable] 3693 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastProgressAsnRead’: objblst3.c:3846:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 3846 | AsnReadFunc func; | ^~~~ objblst3.c:3845:12: warning: unused variable ‘isError’ [-Wunused-variable] 3845 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastDeflineAsnRead’: objblst3.c:4000:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4000 | AsnReadFunc func; | ^~~~ objblst3.c:3999:12: warning: unused variable ‘isError’ [-Wunused-variable] 3999 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘BlastVersionAsnRead’: objblst3.c:4168:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4168 | AsnReadFunc func; | ^~~~ objblst3.c:4167:12: warning: unused variable ‘isError’ [-Wunused-variable] 4167 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘MegaBlastHitAsnRead’: objblst3.c:4335:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4335 | AsnReadFunc func; | ^~~~ objblst3.c:4334:12: warning: unused variable ‘isError’ [-Wunused-variable] 4334 | Boolean isError = FALSE; | ^~~~~~~ objblst3.c: In function ‘MegaBlastResultsAsnRead’: objblst3.c:4546:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 4546 | AsnReadFunc func; | ^~~~ objblst3.c: In function ‘BlastRequestAsnRead’: objblst3.c:430:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 430 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c:336:10: note: ‘choice’ was declared here 336 | Uint1 choice; | ^~~~~~ objblst3.c: In function ‘BlastResponseAsnRead’: objblst3.c:791:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 791 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c:643:10: note: ‘choice’ was declared here 643 | Uint1 choice; | ^~~~~~ In function ‘Cutoff_cutoffAsnRead’, inlined from ‘BlastParametersAsnRead’ at objblst3.c:1077:30: objblst3.c:1840:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1840 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1787:10: note: ‘choice’ was declared here 1787 | Uint1 choice; | ^~~~~~ In function ‘Cutoff2_cutoff2AsnRead’, inlined from ‘BlastParametersAsnRead’ at objblst3.c:1084:32: objblst3.c:1474:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 1474 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objblst3.c: In function ‘BlastParametersAsnRead’: objblst3.c:1421:10: note: ‘choice’ was declared here 1421 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" netblap3.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from netblap3.c:359: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ netblap3.c: In function ‘BlastNetBioseqFetchFunc’: netblap3.c:1835:23: warning: variable ‘omdp’ set but not used [-Wunused-but-set-variable] 1835 | OMUserDataPtr omdp; | ^~~~ netblap3.c: In function ‘MegaBlastSeqLocNetCore’: netblap3.c:2049:15: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 2049 | Uint2 entityID = 0; | ^~~~~~~~ In file included from ../include/netblap3.h:135, from netblap3.c:364: ../include/objblst3.h: At top level: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ netblap3.c:452:1: warning: ‘BlastResetOldHook’ defined but not used [-Wunused-function] 452 | BlastResetOldHook(void) | ^~~~~~~~~~~~~~~~~ netblap3.c:445:1: warning: ‘BlastGetErrorStatus’ defined but not used [-Wunused-function] 445 | BlastGetErrorStatus(void) | ^~~~~~~~~~~~~~~~~~~ netblap3.c:438:1: warning: ‘BlastSetErrorStatus’ defined but not used [-Wunused-function] 438 | BlastSetErrorStatus(Boolean status) | ^~~~~~~~~~~~~~~~~~~ netblap3.c:430:1: warning: ‘BlastSetErrorHook’ defined but not used [-Wunused-function] 430 | BlastSetErrorHook(void) | ^~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ netblap3.c: In function ‘BlastNetMatrixToBlastMatrix’: netblap3.c:1212:42: warning: ‘index2’ may be used uninitialized [-Wmaybe-uninitialized] 1212 | if (index1 != blast_matrix->rows || index2 != blast_matrix->columns) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ netblap3.c:1181:18: note: ‘index2’ was declared here 1181 | Int4 index1, index2; | ^~~~~~ netblap3.c: In function ‘TraditionalBlastReportEngine’: netblap3.c:2570:12: warning: ‘next_seqalign’ may be used uninitialized [-Wmaybe-uninitialized] 2570 | while (seqalign) { | ^~~~~~~~ netblap3.c:2452:39: note: ‘next_seqalign’ was declared here 2452 | SeqAlignPtr seqalign = NULL, sap, next_seqalign; | ^~~~~~~~~~~~~ rm -f libnetblast.a ar cru libnetblast.a objblst3.o netblap3.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libnetblast.a ../lib ranlib ../lib/libnetblast.a x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -DNLM_OBJ_INCL=\"mapmla.h\" objmla.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from objmla.c:1: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ objmla.c: In function ‘MlaRequestFree’: objmla.c:49:12: warning: variable ‘pnt’ set but not used [-Wunused-but-set-variable] 49 | Pointer pnt; | ^~~ objmla.c: In function ‘MlaRequestAsnRead’: objmla.c:96:12: warning: unused variable ‘isError’ [-Wunused-variable] 96 | Boolean isError = FALSE; | ^~~~~~~ objmla.c: In function ‘TitleMsgAsnRead’: objmla.c:447:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 447 | AsnReadFunc func; | ^~~~ objmla.c:446:12: warning: unused variable ‘isError’ [-Wunused-variable] 446 | Boolean isError = FALSE; | ^~~~~~~ objmla.c: In function ‘TitleMsgListAsnRead’: objmla.c:612:16: warning: variable ‘func’ set but not used [-Wunused-but-set-variable] 612 | AsnReadFunc func; | ^~~~ objmla.c: In function ‘MlaRequestAsnRead’: objmla.c:249:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 249 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla.c:95:10: note: ‘choice’ was declared here 95 | Uint1 choice; | ^~~~~~ objmla.c: In function ‘MlaBackAsnRead’: objmla.c:902:16: warning: ‘choice’ may be used uninitialized [-Wmaybe-uninitialized] 902 | anp->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ objmla.c:785:10: note: ‘choice’ was declared here 785 | Uint1 choice; | ^~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medarch.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/ni_types.h:84, from ../include/ncbinet.h:84, from medarch.c:122: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medarch.c:758:8: warning: ‘s_MedArchPubSetEntryGetUid’ defined but not used [-Wunused-function] 758 | /*FCN*/s_MedArchPubSetEntryGetUid ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:710:8: warning: ‘s_MedArchPubSetEntryGetPmId’ defined but not used [-Wunused-function] 710 | /*FCN*/s_MedArchPubSetEntryGetPmId ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c: In function ‘MedArchPubSetCreate’: medarch.c:1655:5: warning: ‘startAtp’ may be used uninitialized [-Wmaybe-uninitialized] 1655 | AsnWrite (aip, startAtp, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:1624:16: note: ‘startAtp’ was declared here 1624 | AsnTypePtr startAtp; | ^~~~~~~~ In file included from ../include/ni_types.h:85: ../include/asn.h:494:29: warning: ‘pubSetAtp’ may be used uninitialized [-Wmaybe-uninitialized] 494 | #define AsnStartStruct(x,y) AsnOpenStruct(x, y, NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c:1625:16: note: ‘pubSetAtp’ was declared here 1625 | AsnTypePtr pubSetAtp; | ^~~~~~~~~ In function ‘s_MedArchPubSetEntryGet’, inlined from ‘MedArchPubSetCreate’ at medarch.c:1669:19: medarch.c:683:9: warning: ‘pubSetEAtp’ may be used uninitialized [-Wmaybe-uninitialized] 683 | MedlineEntryAsnWrite (lastmep, aip, atp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ medarch.c: In function ‘MedArchPubSetCreate’: medarch.c:1626:16: note: ‘pubSetEAtp’ was declared here 1626 | AsnTypePtr pubSetEAtp; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" medutil.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/medutil.h:79, from medutil.c:58: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ medutil.c: In function ‘FixPubEquiv’: medutil.c:1134:16: warning: variable ‘got’ set but not used [-Wunused-but-set-variable] 1134 | Boolean got; | ^~~ rm -f libncbimla.a ar cru libncbimla.a objmla.o medarch.o medutil.o ar: `u' modifier ignored since `D' is the default (see `U') cp -p libncbimla.a ../lib ranlib ../lib/libncbimla.a x86_64-linux-gnu-gcc -o Psequin -I. -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c sequin7.c sequin8.c sequin9.c sequin10.c sequinx.c \ -lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb \ -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla \ -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lconnssl -lncbi \ -lm sequin1.c:46:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 46 | static char *date_of_compilation = __DATE__; | ^~~~~~~~ sequin1.c:47:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 47 | static char *time_of_compilation = __TIME__; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin1.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin1.c: In function ‘SQACT_GuessWhatIAm’: sequin1.c:4884:76: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 4884 | if ((Int4)(*cp) < 0 || (Int4)(*cp) >= 256 || ! isprint ((Int4)(*cp)) && ! isspace ((Int4)(*cp))) | ^ sequin1.c: In function ‘FinishAlignmentRead’: sequin1.c:5196:16: warning: variable ‘rsult’ set but not used [-Wunused-but-set-variable] 5196 | Boolean rsult; | ^~~~~ sequin1.c: In function ‘BioseqViewFormMenus’: sequin1.c:8357:18: warning: variable ‘mssgext’ set but not used [-Wunused-but-set-variable] 8357 | Int2 mssgext; | ^~~~~~~ sequin1.c: In function ‘DeleteSelectedFeatureOrDescriptor’: sequin1.c:8894:19: warning: variable ‘itemtype’ set but not used [-Wunused-but-set-variable] 8894 | Uint2 itemtype; | ^~~~~~~~ sequin1.c:8893:19: warning: variable ‘itemID’ set but not used [-Wunused-but-set-variable] 8893 | Uint4 itemID; | ^~~~~~ sequin1.c:8891:19: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 8891 | Uint2 entityID; | ^~~~~~~~ sequin1.c: In function ‘IsolationSourceOk’: sequin1.c:14815:11: warning: unused variable ‘specific_bad_fmt’ [-Wunused-variable] 14815 | CharPtr specific_bad_fmt = "isolation-source should have a value like seawater, soil, etc. '%s' is not a valid isolation-source."; | ^~~~~~~~~~~~~~~~ sequin1.c:14811:11: warning: unused variable ‘is_ambiguous’ [-Wunused-variable] 14811 | Boolean is_ambiguous = FALSE; | ^~~~~~~~~~~~ sequin1.c: In function ‘WizardTrackerFree’: sequin1.c:15809:20: warning: variable ‘sep_next’ set but not used [-Wunused-but-set-variable] 15809 | SeqEntryPtr sep, sep_next; | ^~~~~~~~ sequin1.c: In function ‘AddCodingRegionFromWizard’: sequin1.c:15881:33: warning: variable ‘nsep’ set but not used [-Wunused-but-set-variable] 15881 | SeqEntryPtr old, psep, nsep; | ^~~~ sequin1.c: In function ‘SetWizardTrackerBaseSrcQuals’: sequin1.c:16157:7: warning: enumeration value ‘eVirusClass_Unknown’ not handled in switch [-Wswitch] 16157 | switch (wiz->virus_class) { | ^~~~~~ sequin1.c:16204:7: warning: enumeration value ‘eCulturedKingdom_Unknown’ not handled in switch [-Wswitch] 16204 | switch (wiz->cultured_kingdom) { | ^~~~~~ sequin1.c:16140:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 16140 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c: In function ‘SetWizardTrackerExtraSrcQuals’: sequin1.c:16328:7: warning: enumeration value ‘eVirusClass_Unknown’ not handled in switch [-Wswitch] 16328 | switch (wiz->virus_class) { | ^~~~~~ sequin1.c:16354:7: warning: enumeration value ‘eCulturedKingdom_Unknown’ not handled in switch [-Wswitch] 16354 | switch (wiz->cultured_kingdom) { | ^~~~~~ sequin1.c:16321:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 16321 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c: In function ‘AddWizardFeatureCallback’: sequin1.c:16687:3: warning: enumeration value ‘eVirusFeat_None’ not handled in switch [-Wswitch] 16687 | switch (wiz->virus_feat) { | ^~~~~~ sequin1.c:16687:3: warning: enumeration value ‘eVirusFeat_CDS’ not handled in switch [-Wswitch] sequin1.c: In function ‘GetWGSNote’: sequin1.c:17010:11: warning: unused variable ‘fmt’ [-Wunused-variable] 17010 | CharPtr fmt = "[%s][WGS wizard]"; | ^~~ sequin1.c: In function ‘FinishWizardAndLaunchSequin’: sequin1.c:17052:5: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 17052 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c: In function ‘HaveUniqueCombinationOfQuals’: sequin1.c:17401:15: warning: variable ‘num_quals’ set but not used [-Wunused-but-set-variable] 17401 | Int4 num_quals; | ^~~~~~~~~ sequin1.c: In function ‘GetWizardQualifierProblems’: sequin1.c:20626:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 20626 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:20626:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘VirusQualsOk’: sequin1.c:20931:5: warning: enumeration value ‘eVirusClass_Unknown’ not handled in switch [-Wswitch] 20931 | switch (wiz->virus_class) { | ^~~~~~ sequin1.c: In function ‘CulturedSamplesOk’: sequin1.c:21036:5: warning: enumeration value ‘eCulturedKingdom_Unknown’ not handled in switch [-Wswitch] 21036 | switch (wiz->cultured_kingdom) { | ^~~~~~ sequin1.c: In function ‘WizardSrcQualsOk’: sequin1.c:21347:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 21347 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c: In function ‘CreateWizardSrcQualsForm’: sequin1.c:22401:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 22401 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:22401:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘CheckFeatureQualsUniqueness’: sequin1.c:22719:8: warning: variable ‘num_rows’ set but not used [-Wunused-but-set-variable] 22719 | Int4 num_rows, row_num; | ^~~~~~~~ sequin1.c: In function ‘WizardFeatureQualsOk’: sequin1.c:22810:11: warning: variable ‘num_features’ set but not used [-Wunused-but-set-variable] 22810 | Int4 num_features; | ^~~~~~~~~~~~ sequin1.c: In function ‘TabTableToMultiModTabTable’: sequin1.c:23178:16: warning: unused variable ‘bsp’ [-Wunused-variable] 23178 | BioseqPtr bsp = NULL; | ^~~ sequin1.c: In function ‘MultiModTableToTabTable’: sequin1.c:23257:21: warning: variable ‘fq’ set but not used [-Wunused-but-set-variable] 23257 | WizardFeatQualPtr fq; | ^~ sequin1.c: In function ‘ShowAllFeatureQualSequences’: sequin1.c:23777:15: warning: variable ‘show_all’ set but not used [-Wunused-but-set-variable] 23777 | Boolean show_all = TRUE; | ^~~~~~~~ sequin1.c: In function ‘TabTableLineFromFeature’: sequin1.c:24725:14: warning: unused variable ‘vals’ [-Wunused-variable] 24725 | ValNodePtr vals = NULL, q_vnp; | ^~~~ sequin1.c: In function ‘PregenerateFeatures’: sequin1.c:24775:22: warning: unused variable ‘problems’ [-Wunused-variable] 24775 | CharPtr PNTR problems = NULL; | ^~~~~~~~ sequin1.c: In function ‘SetQualForSequencesFromWizardList’: sequin1.c:26026:20: warning: unused variable ‘rval’ [-Wunused-variable] 26026 | Boolean rval = FALSE; | ^~~~ sequin1.c: In function ‘CollectWizardSetType’: sequin1.c:27538:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 27538 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:27538:3: warning: enumeration value ‘eWizardType_Microsatellite’ not handled in switch [-Wswitch] sequin1.c:27538:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘SequencingMethodToDialog’: sequin1.c:28361:27: warning: variable ‘info’ set but not used [-Wunused-but-set-variable] 28361 | SequencingMethodInfoPtr info; | ^~~~ sequin1.c: In function ‘CollectWizardSourceType’: sequin1.c:28943:5: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 28943 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:28943:5: warning: enumeration value ‘eWizardType_Microsatellite’ not handled in switch [-Wswitch] sequin1.c:28943:5: warning: enumeration value ‘eWizardType_DLoop’ not handled in switch [-Wswitch] sequin1.c:28943:5: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘HaveWizardSourceType’: sequin1.c:28976:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 28976 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:28976:3: warning: enumeration value ‘eWizardType_UnculturedSamples’ not handled in switch [-Wswitch] sequin1.c:28976:3: warning: enumeration value ‘eWizardType_Microsatellite’ not handled in switch [-Wswitch] sequin1.c:28976:3: warning: enumeration value ‘eWizardType_DLoop’ not handled in switch [-Wswitch] sequin1.c:28976:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘WizardSourceTypeForm’: sequin1.c:29038:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 29038 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:29038:3: warning: enumeration value ‘eWizardType_UnculturedSamples’ not handled in switch [-Wswitch] sequin1.c:29038:3: warning: enumeration value ‘eWizardType_Microsatellite’ not handled in switch [-Wswitch] sequin1.c:29038:3: warning: enumeration value ‘eWizardType_DLoop’ not handled in switch [-Wswitch] sequin1.c:29038:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘PopulateAAPopup’: sequin1.c:29856:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 29856 | Uint1 first; | ^~~~~ sequin1.c: In function ‘CountAmbiProc’: sequin1.c:31452:11: warning: unused variable ‘normal’ [-Wunused-variable] 31452 | Int4 normal = 0; | ^~~~~~ sequin1.c: In function ‘OkToTrimAmbiguous’: sequin1.c:31765:25: warning: variable ‘p2’ set but not used [-Wunused-but-set-variable] 31765 | GrouP p2 = NULL; | ^~ sequin1.c:31764:25: warning: variable ‘p1’ set but not used [-Wunused-but-set-variable] 31764 | PrompT p1, title = NULL, pr = NULL, pt = NULL; | ^~ sequin1.c: In function ‘WGSVectorScreen’: sequin1.c:32753:15: warning: unused variable ‘reasons’ [-Wunused-variable] 32753 | CharPtr reasons[] = {"Low Quality", "Vector Contamination", "Low Quality and Vector Contamination"}; | ^~~~~~~ sequin1.c: In function ‘WGSSequenceAdjustment’: sequin1.c:32916:31: warning: too many arguments for format [-Wformat-extra-args] 32916 | fprintf (lip->fp, "%s (too short)\n", a->id, "Low Quality"); | ^~~~~~~~~~~~~~~~~~ sequin1.c:32841:15: warning: unused variable ‘quit_problems’ [-Wunused-variable] 32841 | CharPtr quit_problems = NULL; | ^~~~~~~~~~~~~ sequin1.c:32839:15: warning: unused variable ‘max_dist’ [-Wunused-variable] 32839 | Int4 max_dist = 20; | ^~~~~~~~ sequin1.c: In function ‘SetFastaText’: sequin1.c:33423:15: warning: unused variable ‘intro’ [-Wunused-variable] 33423 | CharPtr intro = NULL; | ^~~~~ sequin1.c: In function ‘ImportSeqCallback’: sequin1.c:33567:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable] 33567 | Int4 x = 0; | ^ sequin1.c: In function ‘ExportWizardFASTA’: sequin1.c:33590:17: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 33590 | Boolean rval = FALSE; | ^~~~ sequin1.c: In function ‘ImportWizardFASTA’: sequin1.c:33624:15: warning: unused variable ‘changed’ [-Wunused-variable] 33624 | Boolean changed = FALSE; | ^~~~~~~ sequin1.c: In function ‘WizardFASTAFwd’: sequin1.c:33916:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 33916 | switch (frm->wiz->wizard_type) { | ^~~~~~ sequin1.c:33916:3: warning: enumeration value ‘eWizardType_UnculturedSamples’ not handled in switch [-Wswitch] sequin1.c:33916:3: warning: enumeration value ‘eWizardType_Viruses’ not handled in switch [-Wswitch] sequin1.c:33916:3: warning: enumeration value ‘eWizardType_CulturedSamples’ not handled in switch [-Wswitch] sequin1.c:33916:3: warning: enumeration value ‘eWizardType_IGS’ not handled in switch [-Wswitch] sequin1.c:33916:3: warning: enumeration value ‘eWizardType_Microsatellite’ not handled in switch [-Wswitch] sequin1.c:33916:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘WizardFASTABack’: sequin1.c:34038:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 34038 | switch (frm->wiz->wizard_type) { | ^~~~~~ sequin1.c:34038:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] sequin1.c: In function ‘WizardFastaHelpBtn’: sequin1.c:34089:3: warning: enumeration value ‘eWizardType_NormalDialogs’ not handled in switch [-Wswitch] 34089 | switch (wiz->wizard_type) { | ^~~~~~ sequin1.c:34089:3: warning: enumeration value ‘eWizardType_WGS’ not handled in switch [-Wswitch] In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from ../include/accutils.h:119, from sequin1.c:78: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from sequin1.c:84: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:135, from ../include/ingenwin.h:62, from sequin1.c:89: ../include/objblst3.h:180:35: warning: ‘Cutoff2_cutoff2Free’ declared ‘static’ but never defined [-Wunused-function] 180 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:181:35: warning: ‘Cutoff2_cutoff2AsnRead’ declared ‘static’ but never defined [-Wunused-function] 181 | static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:182:24: warning: ‘Cutoff2_cutoff2AsnWrite’ declared ‘static’ but never defined [-Wunused-function] 182 | static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:199:33: warning: ‘Cutoff_cutoffFree’ declared ‘static’ but never defined [-Wunused-function] 199 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objblst3.h:200:33: warning: ‘Cutoff_cutoffAsnRead’ declared ‘static’ but never defined [-Wunused-function] 200 | static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objblst3.h:201:24: warning: ‘Cutoff_cutoffAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 201 | static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sequin1.c:92: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ In file included from sequin1.c:117: ../include/objmime.h:145:29: warning: ‘Data_dataFree’ declared ‘static’ but never defined [-Wunused-function] 145 | static Data_dataPtr LIBCALL Data_dataFree PROTO ((Data_dataPtr )); | ^~~~~~~~~~~~~ ../include/objmime.h:146:29: warning: ‘Data_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 146 | static Data_dataPtr LIBCALL Data_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~ ../include/objmime.h:147:24: warning: ‘Data_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 147 | static Boolean LIBCALL Data_dataAsnWrite PROTO (( Data_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~ ../include/objmime.h:285:47: warning: ‘SeqAlignData_seq_align_dataFree’ declared ‘static’ but never defined [-Wunused-function] 285 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataFree PROTO ((SeqAlignData_seq_align_dataPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:286:47: warning: ‘SeqAlignData_seq_align_dataAsnRead’ declared ‘static’ but never defined [-Wunused-function] 286 | static SeqAlignData_seq_align_dataPtr LIBCALL SeqAlignData_seq_align_dataAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmime.h:287:24: warning: ‘SeqAlignData_seq_align_dataAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 287 | static Boolean LIBCALL SeqAlignData_seq_align_dataAsnWrite PROTO (( SeqAlignData_seq_align_dataPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin1.c: In function ‘LaunchedGoogleEarth’: sequin1.c:1504:11: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1504 | system (cmmd); | ^~~~~~~~~~~~~ sequin1.c: In function ‘Entrez2QueryProc’: sequin1.c:9715:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9715 | system ("entrez2 &"); | ^~~~~~~~~~~~~~~~~~~~ sequin1.c: At top level: sequin1.c:33848:16: warning: ‘IsSequencingMethodOkForTSA’ defined but not used [-Wunused-function] 33848 | static Boolean IsSequencingMethodOkForTSA (WizardTrackerPtr wiz) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ sequin1.c:33103:16: warning: ‘s_TSAFastaExample’ defined but not used [-Wunused-variable] 33103 | static CharPtr s_TSAFastaExample[] = { | ^~~~~~~~~~~~~~~~~ sequin1.c:32740:13: warning: ‘WGSVectorScreen’ defined but not used [-Wunused-function] 32740 | static void WGSVectorScreen (WizardTrackerPtr wiz, ValNodeBlockPtr block, Int4 min_length, Int4 max_dist) | ^~~~~~~~~~~~~~~ sequin1.c:32059:13: warning: ‘TrimTSABases’ defined but not used [-Wunused-function] 32059 | static void TrimTSABases (SeqEntryPtr PNTR sequences) | ^~~~~~~~~~~~ sequin1.c:29180:16: warning: ‘WizardAssemblyDescriptionForm’ defined but not used [-Wunused-function] 29180 | static Boolean WizardAssemblyDescriptionForm (WizardTrackerPtr wiz) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin1.c:29123:16: warning: ‘WizardCommentForm’ defined but not used [-Wunused-function] 29123 | static Boolean WizardCommentForm (WizardTrackerPtr wiz) | ^~~~~~~~~~~~~~~~~ sequin1.c:21709:16: warning: ‘s_TSASrcTblHelpMsgs’ defined but not used [-Wunused-variable] 21709 | static CharPtr s_TSASrcTblHelpMsgs[] = { | ^~~~~~~~~~~~~~~~~~~ sequin1.c:21228:16: warning: ‘TSASrcQualsOk’ defined but not used [-Wunused-function] 21228 | static Boolean TSASrcQualsOk (WizardTrackerPtr wiz) | ^~~~~~~~~~~~~ sequin1.c:20543:21: warning: ‘GetTSAQualifiersProblems’ defined but not used [-Wunused-function] 20543 | static CharPtr PNTR GetTSAQualifiersProblems (WizardTrackerPtr wiz) | ^~~~~~~~~~~~~~~~~~~~~~~~ sequin1.c:10760:13: warning: ‘ObjMgrReport’ defined but not used [-Wunused-function] 10760 | static void ObjMgrReport (IteM i) | ^~~~~~~~~~~~ In file included from ../include/netblap3.h:134: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ sequin1.c: In function ‘LaunchedGoogleEarth.constprop.0’: sequin1.c:1503:32: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 1503 | sprintf (cmmd, "open %s", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘LaunchedGoogleEarth.constprop.0’ at sequin1.c:1503:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 4101 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:133: sequin1.c: In function ‘BioseqViewFormMenus’: ../include/vibforms.h:522:25: warning: ‘mssgupd_idx’ may be used uninitialized [-Wmaybe-uninitialized] 522 | #define SetFormMenuItem Nlm_SetFormMenuItem sequin1.c:8356:27: note: ‘mssgupd_idx’ was declared here 8356 | Int2 mssgupd, mssgupd_idx; | ^~~~~~~~~~~ sequin1.c: In function ‘SubtoolDoneFuncEx’: sequin1.c:2000:35: warning: ‘bfp’ may be used uninitialized [-Wmaybe-uninitialized] 2000 | SeqMgrClearFeatureIndexes (bfp->input_entityID, NULL); | ~~~^~~~~~~~~~~~~~~~ sequin1.c:1938:16: note: ‘bfp’ was declared here 1938 | BaseFormPtr bfp; | ^~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin2.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin2.c: In function ‘ValidateModifierTableSequenceIDs’: sequin2.c:2847:16: warning: variable ‘deleted_rows’ set but not used [-Wunused-but-set-variable] 2847 | Int4 deleted_rows; | ^~~~~~~~~~~~ sequin2.c: In function ‘ImportFastaDialog’: sequin2.c:4587:17: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 4587 | SeqEntryPtr sep, new_sep_list, new_sep, test_sep; | ^~~ sequin2.c: In function ‘ExportOneRawSequence’: sequin2.c:4859:15: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] 4859 | Char buffer [EXPORT_PAGE_WIDTH + 1]; | ^~~~~~ sequin2.c: In function ‘ExportOneDeltaBioseq’: sequin2.c:4958:15: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] 4958 | Char buffer [EXPORT_PAGE_WIDTH + 1]; | ^~~~~~ sequin2.c: In function ‘FindBioseqWithValue’: sequin2.c:7807:17: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 7807 | BioseqPtr bsp = NULL; | ^~~ sequin2.c: In function ‘CollectNucleotideProteinAssociations’: sequin2.c:9174:73: warning: variable ‘p_msg’ set but not used [-Wunused-but-set-variable] 9174 | GrouP h, title_grp, all_gene_grp, all_prot_grp, k, c, p_msg; | ^~~~~ sequin2.c: In function ‘AddCDSToSeqEntry’: sequin2.c:9713:37: warning: unused variable ‘scope’ [-Wunused-variable] 9713 | SeqEntryPtr setsep = NULL, scope, old_scope; | ^~~~~ sequin2.c: In function ‘GetModNameStartFromEqLoc’: sequin2.c:11770:11: warning: variable ‘match_quote’ set but not used [-Wunused-but-set-variable] 11770 | Char match_quote; | ^~~~~~~~~~~ sequin2.c: In function ‘GetValueFromTitle’: sequin2.c:12334:15: warning: variable ‘is_nontext’ set but not used [-Wunused-but-set-variable] 12334 | Boolean is_nontext; | ^~~~~~~~~~ sequin2.c: In function ‘PrepareSourceAssistantTableData’: sequin2.c:13585:36: warning: variable ‘num_columns’ set but not used [-Wunused-but-set-variable] 13585 | Int4 column_width, num_columns = 0; | ^~~~~~~~~~~ sequin2.c: In function ‘SetOrganismText’: sequin2.c:13787:30: warning: variable ‘changed_val’ set but not used [-Wunused-but-set-variable] 13787 | Boolean changed_val = FALSE; | ^~~~~~~~~~~ sequin2.c: In function ‘ApplyRowListToIDAndTitleEdit’: sequin2.c:15438:32: warning: variable ‘next_org’ set but not used [-Wunused-but-set-variable] 15438 | CharPtr org_loc, org_end, next_org; | ^~~~~~~~ sequin2.c: In function ‘EditOrgModColumn’: sequin2.c:16349:26: warning: variable ‘row_list’ set but not used [-Wunused-but-set-variable] 16349 | ValNodePtr row_list = NULL; | ^~~~~~~~ sequin2.c: In function ‘ApplyOrgModColumn’: sequin2.c:17198:11: warning: variable ‘is_nontext’ set but not used [-Wunused-but-set-variable] 17198 | Boolean is_nontext; | ^~~~~~~~~~ sequin2.c: In function ‘PrepareSequenceAssistantTableData’: sequin2.c:18172:36: warning: variable ‘num_columns’ set but not used [-Wunused-but-set-variable] 18172 | Int4 column_width, num_columns = 0; | ^~~~~~~~~~~ sequin2.c: In function ‘UpdateIdAndTitleEditDialog’: sequin2.c:19591:50: warning: variable ‘has_space’ set but not used [-Wunused-but-set-variable] 19591 | Boolean has_dups, has_missing, has_bracket, has_space, has_unrec_mods = FALSE; | ^~~~~~~~~ sequin2.c: In function ‘SetIDAndTitleEditDialogErrorColumn’: sequin2.c:19741:74: warning: variable ‘has_space’ set but not used [-Wunused-but-set-variable] 19741 | Boolean has_dups, has_missing, has_bracket, has_unrec_mods = FALSE, has_space; | ^~~~~~~~~ sequin2.c: In function ‘GetDiffDlgCoord’: sequin2.c:20911:19: warning: variable ‘start_col’ set but not used [-Wunused-but-set-variable] 20911 | Int4 start_row, start_col; | ^~~~~~~~~ sequin2.c:20911:8: warning: variable ‘start_row’ set but not used [-Wunused-but-set-variable] 20911 | Int4 start_row, start_col; | ^~~~~~~~~ sequin2.c: In function ‘DownloadAndDisplay’: sequin2.c:26575:17: warning: variable ‘dbname’ set but not used [-Wunused-but-set-variable] 26575 | CharPtr dbname; | ^~~~~~ sequin2.c: In function ‘DownloadProc’: sequin2.c:26725:17: warning: variable ‘dbname’ set but not used [-Wunused-but-set-variable] 26725 | CharPtr dbname; | ^~~~~~ sequin2.c: In function ‘LoadSecondaryAccessionNumbersPlusHistFromFile’: sequin2.c:27908:17: warning: variable ‘need_seqid’ set but not used [-Wunused-but-set-variable] 27908 | Boolean need_seqid; | ^~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/aliparse.h:15, from sequin2.c:66: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sequin2.c:26330:13: warning: ‘GetRawBsps’ defined but not used [-Wunused-function] 26330 | static void GetRawBsps (BioseqPtr bsp, Pointer userdata) | ^~~~~~~~~~ sequin2.c:24919:1: warning: ‘SequenceAssistantValidateSegments’ defined but not used [-Wunused-function] 24919 | SequenceAssistantValidateSegments | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin2.c:10685:17: warning: ‘GetSeqIdFromSeqEntryPtr’ defined but not used [-Wunused-function] 10685 | static SeqIdPtr GetSeqIdFromSeqEntryPtr (SeqEntryPtr sep) | ^~~~~~~~~~~~~~~~~~~~~~~ sequin2.c:8106:20: warning: ‘FindSeqEntryWithTranscriptID’ defined but not used [-Wunused-function] 8106 | static SeqEntryPtr FindSeqEntryWithTranscriptID (SeqEntryPtr sep, CharPtr transcript_id) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin2.c:6863:13: warning: ‘ParseDeflineToBiop’ defined but not used [-Wunused-function] 6863 | static void ParseDeflineToBiop(CharPtr defline, BioSourcePtr biop) | ^~~~~~~~~~~~~~~~~~ sequin2.c:3922:1: warning: ‘ReadOneSegSet’ defined but not used [-Wunused-function] 3922 | ReadOneSegSet | ^~~~~~~~~~~~~ In file included from ../include/ncbi.h:62: In function ‘SummarizeModifiers’, inlined from ‘SeqEntryPtrToOrgDoc’ at sequin2.c:13286:5: ../include/ncbistr.h:331:25: warning: ‘row_status’ may be used uninitialized [-Wmaybe-uninitialized] 331 | #define StringLen Nlm_StringLen sequin2.c: In function ‘SeqEntryPtrToOrgDoc’: sequin2.c:12964:14: note: ‘row_status’ was declared here 12964 | CharPtr row_status; | ^~~~~~~~~~ sequin2.c: In function ‘InsertMostUsedFeatureValNodes’: sequin2.c:28172:6: warning: ‘new_item’ may be used uninitialized [-Wmaybe-uninitialized] 28172 | if (new_item != NULL) | ^ sequin2.c:28155:24: note: ‘new_item’ was declared here 28155 | ValNodePtr new_list, new_item, old_item; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin3.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin3.c: In function ‘FarToNearProc’: sequin3.c:542:12: warning: variable ‘olddelta’ set but not used [-Wunused-but-set-variable] 542 | Pointer olddelta; | ^~~~~~~~ sequin3.c: In function ‘FixLocus’: sequin3.c:1019:22: warning: variable ‘embl_code’ set but not used [-Wunused-but-set-variable] 1019 | CharPtr ptr, embl_code; | ^~~~~~~~~ sequin3.c: In function ‘RemoveGeneXrefsOnBioseqs’: sequin3.c:2237:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 2237 | Int2 count; | ^~~~~ sequin3.c: In function ‘MakeCDS’: sequin3.c:7040:27: warning: variable ‘nsep’ set but not used [-Wunused-but-set-variable] 7040 | SeqEntryPtr psep, nsep, old, topsep; | ^~~~ sequin3.c: In function ‘ConvertOneCDSToMiscFeat’: sequin3.c:9217:26: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 9217 | || must_have_stops && !HasInternalStops (sfp)) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ sequin3.c: In function ‘SuppressGenesOnFeatures’: sequin3.c:11108:20: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 11108 | ButtoN b; | ^ sequin3.c: In function ‘CheckForExistingMolInfo’: sequin3.c:12443:17: warning: variable ‘bsp’ set but not used [-Wunused-but-set-variable] 12443 | BioseqPtr bsp; | ^~~ sequin3.c: In function ‘RemoveNthCDS’: sequin3.c:19694:17: warning: variable ‘segCount’ set but not used [-Wunused-but-set-variable] 19694 | Int4 segCount; | ^~~~~~~~ sequin3.c: In function ‘InstantiateGapFeatCallback’: sequin3.c:20956:15: warning: variable ‘fuzz’ set but not used [-Wunused-but-set-variable] 20956 | IntFuzzPtr fuzz; | ^~~~ sequin3.c: In function ‘GlobalDisableStrainForwarding’: sequin3.c:23530:14: warning: unused variable ‘lip’ [-Wunused-variable] 23530 | LogInfoPtr lip; | ^~~ In file included from ../include/tax3api.h:51, from sequin3.c:71: ../include/objtax3.h: At top level: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sequin3.c:73: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sequin3.c:23279:16: warning: ‘SummarizeFieldDiff’ defined but not used [-Wunused-function] 23279 | static CharPtr SummarizeFieldDiff (FieldDiffPtr diff) | ^~~~~~~~~~~~~~~~~~ sequin3.c:22333:13: warning: ‘TestSegregateByList’ defined but not used [-Wunused-function] 22333 | static void TestSegregateByList (IteM i) | ^~~~~~~~~~~~~~~~~~~ sequin3.c:21921:13: warning: ‘LabelFungalRNAs’ defined but not used [-Wunused-function] 21921 | static void LabelFungalRNAs (IteM i) | ^~~~~~~~~~~~~~~ sequin3.c:21906:13: warning: ‘WriteAccessionsCallback’ defined but not used [-Wunused-function] 21906 | static void WriteAccessionsCallback (BioseqPtr bsp, Pointer data) | ^~~~~~~~~~~~~~~~~~~~~~~ sequin3.c:21398:13: warning: ‘ModernizeGenes’ defined but not used [-Wunused-function] 21398 | static void ModernizeGenes (IteM i) | ^~~~~~~~~~~~~~ sequin3.c:21371:13: warning: ‘ModernizeRNAs’ defined but not used [-Wunused-function] 21371 | static void ModernizeRNAs (IteM i) | ^~~~~~~~~~~~~ sequin3.c:21344:13: warning: ‘ModernizePCRs’ defined but not used [-Wunused-function] 21344 | static void ModernizePCRs (IteM i) | ^~~~~~~~~~~~~ sequin3.c:21234:13: warning: ‘TestTax3B’ defined but not used [-Wunused-function] 21234 | static void TestTax3B (IteM i) | ^~~~~~~~~ sequin3.c:21228:13: warning: ‘TestTax3A’ defined but not used [-Wunused-function] 21228 | static void TestTax3A (IteM i) | ^~~~~~~~~ sequin3.c:21095:13: warning: ‘NewAligmentViewer’ defined but not used [-Wunused-function] 21095 | static void NewAligmentViewer (IteM i) | ^~~~~~~~~~~~~~~~~ sequin3.c:21064:13: warning: ‘AddAllDbxrefsMenuItem’ defined but not used [-Wunused-function] 21064 | static void AddAllDbxrefsMenuItem (IteM i) | ^~~~~~~~~~~~~~~~~~~~~ sequin3.c:17134:16: warning: ‘s_NextQualifies’ defined but not used [-Wunused-function] 17134 | static Boolean s_NextQualifies (SeqFeatPtr sfp, | ^~~~~~~~~~~~~~~ sequin3.c:14836:25: warning: ‘FsaStreamProc’ defined but not used [-Wunused-function] 14836 | static void LIBCALLBACK FsaStreamProc ( | ^~~~~~~~~~~~~ sequin3.c:13705:13: warning: ‘PrepareTaxListProc’ defined but not used [-Wunused-function] 13705 | static void PrepareTaxListProc (IteM i) | ^~~~~~~~~~~~~~~~~~ sequin3.c:11155:19: warning: ‘CopyGeneRef’ defined but not used [-Wunused-function] 11155 | static GeneRefPtr CopyGeneRef (GeneRefPtr srcGrp) | ^~~~~~~~~~~ sequin3.c:5388:13: warning: ‘InstantiateAssemblyGapFeats’ defined but not used [-Wunused-function] 5388 | static void InstantiateAssemblyGapFeats (BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin3.c:5310:16: warning: ‘ValidateAssemblyGapFeat’ defined but not used [-Wunused-function] 5310 | static Boolean ValidateAssemblyGapFeat (SeqFeatPtr sfp, BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~~~~ sequin3.c:5268:13: warning: ‘linkEvValues’ defined but not used [-Wunused-variable] 5268 | static Int4 linkEvValues [] = { | ^~~~~~~~~~~~ sequin3.c:5253:16: warning: ‘linkEvStrings’ defined but not used [-Wunused-variable] 5253 | static CharPtr linkEvStrings [] = { | ^~~~~~~~~~~~~ sequin3.c:5237:13: warning: ‘gapTypeValues’ defined but not used [-Wunused-variable] 5237 | static Int4 gapTypeValues [] = { | ^~~~~~~~~~~~~ sequin3.c:5220:16: warning: ‘gapTypeStrings’ defined but not used [-Wunused-variable] 5220 | static CharPtr gapTypeStrings [] = { | ^~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: sequin3.c: In function ‘AddMissingFieldsFromBioSample’: ../include/vibdefns.h:318:18: warning: ‘summ’ may be used uninitialized [-Wmaybe-uninitialized] 318 | #define CheckBox Nlm_CheckBox sequin3.c:23379:14: note: ‘summ’ was declared here 23379 | CharPtr summ, prev = NULL; | ^~~~ sequin3.c: In function ‘MakeBioSampleUpdateTable’: sequin3.c:23057:46: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 23057 | || StringCmp (prev_biosample_id, diff->biosample_id) != 0) { | ~~~~^~~~~~~~~~~~~~ sequin3.c:22980:30: note: ‘diff’ was declared here 22980 | FieldDiffPtr sdiff, ddiff, diff; | ^~~~ sequin3.c: In function ‘CompareWithBioSampleEx’: sequin3.c:23175:46: warning: ‘diff’ may be used uninitialized [-Wmaybe-uninitialized] 23175 | || StringCmp (prev_biosample_id, diff->biosample_id) != 0) { | ~~~~^~~~~~~~~~~~~~ sequin3.c:23104:30: note: ‘diff’ was declared here 23104 | FieldDiffPtr sdiff, ddiff, diff; | ^~~~ sequin3.c: In function ‘DoFixupSegSet’: sequin3.c:1126:18: warning: ‘%s’ directive writing up to 127 bytes into a region of size 32 [-Wformat-overflow=] 1126 | sprintf (str, "%sS%s", prefix, digs); | ^~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DoFixPartLocus’ at sequin3.c:1126:3, inlined from ‘DoFixupSegSet’ at sequin3.c:1210:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 2 and 144 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin3.c: In function ‘DoFixupSegSet’: sequin3.c:1226:22: warning: ‘%s’ directive writing up to 127 bytes into a region of size 28 [-Wformat-overflow=] 1226 | sprintf (str, "SEG_%sS", prefix); | ^~ In function ‘sprintf’, inlined from ‘DoFixupSegSet’ at sequin3.c:1226:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 133 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin4.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin4.c: In function ‘SplitSegmentedFeatsOnOneSet’: sequin4.c:1621:20: warning: variable ‘set_sep’ set but not used [-Wunused-but-set-variable] 1621 | SeqEntryPtr sep, set_sep; | ^~~~~~~ sequin4.c: In function ‘RemoveOneSegSet’: sequin4.c:2295:30: warning: variable ‘seg_bssp’ set but not used [-Wunused-but-set-variable] 2295 | BioseqSetPtr seg_nuc_prot, seg_bssp; | ^~~~~~~~ sequin4.c: In function ‘NewUpdateSeqAlign’: sequin4.c:3142:20: warning: variable ‘bssp’ set but not used [-Wunused-but-set-variable] 3142 | BioseqSetPtr bssp; | ^~~~ sequin4.c: In function ‘LaunchOrfViewer’: sequin4.c:7256:16: warning: variable ‘qu’ set but not used [-Wunused-but-set-variable] 7256 | ButtoN qu, b1; | ^~ sequin4.c: In function ‘MRnaFromCdsCallback’: sequin4.c:7624:17: warning: variable ‘entityID’ set but not used [-Wunused-but-set-variable] 7624 | Uint2 entityID; | ^~~~~~~~ sequin4.c: In function ‘FindNonACGT’: sequin4.c:8773:21: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 8773 | Int4 len; | ^~~ sequin4.c: In function ‘GetPubStatus’: sequin4.c:10801:14: warning: variable ‘csp’ set but not used [-Wunused-but-set-variable] 10801 | CitSubPtr csp; | ^~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from sequin4.c:72: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sequin4.c:14157:13: warning: ‘CleanupTruncateByProtAlignForm’ defined but not used [-Wunused-function] 14157 | static void CleanupTruncateByProtAlignForm (GraphiC g, VoidPtr data) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin4.c:13699:25: warning: ‘FeatToDeltaSeq’ defined but not used [-Wunused-function] 13699 | static Int2 LIBCALLBACK FeatToDeltaSeq (Pointer data) | ^~~~~~~~~~~~~~ sequin4.c:13659:16: warning: ‘ListRawSequencesInAlignments’ defined but not used [-Wunused-function] 13659 | static Boolean ListRawSequencesInAlignments (GatherContextPtr gcp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin4.c:9889:13: warning: ‘PubConstraintClearText’ defined but not used [-Wunused-function] 9889 | static void PubConstraintClearText (PubConstraintPtr pcp) | ^~~~~~~~~~~~~~~~~~~~~~ sequin4.c:8853:18: warning: ‘RevStringUpper’ defined but not used [-Wunused-function] 8853 | static void NEAR RevStringUpper (CharPtr str) | ^~~~~~~~~~~~~~ sequin4.c:8504:13: warning: ‘MakeGeneXref’ defined but not used [-Wunused-function] 8504 | static void MakeGeneXref (SeqFeatPtr sfpr, SeqFeatPtr sfpg) | ^~~~~~~~~~~~ sequin4.c:6747:13: warning: ‘AddOrfListToDoc’ defined but not used [-Wunused-function] 6747 | static void AddOrfListToDoc(DoC doc, ValNodePtr list) | ^~~~~~~~~~~~~~~ sequin4.c:3264:17: warning: ‘CorrectIDsForSeqHistAlign’ defined but not used [-Wunused-function] 3264 | static SeqIdPtr CorrectIDsForSeqHistAlign (TAlignmentFilePtr afp, SeqEntryPtr sep) | ^~~~~~~~~~~~~~~~~~~~~~~~~ sequin4.c:3237:18: warning: ‘FindBioseqForSeqHist’ defined but not used [-Wunused-function] 3237 | static BioseqPtr FindBioseqForSeqHist (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~ In file included from ../include/asn2ff6.h:142, from ../include/asn2ffp.h:50, from sequin4.c:55: ../include/asnprt.h:61:21: warning: ‘amp’ defined but not used [-Wunused-variable] 61 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnprt.h:60:19: warning: ‘at’ defined but not used [-Wunused-variable] 60 | static AsnTypePtr at = atx; | ^~ ../include/asnprt.h:59:23: warning: ‘avn’ defined but not used [-Wunused-variable] 59 | static AsnValxNodePtr avn = NULL; | ^~~ ../include/asnprt.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnprt.h60"; | ^~~~~~~~~~~ In function ‘MakeExonsAndIntronsFromFeature’, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5967:3, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5952:13: sequin4.c:5908:16: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 5908 | intron = AddIntronForInterval (start, -1, last, strand, bsp, fuzz_from, fuzz_to, part_number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin4.c: In function ‘MakeExonsFromFeatureIntervalsVisitFunc’: sequin4.c:5799:15: note: ‘start’ was declared here 5799 | Int4 start; | ^~~~~ In function ‘MakeExonsAndIntronsFromFeature’, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5967:3, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5952:13: sequin4.c:5910:16: warning: ‘stop’ may be used uninitialized [-Wmaybe-uninitialized] 5910 | intron = AddIntronForInterval (bsp->length, stop, last, strand, bsp, fuzz_from, fuzz_to, part_number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin4.c: In function ‘MakeExonsFromFeatureIntervalsVisitFunc’: sequin4.c:5800:15: note: ‘stop’ was declared here 5800 | Int4 stop; | ^~~~ In function ‘MakeExonsAndIntronsFromFeature’, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5967:3, inlined from ‘MakeExonsFromFeatureIntervalsVisitFunc’ at sequin4.c:5952:13: sequin4.c:5907:8: warning: ‘strand’ may be used uninitialized [-Wmaybe-uninitialized] 5907 | if (strand == Seq_strand_minus) { | ^ sequin4.c: In function ‘MakeExonsFromFeatureIntervalsVisitFunc’: sequin4.c:5801:15: note: ‘strand’ was declared here 5801 | Uint1 strand; | ^~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin5.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin5.c: In function ‘GeneExtendFunc’: sequin5.c:247:18: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 247 | GeneRefPtr grp; | ^~~ sequin5.c: In function ‘RemoveGBIDsProc’: sequin5.c:1372:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 1372 | SeqIdPtr nextid, sip; | ^~~~~~ sequin5.c: In function ‘RemoveGBProtIDsProc’: sequin5.c:1422:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 1422 | SeqIdPtr nextid, sip; | ^~~~~~ sequin5.c: In function ‘RemoveGIProc’: sequin5.c:1473:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 1473 | SeqIdPtr nextid, sip; | ^~~~~~ sequin5.c: In function ‘SetmRNAFieldString’: sequin5.c:6548:17: warning: variable ‘field_choice’ set but not used [-Wunused-but-set-variable] 6548 | Int4 field_choice; | ^~~~~~~~~~~~ sequin5.c: In function ‘GetCDSGeneProtField’: sequin5.c:7233:11: warning: variable ‘field_choice’ set but not used [-Wunused-but-set-variable] 7233 | Int4 field_choice; | ^~~~~~~~~~~~ sequin5.c: In function ‘GetRNAFieldString’: sequin5.c:7628:21: warning: variable ‘field_choice’ set but not used [-Wunused-but-set-variable] 7628 | Int4 field_choice; | ^~~~~~~~~~~~ sequin5.c:7622:14: warning: variable ‘rrp’ set but not used [-Wunused-but-set-variable] 7622 | RnaRefPtr rrp; | ^~~ sequin5.c: In function ‘SetRNAFieldString’: sequin5.c:7863:17: warning: variable ‘rrp’ set but not used [-Wunused-but-set-variable] 7863 | RnaRefPtr rrp; | ^~~ sequin5.c: In function ‘BioseqConstrainedFeaturesCallback’: sequin5.c:11293:21: warning: variable ‘cop’ set but not used [-Wunused-but-set-variable] 11293 | ConstraintOpPtr cop; | ^~~ sequin5.c: In function ‘SampleDialogCopy’: sequin5.c:13545:53: warning: variable ‘last_col’ set but not used [-Wunused-but-set-variable] 13545 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~ sequin5.c:13545:42: warning: variable ‘first_col’ set but not used [-Wunused-but-set-variable] 13545 | Int2 start_col = 0, end_col = 0, first_col, last_col; | ^~~~~~~~~ sequin5.c: In function ‘TestFeatureFieldChoice’: sequin5.c:14066:31: warning: variable ‘dlg’ set but not used [-Wunused-but-set-variable] 14066 | FeatureFieldChoiceDialogPtr dlg; | ^~~ sequin5.c: In function ‘CreateClickableListForSourceFeats’: sequin5.c:14854:27: warning: variable ‘insertion_seq_txt’ set but not used [-Wunused-but-set-variable] 14854 | CharPtr transposon_txt, insertion_seq_txt, note_txt; | ^~~~~~~~~~~~~~~~~ sequin5.c:14854:11: warning: variable ‘transposon_txt’ set but not used [-Wunused-but-set-variable] 14854 | CharPtr transposon_txt, insertion_seq_txt, note_txt; | ^~~~~~~~~~~~~~ sequin5.c: In function ‘CDSToMiscFeatConvertFunc’: sequin5.c:15014:24: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 15014 | Boolean rval = FALSE; | ^~~~ sequin5.c: In function ‘GetRegionOpts’: sequin5.c:15152:25: warning: unused variable ‘rval’ [-Wunused-variable] 15152 | Boolean rval = FALSE; | ^~~~ sequin5.c: In function ‘NewConvertFeaturesByList’: sequin5.c:15322:14: warning: unused variable ‘only_pseudo’ [-Wunused-variable] 15322 | Boolean only_pseudo = FALSE; | ^~~~~~~~~~~ sequin5.c: In function ‘FeatureRemoveOrConvertAction’: sequin5.c:15588:25: warning: variable ‘sfp’ set but not used [-Wunused-but-set-variable] 15588 | SeqFeatPtr sfp; | ^~~ sequin5.c: In function ‘CDSGeneProtAECRDialog’: sequin5.c:18564:25: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 18564 | SeqEntryPtr sep; | ^~~ sequin5.c: In function ‘CDSGeneProtConvert’: sequin5.c:18931:18: warning: unused variable ‘str_dst’ [-Wunused-variable] 18931 | CharPtr str_dst = NULL; | ^~~~~~~ sequin5.c: In function ‘CDSGeneProtParse’: sequin5.c:19141:18: warning: variable ‘avd’ set but not used [-Wunused-but-set-variable] 19141 | ApplyValueData avd; | ^~~ sequin5.c: In function ‘RNAQualListDialog’: sequin5.c:21603:22: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 21603 | SeqEntryPtr sep; | ^~~ sequin5.c: In function ‘GetRNAFeatureList’: sequin5.c:21792:14: warning: variable ‘matches’ set but not used [-Wunused-but-set-variable] 21792 | Boolean matches; | ^~~~~~~ sequin5.c: In function ‘RNAQualConvertSwapParseList’: sequin5.c:21924:26: warning: variable ‘avd’ set but not used [-Wunused-but-set-variable] 21924 | ApplyValueData avd; | ^~~ sequin5.c: In function ‘RNAQualEditRemoveList’: sequin5.c:22021:20: warning: unused variable ‘rval’ [-Wunused-variable] 22021 | Boolean rval = TRUE; | ^~~~ sequin5.c: In function ‘GetGBQualSampleName’: sequin5.c:22729:14: warning: variable ‘num_feature_choices’ set but not used [-Wunused-but-set-variable] 22729 | Int4 num_feature_choices; | ^~~~~~~~~~~~~~~~~~~ sequin5.c: In function ‘ConvertGeneLocusTagToOldLocusTagCallback’: sequin5.c:22964:28: warning: variable ‘mp’ set but not used [-Wunused-but-set-variable] 22964 | LocusTagToOldLocusTagPtr mp; | ^~ sequin5.c: In function ‘NewSegregateBioseqSet’: sequin5.c:26425:22: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 26425 | PrompT p, p2; | ^ sequin5.c: In function ‘CompareBulkRows’: sequin5.c:27910:8: warning: variable ‘col’ set but not used [-Wunused-but-set-variable] 27910 | Int4 col; | ^~~ sequin5.c: In function ‘ResortBulkEditorRows’: sequin5.c:28177:20: warning: unused variable ‘matches’ [-Wunused-variable] 28177 | ValNodePtr matches = NULL, vnp; | ^~~~~~~ sequin5.c:28174:26: warning: unused variable ‘last_inserted’ [-Wunused-variable] 28174 | Int4 row_num, sub_num, last_inserted = 0, comp, col; | ^~~~~~~~~~~~~ sequin5.c: In function ‘UpdateBulkEdDisplay’: sequin5.c:29258:17: warning: unused variable ‘text_len’ [-Wunused-variable] 29258 | Int4 i, text_len = 0, sub_num; | ^~~~~~~~ sequin5.c: In function ‘AddColumnToRowList’: sequin5.c:29993:11: warning: unused variable ‘m’ [-Wunused-variable] 29993 | Int4 i, m = 0, f = 0, num_columns = 1; | ^ sequin5.c: In function ‘ApplyBulkEditCommon’: sequin5.c:30418:23: warning: unused variable ‘need_redraw’ [-Wunused-variable] 30418 | Boolean need_redraw = FALSE; | ^~~~~~~~~~~ sequin5.c: In function ‘CopyAllFieldsFromList’: sequin5.c:30773:8: warning: unused variable ‘num_full’ [-Wunused-variable] 30773 | Int4 num_full = 0; | ^~~~~~~~ sequin5.c: In function ‘BulkEditorObjectList’: sequin5.c:32741:22: warning: unused variable ‘subtype’ [-Wunused-variable] 32741 | Uint1 subtype = 0; | ^~~~~~~ sequin5.c: In function ‘BulkEditorBaseForm’: sequin5.c:32798:22: warning: variable ‘field_list’ set but not used [-Wunused-but-set-variable] 32798 | BulkEdFieldPtr field_list = NULL; | ^~~~~~~~~~ sequin5.c: In function ‘GetSpecificHostCorrectionCategory’: sequin5.c:33567:22: warning: unused variable ‘fmt’ [-Wunused-variable] 33567 | CharPtr fmt = "Unable to suggest correction for '%s'"; | ^~~ In file included from ../include/tax3api.h:51, from sequin5.c:78: ../include/objtax3.h: At top level: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sequin5.c:32057:13: warning: ‘BulkSrcSetOrgModDescTF’ defined but not used [-Wunused-function] 32057 | static void BulkSrcSetOrgModDescTF (Pointer target, Pointer data, Uint2 mod_type) | ^~~~~~~~~~~~~~~~~~~~~~ sequin5.c:32036:16: warning: ‘BulkSrcGetOrgModDescTF’ defined but not used [-Wunused-function] 32036 | static Pointer BulkSrcGetOrgModDescTF (Uint1 data_choice, Pointer data, Uint2 mod_type) | ^~~~~~~~~~~~~~~~~~~~~~ sequin5.c:31734:23: warning: ‘GetBulkEditorFieldListForFeature’ defined but not used [-Wunused-function] 31734 | static BulkEdFieldPtr GetBulkEditorFieldListForFeature (SeqFeatPtr sfp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin5.c:31268:16: warning: ‘BulkGetPseudo’ defined but not used [-Wunused-function] 31268 | static Pointer BulkGetPseudo (Pointer data) | ^~~~~~~~~~~~~ sequin5.c:31257:13: warning: ‘BulkSetPseudo’ defined but not used [-Wunused-function] 31257 | static void BulkSetPseudo (Pointer target, Pointer val) | ^~~~~~~~~~~~~ sequin5.c:31246:16: warning: ‘BulkReleaseTrueFalse’ defined but not used [-Wunused-function] 31246 | static Pointer BulkReleaseTrueFalse (Pointer p) | ^~~~~~~~~~~~~~~~~~~~ sequin5.c:31080:15: warning: ‘BulkNucLocationDialog’ defined but not used [-Wunused-function] 31080 | static DialoG BulkNucLocationDialog (GrouP g, CharPtr name, SeqEntryPtr sep) | ^~~~~~~~~~~~~~~~~~~~~ sequin5.c:28858:28: warning: ‘TwoFieldBulkEditNew’ defined but not used [-Wunused-function] 28858 | static TwoFieldBulkEditPtr TwoFieldBulkEditNew (void) | ^~~~~~~~~~~~~~~~~~~ sequin5.c:28605:28: warning: ‘OneFieldBulkEditNew’ defined but not used [-Wunused-function] 28605 | static OneFieldBulkEditPtr OneFieldBulkEditNew (void) | ^~~~~~~~~~~~~~~~~~~ sequin5.c:28101:13: warning: ‘FlatCopyRows’ defined but not used [-Wunused-function] 28101 | static Int4 FlatCopyRows (BulkEditorRowPtr new_rows, BulkEditorRowPtr orig_rows, BulkEdFieldPtr field_list) | ^~~~~~~~~~~~ sequin5.c:27569:13: warning: ‘FreeBulkEditorValuesList’ defined but not used [-Wunused-function] 27569 | static void FreeBulkEditorValuesList (ValNodePtr PNTR values_list, Int4 num_rows, BulkEdFieldPtr field_list) | ^~~~~~~~~~~~~~~~~~~~~~~~ sequin5.c:21287:23: warning: ‘AECRRNAQualFree’ defined but not used [-Wunused-function] 21287 | static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap) | ^~~~~~~~~~~~~~~ sequin5.c:12796:25: warning: ‘ParseFieldSrcFree’ defined but not used [-Wunused-function] 12796 | static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp) | ^~~~~~~~~~~~~~~~~ sequin5.c:438:13: warning: ‘ProcessOligo’ defined but not used [-Wunused-function] 438 | static void ProcessOligo (SeqEntryPtr sep, CharPtr sequence, CharPtr title) | ^~~~~~~~~~~~ sequin5.c:171:16: warning: ‘GetSequenceString’ defined but not used [-Wunused-function] 171 | static CharPtr GetSequenceString (BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~ sequin5.c:88:13: warning: ‘CommonLaunchBioseqViewer’ defined but not used [-Wunused-function] 88 | static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor) | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/netblap3.h:134, from sequin5.c:53: ../include/blstspc.h:229:21: warning: ‘amp’ defined but not used [-Wunused-variable] 229 | static AsnModulePtr amp = ampx; | ^~~ ../include/blstspc.h:228:19: warning: ‘at’ defined but not used [-Wunused-variable] 228 | static AsnTypePtr at = atx; | ^~ ../include/blstspc.h:227:23: warning: ‘avn’ defined but not used [-Wunused-variable] 227 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/blstspc.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "blstspc.h23"; | ^~~~~~~~~~~ sequin5.c: In function ‘ConvertDescriptorFieldCallback’: sequin5.c:5784:18: warning: ‘dst_text’ may be used uninitialized [-Wmaybe-uninitialized] 5784 | avd.new_text = dst_text; | ~~~~~~~~~~~~~^~~~~~~~~~ sequin5.c:5709:19: note: ‘dst_text’ was declared here 5709 | CharPtr dst_text; | ^~~~~~~~ sequin5.c: In function ‘EditLocusActnProc’: sequin5.c:605:28: warning: ‘%s’ directive writing up to 15 bytes into a region of size between 13 and 76 [-Wformat-overflow=] 605 | sprintf (tmp, "%s%s", str, num); | ^~ ~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘EditLocusActnProc’ at sequin5.c:605:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 1 and 79 bytes into a destination of size 76 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: sequin5.c: In function ‘ApplyEditConvertRemoveCombo.constprop.0’: ../include/vibdefns.h:535:22: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 535 | #define AlignObjects Nlm_AlignObjects sequin5.c:17563:42: note: ‘m’ was declared here 17563 | GrouP h, g1, k, n, m; | ^ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin6.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin6.c: In function ‘RemoveOrgModText’: sequin6.c:3069:35: warning: variable ‘next_mod’ set but not used [-Wunused-but-set-variable] 3069 | OrgModPtr mod, prev_mod = NULL, next_mod; | ^~~~~~~~ sequin6.c: In function ‘TrimCodingRegionsFoNsCallback’: sequin6.c:4576:31: warning: unused variable ‘cut’ [-Wunused-variable] 4576 | SeqLocPtr slp, sp, cut; | ^~~ sequin6.c:4576:22: warning: unused variable ‘slp’ [-Wunused-variable] 4576 | SeqLocPtr slp, sp, cut; | ^~~ sequin6.c: In function ‘GapLocationsFromNs’: sequin6.c:4750:15: warning: variable ‘seq_ext’ set but not used [-Wunused-but-set-variable] 4750 | ValNodePtr seq_ext; | ^~~~~~~ sequin6.c:4749:15: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 4749 | Int4 len; | ^~~ sequin6.c: In function ‘ApplyBioFeatToList’: sequin6.c:6400:23: warning: variable ‘oldscope’ set but not used [-Wunused-but-set-variable] 6400 | SeqEntryPtr nsep, oldscope; | ^~~~~~~~ sequin6.c: In function ‘ParseHelpFile’: sequin6.c:11491:17: warning: the comparison will always evaluate as ‘false’ for the address of ‘file’ will never be NULL [-Waddress] 11491 | if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; | ^~ sequin6.c:11404:18: note: ‘file’ declared here 11404 | Char file [PATH_MAX]; | ^~~~ sequin6.c: In function ‘PopulateHelpForm’: sequin6.c:11766:17: warning: the comparison will always evaluate as ‘false’ for the address of ‘file’ will never be NULL [-Waddress] 11766 | if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; | ^~ sequin6.c:11404:18: note: ‘file’ declared here 11404 | Char file [PATH_MAX]; | ^~~~ sequin6.c: In function ‘RNAWordsFromString’: sequin6.c:13298:32: warning: variable ‘last_pos’ set but not used [-Wunused-but-set-variable] 13298 | CharPtr last_hit = NULL, last_pos = NULL; | ^~~~~~~~ sequin6.c:13298:15: warning: variable ‘last_hit’ set but not used [-Wunused-but-set-variable] 13298 | CharPtr last_hit = NULL, last_pos = NULL; | ^~~~~~~~ sequin6.c: In function ‘FeatureEditorActionGroup’: sequin6.c:14382:15: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 14382 | SeqEntryPtr sep; | ^~~ sequin6.c: In function ‘DoPartialFeatureProc’: sequin6.c:14631:16: warning: variable ‘dash_at_end’ set but not used [-Wunused-but-set-variable] 14631 | Boolean dash_at_end = FALSE; | ^~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from sequin6.c:60: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ sequin6.c:9215:13: warning: ‘LongestMatch’ defined but not used [-Wunused-function] 9215 | static Int2 LongestMatch ( | ^~~~~~~~~~~~ sequin6.c:9121:13: warning: ‘RevcompString’ defined but not used [-Wunused-function] 9121 | static void RevcompString ( | ^~~~~~~~~~~~~ sequin6.c:9093:13: warning: ‘ExtractString’ defined but not used [-Wunused-function] 9093 | static void ExtractString ( | ^~~~~~~~~~~~~ sequin6.c:5459:1: warning: ‘RemoveTerminalNsFromLocation’ defined but not used [-Wunused-function] 5459 | RemoveTerminalNsFromLocation | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin6.c:5046:13: warning: ‘AppendFirstToFeat’ defined but not used [-Wunused-function] 5046 | static void AppendFirstToFeat (SeqFeatPtr sfp, Pointer userdata) | ^~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: sequin6.c: In function ‘CreateFieldSubfieldDlg.constprop.0’: ../include/vibdefns.h:535:22: warning: ‘g2’ may be used uninitialized [-Wmaybe-uninitialized] 535 | #define AlignObjects Nlm_AlignObjects sequin6.c:430:29: note: ‘g2’ was declared here 430 | GrouP p, g, g2; | ^~ sequin7.c:46:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 46 | static char *date_of_compilation = __DATE__; | ^~~~~~~~ sequin7.c:47:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 47 | static char *time_of_compilation = __TIME__; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin7.c:53: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin7.c: In function ‘GeneExtendFunc’: sequin7.c:959:18: warning: variable ‘grp’ set but not used [-Wunused-but-set-variable] 959 | GeneRefPtr grp; | ^~~ sequin7.c: In function ‘FinishConvertingToCDS’: sequin7.c:2771:17: warning: variable ‘nsep’ set but not used [-Wunused-but-set-variable] 2771 | SeqEntryPtr nsep; | ^~~~ sequin7.c: In function ‘SetBestFrame’: sequin7.c:5218:26: warning: variable ‘seq_str2’ set but not used [-Wunused-but-set-variable] 5218 | CharPtr seq_str1, seq_str2; | ^~~~~~~~ sequin7.c:5218:16: warning: variable ‘seq_str1’ set but not used [-Wunused-but-set-variable] 5218 | CharPtr seq_str1, seq_str2; | ^~~~~~~~ sequin7.c: In function ‘RemoveProteinsAndOptionallyRenormalize’: sequin7.c:5679:18: warning: unused variable ‘tmp’ [-Wunused-variable] 5679 | ValNodePtr tmp; | ^~~ sequin7.c:5675:18: warning: unused variable ‘ompc’ [-Wunused-variable] 5675 | OMProcControl ompc; | ^~~~ sequin7.c:5672:18: warning: unused variable ‘itemID’ [-Wunused-variable] 5672 | Uint4 itemID; | ^~~~~~ sequin7.c:5671:18: warning: unused variable ‘bsp’ [-Wunused-variable] 5671 | BioseqPtr bsp; | ^~~ sequin7.c: In function ‘RNABlastOptionNew’: sequin7.c:7045:24: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 7045 | Int2 rval; | ^~~~ sequin7.c: In function ‘GetSubListForRNAStrandCorrection’: sequin7.c:7325:27: warning: variable ‘found_id’ set but not used [-Wunused-but-set-variable] 7325 | Boolean found_id; | ^~~~~~~~ sequin7.c: In function ‘ShowClickableItemListEx’: sequin7.c:9473:28: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 9473 | SeqEntryPtr sep; | ^~~ sequin7.c: In function ‘ChooseFeaturesForConversion’: sequin7.c:9614:28: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 9614 | SeqEntryPtr sep; | ^~~ sequin7.c: In function ‘GetTableOptions’: sequin7.c:13793:30: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 13793 | SeqEntryPtr sep; | ^~~ sequin7.c: In function ‘RemoveCDSandmRNAForGene’: sequin7.c:14076:27: warning: variable ‘prev_xref’ set but not used [-Wunused-but-set-variable] 14076 | SeqFeatXrefPtr xref, prev_xref, next_xref; | ^~~~~~~~~ sequin7.c: In function ‘CombineToCreatePseudoGene’: sequin7.c:14159:48: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 14159 | || best_left == fcontext.left && best_right < fcontext.right) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c: In function ‘TrimTaxFix’: sequin7.c:15679:46: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 15679 | || word_break - t->suggested_fix == 10 && StringNICmp (t->suggested_fix, "uncultured ", 11) == 0) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c: In function ‘FindBestNTrimSites’: sequin7.c:16522:21: warning: unused variable ‘trim_list’ [-Wunused-variable] 16522 | ValNodePtr trim_list = NULL; | ^~~~~~~~~ sequin7.c: In function ‘BarcodeBlastOptionNew’: sequin7.c:16791:24: warning: variable ‘rval’ set but not used [-Wunused-but-set-variable] 16791 | Int2 rval; | ^~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sequin7.c:74: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sequin7.c:77: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sequin7.c: In function ‘GetSubListForRNAStrandCorrection’: sequin7.c:7390:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7390 | system (cmmd); | ^~~~~~~~~~~~~ sequin7.c: At top level: sequin7.c:14322:13: warning: ‘FindBadLatLonSourceFeat’ defined but not used [-Wunused-function] 14322 | static void FindBadLatLonSourceFeat (SeqFeatPtr sfp, Pointer userdata) | ^~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:12208:13: warning: ‘RemoveBarcodeKeywordsFromLowTrace’ defined but not used [-Wunused-function] 12208 | static void RemoveBarcodeKeywordsFromLowTrace (ButtoN b) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:6629:16: warning: ‘DoesBioseqMatchStringConstraint’ defined but not used [-Wunused-function] 6629 | static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintXPtr scp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:4781:13: warning: ‘RemoveMultipleTitles’ defined but not used [-Wunused-function] 4781 | static void RemoveMultipleTitles (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) | ^~~~~~~~~~~~~~~~~~~~ sequin7.c:47:14: warning: ‘time_of_compilation’ defined but not used [-Wunused-variable] 47 | static char *time_of_compilation = __TIME__; | ^~~~~~~~~~~~~~~~~~~ sequin7.c: In function ‘CombineToCreatePseudoGene’: sequin7.c:14158:18: warning: ‘best_left’ may be used uninitialized [-Wmaybe-uninitialized] 14157 | } else if (feat_list == NULL | ~~~~~~~~~~~~~~~~~ 14158 | || best_left > fcontext.left | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:14125:21: note: ‘best_left’ was declared here 14125 | Int4 best_left, best_right; | ^~~~~~~~~ sequin7.c:14159:48: warning: ‘best_right’ may be used uninitialized [-Wmaybe-uninitialized] 14159 | || best_left == fcontext.left && best_right < fcontext.right) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:14125:32: note: ‘best_right’ was declared here 14125 | Int4 best_left, best_right; | ^~~~~~~~~~ sequin7.c:14204:16: warning: ‘int_strand’ may be used uninitialized [-Wmaybe-uninitialized] 14204 | cds_list = GetCDSListForInterval (int_left, int_right, int_strand, first_sfp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin7.c:14127:21: note: ‘int_strand’ was declared here 14127 | Uint1 int_strand; | ^~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin8.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin8.c: In function ‘PopulateAAPopup’: sequin8.c:1198:20: warning: variable ‘first’ set but not used [-Wunused-but-set-variable] 1198 | Uint1 first; | ^~~~~ sequin8.c: In function ‘SelectBestRepeatsFromList’: sequin8.c:7867:18: warning: variable ‘best_len’ set but not used [-Wunused-but-set-variable] 7867 | Int4 best_len; | ^~~~~~~~ sequin8.c:7862:18: warning: variable ‘strand2’ set but not used [-Wunused-but-set-variable] 7862 | Uint1 strand1, strand2; | ^~~~~~~ sequin8.c:7862:9: warning: variable ‘strand1’ set but not used [-Wunused-but-set-variable] 7862 | Uint1 strand1, strand2; | ^~~~~~~ sequin8.c: In function ‘ExamineAln’: sequin8.c:8328:8: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 8328 | Int4 len, num_aln = 0; | ^~~ sequin8.c: In function ‘FindIntervalConflict’: sequin8.c:10165:39: warning: self-comparison always evaluates to true [-Wtautological-compare] 10165 | } else if (left2 <= left1 && right2 >= right2) { | ^~ sequin8.c: In function ‘BuildConflictLists’: sequin8.c:10507:69: warning: self-comparison always evaluates to false [-Wtautological-compare] 10507 | if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { | ^~ sequin8.c:10513:69: warning: self-comparison always evaluates to false [-Wtautological-compare] 10513 | if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) { | ^~ sequin8.c: In function ‘ScrollToDiscrepancyItem’: sequin8.c:14861:17: warning: variable ‘special_flag’ set but not used [-Wunused-but-set-variable] 14861 | Boolean special_flag = FALSE; | ^~~~~~~~~~~~ sequin8.c: In function ‘SortVnpByLinkStatus’: sequin8.c:17767:33: warning: self-comparison always evaluates to false [-Wtautological-compare] 17767 | } else if (fcontext2.itemID < fcontext2.itemID) { | ^ sequin8.c: In function ‘SortVnpBymRNAPos’: sequin8.c:17784:22: warning: variable ‘mrna2’ set but not used [-Wunused-but-set-variable] 17784 | SeqFeatPtr mrna1, mrna2; | ^~~~~ sequin8.c:17784:15: warning: variable ‘mrna1’ set but not used [-Wunused-but-set-variable] 17784 | SeqFeatPtr mrna1, mrna2; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sequin8.c:57: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sequin8.c:63: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sequin8.c:18941:19: warning: ‘DivideClickableItemListByEntityID’ defined but not used [-Wunused-function] 18941 | static ValNodePtr DivideClickableItemListByEntityID (ValNodePtr clickable_list) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin8.c:14351:13: warning: ‘VisitFeaturesInViewedBioseqs’ defined but not used [-Wunused-function] 14351 | static void VisitFeaturesInViewedBioseqs (Pointer userdata, VisitFeaturesFunc callback) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin8.c:12559:13: warning: ‘MakeProteinTitlesInSequinStyle’ defined but not used [-Wunused-function] 12559 | static void MakeProteinTitlesInSequinStyle (Uint2 entityID, SeqEntryPtr sep) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin8.c:12367:13: warning: ‘ShowAssemblyAlignment’ defined but not used [-Wunused-function] 12367 | static void ShowAssemblyAlignment (SeqAlignPtr salp) | ^~~~~~~~~~~~~~~~~~~~~ sequin8.c:8326:13: warning: ‘ExamineAln’ defined but not used [-Wunused-function] 8326 | static void ExamineAln (SeqAlignPtr sap) | ^~~~~~~~~~ sequin8.c:7262:16: warning: ‘DoesFirstRepeatContainAllOtherRepeats’ defined but not used [-Wunused-function] 7262 | static Boolean DoesFirstRepeatContainAllOtherRepeats (ValNodePtr start, ValNodePtr stop) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin8.c:6810:16: warning: ‘DoesRowContainPoint’ defined but not used [-Wunused-function] 6810 | static Boolean DoesRowContainPoint (SeqAlignRowPtr row, Int4 point) | ^~~~~~~~~~~~~~~~~~~ sequin8.c:6475:13: warning: ‘CKA_ShowAln’ defined but not used [-Wunused-function] 6475 | static void CKA_ShowAln(SeqAlignPtr sap, CKA_AccPtr acc_head) | ^~~~~~~~~~~ sequin8.c:6269:16: warning: ‘CKA_ValidateSeqAlign’ defined but not used [-Wunused-function] 6269 | static Boolean CKA_ValidateSeqAlign(SeqAlignPtr sap, CKA_AccPtr acc_head, Int4 bioseqlen, ValNodePtr PNTR errors) | ^~~~~~~~~~~~~~~~~~~~ sequin8.c:1538:18: warning: ‘SqnGetBioseqGivenSeqLoc’ defined but not used [-Wunused-function] 1538 | static BioseqPtr SqnGetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID) | ^~~~~~~~~~~~~~~~~~~~~~~ sequin8.c:536:13: warning: ‘FixReadingFrame’ defined but not used [-Wunused-function] 536 | static void FixReadingFrame ( | ^~~~~~~~~~~~~~~ sequin8.c:309:13: warning: ‘ExtendOnePartialFeatureToEndOrGap’ defined but not used [-Wunused-function] 309 | static void ExtendOnePartialFeatureToEndOrGap (SeqFeatPtr sfp, Pointer userdata) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/objsub.h:76, from ../include/subutil.h:50, from sequin9.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin9.c: In function ‘DoVecScreens’: sequin9.c:629:19: warning: variable ‘hits’ set but not used [-Wunused-but-set-variable] 629 | Int2 hits; | ^~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1529:18: warning: variable ‘choice’ set but not used [-Wunused-but-set-variable] 1529 | Int2 choice; | ^~~~~~ sequin9.c: In function ‘ReadServiceConfigFile’: sequin9.c:2710:12: warning: the comparison will always evaluate as ‘false’ for the address of ‘path’ will never be NULL [-Waddress] 2710 | if (path == NULL || config == NULL || config->data.ptrvalue == NULL) return; | ^~ sequin9.c:2695:17: note: ‘path’ declared here 2695 | Char path [PATH_MAX]; | ^~~~ sequin9.c: In function ‘ExtendBothEnds’: sequin9.c:4838:17: warning: variable ‘oldbsp’ set but not used [-Wunused-but-set-variable] 4838 | BioseqPtr oldbsp; | ^~~~~~ sequin9.c: In function ‘Extend5Prime’: sequin9.c:4906:17: warning: variable ‘oldbsp’ set but not used [-Wunused-but-set-variable] 4906 | BioseqPtr oldbsp; | ^~~~~~ sequin9.c: In function ‘Extend3Prime’: sequin9.c:4966:17: warning: variable ‘oldbsp’ set but not used [-Wunused-but-set-variable] 4966 | BioseqPtr oldbsp; | ^~~~~~ sequin9.c: In function ‘FixProteinString’: sequin9.c:5177:16: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5177 | Int4 start, stop, new_stop, prot_len; | ^~~~~ sequin9.c: In function ‘ShiftStopForLengthChange’: sequin9.c:5254:13: warning: variable ‘start’ set but not used [-Wunused-but-set-variable] 5254 | Int4 start, stop, new_stop; | ^~~~~ sequin9.c: In function ‘ExtendProtein5’: sequin9.c:5447:23: warning: variable ‘new_stop’ set but not used [-Wunused-but-set-variable] 5447 | Int4 stop, new_stop; | ^~~~~~~~ sequin9.c: In function ‘PrepareUpdateAlignmentForProtein’: sequin9.c:5975:17: warning: variable ‘changed_frame’ set but not used [-Wunused-but-set-variable] 5975 | Boolean changed_frame; | ^~~~~~~~~~~~~ sequin9.c: In function ‘DrawAlignDiffs’: sequin9.c:7468:20: warning: variable ‘len2’ set but not used [-Wunused-but-set-variable] 7468 | Int4 len1, len2, i; | ^~~~ sequin9.c:7468:14: warning: variable ‘len1’ set but not used [-Wunused-but-set-variable] 7468 | Int4 len1, len2, i; | ^~~~ sequin9.c: In function ‘MakeAlignDetails’: sequin9.c:7603:12: warning: variable ‘aln_length’ set but not used [-Wunused-but-set-variable] 7603 | Int4 aln_length; | ^~~~~~~~~~ sequin9.c: In function ‘MakeAlignSequence’: sequin9.c:7652:56: warning: variable ‘to’ set but not used [-Wunused-but-set-variable] 7652 | Int4 aln_length, len, lens, start, stop, from, to, i, j; | ^~ sequin9.c:7652:50: warning: variable ‘from’ set but not used [-Wunused-but-set-variable] 7652 | Int4 aln_length, len, lens, start, stop, from, to, i, j; | ^~~~ sequin9.c: In function ‘DrawUpdateAlignmentDiffs’: sequin9.c:12920:20: warning: variable ‘len2’ set but not used [-Wunused-but-set-variable] 12920 | Int4 len1, len2, i; | ^~~~ sequin9.c:12920:14: warning: variable ‘len1’ set but not used [-Wunused-but-set-variable] 12920 | Int4 len1, len2, i; | ^~~~ sequin9.c: In function ‘MakeAlignmentDetailsPicture’: sequin9.c:13005:12: warning: variable ‘aln_length’ set but not used [-Wunused-but-set-variable] 13005 | Int4 aln_length; | ^~~~~~~~~~ sequin9.c: In function ‘MakeUpdateAlignmentSequenceString’: sequin9.c:13087:44: warning: variable ‘to’ set but not used [-Wunused-but-set-variable] 13087 | Int4 len, lens, start, stop, from, to, i, j; | ^~ sequin9.c:13087:38: warning: variable ‘from’ set but not used [-Wunused-but-set-variable] 13087 | Int4 len, lens, start, stop, from, to, i, j; | ^~~~ sequin9.c: In function ‘SetPreviewSequenceSelectionByPosition’: sequin9.c:15261:46: warning: variable ‘curr_scroll’ set but not used [-Wunused-but-set-variable] 15261 | Int4 prevrow, curr_scroll, max_scroll; | ^~~~~~~~~~~ sequin9.c: In function ‘DoTestUpdateOneSequence’: sequin9.c:16366:30: warning: variable ‘update_bsp’ set but not used [-Wunused-but-set-variable] 16366 | BioseqPtr update_bsp = NULL; | ^~~~~~~~~~ sequin9.c:16365:30: warning: variable ‘update_entityID’ set but not used [-Wunused-but-set-variable] 16365 | Uint2 update_entityID = 0; | ^~~~~~~~~~~~~~~ sequin9.c: In function ‘UpdateAllSequences’: sequin9.c:16656:30: warning: unused variable ‘update_entityID’ [-Wunused-variable] 16656 | Uint2 update_entityID = 0; | ^~~~~~~~~~~~~~~ sequin9.c:16655:30: warning: unused variable ‘update_bsp’ [-Wunused-variable] 16655 | BioseqPtr update_bsp = NULL; | ^~~~~~~~~~ sequin9.c: In function ‘CleanupUpdateMultiSequence’: sequin9.c:16976:30: warning: unused variable ‘entityIDList’ [-Wunused-variable] 16976 | ValNodePtr entityIDList = NULL; | ^~~~~~~~~~~~ sequin9.c: In function ‘RemoveIdenticalUpdates’: sequin9.c:17219:30: warning: unused variable ‘update_entityID’ [-Wunused-variable] 17219 | Uint2 update_entityID = 0; | ^~~~~~~~~~~~~~~ sequin9.c: In function ‘UpdateSequenceViaDownload’: sequin9.c:18323:15: warning: variable ‘is_na’ set but not used [-Wunused-but-set-variable] 18323 | Boolean is_na; | ^~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from sequin9.c:47: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from sequin9.c:50: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ../include/sqnutils.h:51, from ../include/alignmgr2.h:111, from ../include/actutils.h:105, from sequin9.c:56: ../include/objentgene.h:177:33: warning: ‘Method_methodFree’ declared ‘static’ but never defined [-Wunused-function] 177 | static Method_methodPtr LIBCALL Method_methodFree PROTO ((Method_methodPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objentgene.h:178:33: warning: ‘Method_methodAsnRead’ declared ‘static’ but never defined [-Wunused-function] 178 | static Method_methodPtr LIBCALL Method_methodAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objentgene.h:179:24: warning: ‘Method_methodAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 179 | static Boolean LIBCALL Method_methodAsnWrite PROTO (( Method_methodPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ sequin9.c:215:13: warning: ‘TruncateCDS’ declared ‘static’ but never defined [-Wunused-function] 215 | static void TruncateCDS (SeqFeatPtr sfp, Uint1 frame, BioseqPtr pbsp); | ^~~~~~~~~~~ sequin9.c:16618:29: warning: ‘FeatureUpdateNew’ defined but not used [-Wunused-function] 16618 | static FeatureUpdateInfoPtr FeatureUpdateNew (BioseqPtr orig_bsp, BioseqPtr update_bsp) | ^~~~~~~~~~~~~~~~ sequin9.c:1466:16: warning: ‘StrSaveNoNullEncodeSpaces’ defined but not used [-Wunused-function] 1466 | static CharPtr StrSaveNoNullEncodeSpaces (CharPtr from) | ^~~~~~~~~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘ListIds’: sequin9.c:16197:14: warning: ‘bssp’ may be used uninitialized [-Wmaybe-uninitialized] 16197 | for (s = bssp->seq_set; s != NULL; s = s->next) { | ~~^~~~~~~~~~~~~~~ sequin9.c:16184:16: note: ‘bssp’ was declared here 16184 | BioseqSetPtr bssp; | ^~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1670:39: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1670 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1670:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1684:37: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1684 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1684:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1635:39: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1635 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1635:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1649:37: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1649 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1649:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1600:39: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1600 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1600:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘AcceptArgumentFormProc’: sequin9.c:1614:37: warning: ‘__sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1614 | sprintf (cpy, "%s=%s", upp->param, last); | ^ In function ‘sprintf’, inlined from ‘AcceptArgumentFormProc’ at sequin9.c:1614:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sequin9.c: In function ‘TruncateSeqGraphValues.isra.0’: sequin9.c:3144:11: warning: ‘fmin’ may be used uninitialized [-Wmaybe-uninitialized] 3144 | FloatHi fmin, fmax; | ^~~~ sequin9.c: In function ‘PrepareUpdateAlignmentForProtein.constprop.0’: sequin9.c:6087:37: warning: ‘gene_sfp’ may be used uninitialized [-Wmaybe-uninitialized] 6087 | if (correct_cds_genes && gene_sfp != NULL) { | ^ sequin9.c:5981:17: note: ‘gene_sfp’ was declared here 5981 | SeqFeatPtr gene_sfp; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequin10.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sequin10.c: In function ‘DoAutoDefLine’: sequin10.c:198:17: warning: unused variable ‘uop’ [-Wunused-variable] 198 | UserObjectPtr uop; | ^~~ sequin10.c: In function ‘ApplyTableQuals’: sequin10.c:4576:26: warning: variable ‘fqtd’ set but not used [-Wunused-but-set-variable] 4576 | FeatureQualTableData fqtd; | ^~~~ sequin10.c: In function ‘OkCancelTellMeMore’: sequin10.c:4937:10: warning: variable ‘p1’ set but not used [-Wunused-but-set-variable] 4937 | PrompT p1; | ^~ sequin10.c: In function ‘LookupJournalTitlesInObjectTable’: sequin10.c:5094:11: warning: unused variable ‘rval’ [-Wunused-variable] 5094 | Boolean rval = TRUE; | ^~~~ sequin10.c: In function ‘EraseAllFieldsWhenBlank’: sequin10.c:5874:19: warning: unused variable ‘columns’ [-Wunused-variable] 5874 | ValNodePtr columns = NULL; | ^~~~~~~ sequin10.c: In function ‘ExternalSourceQualifierTableReader’: sequin10.c:6812:22: warning: variable ‘any_valid’ set but not used [-Wunused-but-set-variable] 6812 | Boolean any_valid = FALSE; | ^~~~~~~~~ sequin10.c: In function ‘LoadFeatureFieldTable’: sequin10.c:9115:24: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 9115 | SeqEntryPtr sep; | ^~~ sequin10.c: In function ‘OrgModListsMatch’: sequin10.c:10856:14: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 10856 | Boolean found; | ^~~~~ sequin10.c: In function ‘SubtypeListsMatch’: sequin10.c:11049:14: warning: variable ‘found’ set but not used [-Wunused-but-set-variable] 11049 | Boolean found; | ^~~~~ sequin10.c: In function ‘TrimSequencesByAlignment’: sequin10.c:12402:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 12402 | ButtoN b; | ^ sequin10.c: In function ‘AddOneFeatureBetween’: sequin10.c:12809:14: warning: variable ‘seqfeattype’ set but not used [-Wunused-but-set-variable] 12809 | Int4 seqfeattype; | ^~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from sequin10.c:63: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from sequin10.c:68: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ sequin10.c:14399:13: warning: ‘PrintTPAHistErrors’ defined but not used [-Wunused-function] 14399 | static void PrintTPAHistErrors (LogInfoPtr lip, ValNodePtr errors) | ^~~~~~~~~~~~~~~~~~ sequin10.c:12050:19: warning: ‘FindGeneInSeqEntryByLocusTag’ defined but not used [-Wunused-function] 12050 | static SeqFeatPtr FindGeneInSeqEntryByLocusTag (SeqEntryPtr sep, CharPtr locus_tag) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequin10.c:9201:16: warning: ‘GetRevSectionInterval’ defined but not used [-Wunused-function] 9201 | static Pointer GetRevSectionInterval (Uint1 data_choice, Pointer data, Pointer metadata) | ^~~~~~~~~~~~~~~~~~~~~ sequin10.c:9183:16: warning: ‘GetRevSectionSequence’ defined but not used [-Wunused-function] 9183 | static Pointer GetRevSectionSequence (Uint1 data_choice, Pointer data, Pointer metadata) | ^~~~~~~~~~~~~~~~~~~~~ sequin10.c:3058:19: warning: ‘FreeTableData’ defined but not used [-Wunused-function] 3058 | static ValNodePtr FreeTableData (ValNodePtr lines) | ^~~~~~~~~~~~~ sequin10.c:1495:19: warning: ‘OrgModTableColumnListFree’ defined but not used [-Wunused-function] 1495 | static ValNodePtr OrgModTableColumnListFree (ValNodePtr vnp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/vibrant.h:130: In function ‘CreateDefLineFormFeatureOptionsGroup’, inlined from ‘CreateDefLineForm’ at sequin10.c:853:15, inlined from ‘AutoDefBaseFormCommon’ at sequin10.c:993:5: ../include/vibdefns.h:318:18: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 318 | #define CheckBox Nlm_CheckBox sequin10.c: In function ‘AutoDefBaseFormCommon’: sequin10.c:726:24: note: ‘k’ was declared here 726 | GrouP p, g1, s1, s2, k, k2; | ^ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sequinx.c:46: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ : Psequin x86_64-linux-gnu-gcc -o sbtedit -I. -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sbtedit.c \ -lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb \ -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla \ -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -lm sbtedit.c:48:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 48 | static char *date_of_compilation = __DATE__; | ^~~~~~~~ sbtedit.c:49:36: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 49 | static char *time_of_compilation = __TIME__; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from ../include/dlogutil.h:48, from sequin.h:82, from sbtedit.c:55: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sbtedit.c: In function ‘LookupTaxonomyFunc’: sbtedit.c:604:15: warning: variable ‘rsult’ set but not used [-Wunused-but-set-variable] 604 | Int4 rsult; | ^~~~~ sbtedit.c: At top level: sbtedit.c:49:14: warning: ‘time_of_compilation’ defined but not used [-Wunused-variable] 49 | static char *time_of_compilation = __TIME__; | ^~~~~~~~~~~~~~~~~~~ sbtedit.c:48:14: warning: ‘date_of_compilation’ defined but not used [-Wunused-variable] 48 | static char *date_of_compilation = __DATE__; | ^~~~~~~~~~~~~~~~~~~ : sbtedit x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" udvmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/explore.h:49, from ../include/udviewer.h:209, from udvmain.c:80: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ udvmain.c: In function ‘Nlm_Main’: udvmain.c:232:25: warning: unused variable ‘rcL’ [-Wunused-variable] 232 | RecT rcL; | ^~~ In file included from ../include/strimprt.h:72, from ../include/mmdbapi1.h:234, from ../include/accentr.h:143, from udvmain.c:81: ../include/objmmdb1.h: At top level: ../include/objmmdb1.h:206:57: warning: ‘VersionOfDatabase_version_of_databaseFree’ declared ‘static’ but never defined [-Wunused-function] 206 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseFree PROTO ((VersionOfDatabase_version_of_databasePtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:207:57: warning: ‘VersionOfDatabase_version_of_databaseAsnRead’ declared ‘static’ but never defined [-Wunused-function] 207 | static VersionOfDatabase_version_of_databasePtr LIBCALL VersionOfDatabase_version_of_databaseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb1.h:208:24: warning: ‘VersionOfDatabase_version_of_databaseAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 208 | static Boolean LIBCALL VersionOfDatabase_version_of_databaseAsnWrite PROTO (( VersionOfDatabase_version_of_databasePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:73: ../include/objmmdb2.h:151:43: warning: ‘Coordinates_coordinatesFree’ declared ‘static’ but never defined [-Wunused-function] 151 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesFree PROTO ((Coordinates_coordinatesPtr )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:152:43: warning: ‘Coordinates_coordinatesAsnRead’ declared ‘static’ but never defined [-Wunused-function] 152 | static Coordinates_coordinatesPtr LIBCALL Coordinates_coordinatesAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:153:24: warning: ‘Coordinates_coordinatesAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 153 | static Boolean LIBCALL Coordinates_coordinatesAsnWrite PROTO (( Coordinates_coordinatesPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:247:35: warning: ‘Surface_surfaceFree’ declared ‘static’ but never defined [-Wunused-function] 247 | static Surface_surfacePtr LIBCALL Surface_surfaceFree PROTO ((Surface_surfacePtr )); | ^~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:248:35: warning: ‘Surface_surfaceAsnRead’ declared ‘static’ but never defined [-Wunused-function] 248 | static Surface_surfacePtr LIBCALL Surface_surfaceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb2.h:249:24: warning: ‘Surface_surfaceAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 249 | static Boolean LIBCALL Surface_surfaceAsnWrite PROTO (( Surface_surfacePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/strimprt.h:74: ../include/objmmdb3.h:287:37: warning: ‘Location_locationFree’ declared ‘static’ but never defined [-Wunused-function] 287 | static Location_locationPtr LIBCALL Location_locationFree PROTO ((Location_locationPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:288:37: warning: ‘Location_locationAsnRead’ declared ‘static’ but never defined [-Wunused-function] 288 | static Location_locationPtr LIBCALL Location_locationAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:289:24: warning: ‘Location_locationAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 289 | static Boolean LIBCALL Location_locationAsnWrite PROTO (( Location_locationPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:310:37: warning: ‘Property_propertyFree’ declared ‘static’ but never defined [-Wunused-function] 310 | static Property_propertyPtr LIBCALL Property_propertyFree PROTO ((Property_propertyPtr )); | ^~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:311:37: warning: ‘Property_propertyAsnRead’ declared ‘static’ but never defined [-Wunused-function] 311 | static Property_propertyPtr LIBCALL Property_propertyAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:312:24: warning: ‘Property_propertyAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 312 | static Boolean LIBCALL Property_propertyAsnWrite PROTO (( Property_propertyPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:419:33: warning: ‘Region_regionFree’ declared ‘static’ but never defined [-Wunused-function] 419 | static Region_regionPtr LIBCALL Region_regionFree PROTO ((Region_regionPtr )); | ^~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:420:33: warning: ‘Region_regionAsnRead’ declared ‘static’ but never defined [-Wunused-function] 420 | static Region_regionPtr LIBCALL Region_regionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~ ../include/objmmdb3.h:421:24: warning: ‘Region_regionAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 421 | static Boolean LIBCALL Region_regionAsnWrite PROTO (( Region_regionPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -o udv -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF udvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib \ -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant \ -lncbitool -lblastcompadj -lncbiobj \ -lncbi -lm x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ddvmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ddvmain.c:138: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ ddvmain.c:147:13: warning: ‘DDV_myargs’ initialized and declared ‘extern’ 147 | extern Args DDV_myargs[NUMARGS] = { | ^~~~~~~~~~ ddvmain.c:267:16: warning: ‘DDV_UseNetwork’ defined but not used [-Wunused-function] 267 | static Boolean DDV_UseNetwork(void) | ^~~~~~~~~~~~~~ ddvmain.c: In function ‘Nlm_Main’: ddvmain.c:441:12: warning: ‘UseNetwork’ may be used uninitialized [-Wmaybe-uninitialized] 441 | if (UseNetwork && EntrezIsInited()) EntrezBioseqFetchDisable(); | ^ ddvmain.c:353:25: note: ‘UseNetwork’ was declared here 353 | Boolean UseNetwork; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -o ddv -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF ddvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib \ -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool \ -lblastcompadj -lncbiobj -lncbi \ -lm x86_64-linux-gnu-gcc -g -o taxblast -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF taxblast_main.c \ -lblastapi -lblast -lnetblast -lncbiid1 -lncbitxc2 -lncbitool -lblastcompadj \ -lnetcli -lncbiobj -lconnssl -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from taxblast_main.c:35: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ taxblast_main.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 1 | static char const rcsid[] = "$Id: taxblast_main.c,v"; | ^~~~~ x86_64-linux-gnu-gcc -g -o idfetch -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF idfetch.c -lncbiid1 -lnetcli -lncbiobj -lconnssl -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from idfetch.c:30: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ idfetch.c: In function ‘Nlm_Main’: idfetch.c:358:46: warning: variable ‘any_type’ set but not used [-Wunused-but-set-variable] 358 | found_colon = FALSE, dna_type = FALSE, any_type = FALSE; | ^~~~~~~~ idfetch.c:358:28: warning: variable ‘dna_type’ set but not used [-Wunused-but-set-variable] 358 | found_colon = FALSE, dna_type = FALSE, any_type = FALSE; | ^~~~~~~~ idfetch.c: In function ‘ProcessOneDocSum’: idfetch.c:803:25: warning: unused variable ‘e2ry’ [-Wunused-variable] 803 | Entrez2ReplyPtr e2ry; | ^~~~ idfetch.c:802:25: warning: unused variable ‘e2rq’ [-Wunused-variable] 802 | Entrez2RequestPtr e2rq; | ^~~~ idfetch.c: In function ‘IdFetch_func’: idfetch.c:852:20: warning: missing braces around initializer [-Wmissing-braces] 852 | SeqId si={SEQID_GI,0,0}; | ^ | {} idfetch.c:859:17: warning: variable ‘group_segs’ set but not used [-Wunused-but-set-variable] 859 | Uint1 group_segs; | ^~~~~~~~~~ idfetch.c: In function ‘BEGetUidsFromQuery’: idfetch.c:1113:14: warning: unused variable ‘e2rp’ [-Wunused-variable] 1113 | E2ReplyPtr e2rp; | ^~~~ idfetch.c: In function ‘GetIntervalAccession’: idfetch.c:1401:5: warning: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation] 1401 | strncpy( pBuff, pAccession, 64); | ^ idfetch.c: In function ‘IdFetch_func’: idfetch.c:961:5: warning: ‘gi_state’ may be used uninitialized [-Wmaybe-uninitialized] 961 | id_print_gi_state(gi_state,buf,sizeof(buf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ idfetch.c:850:28: note: ‘gi_state’ was declared here 850 | Int4 status = 0,gi_state; | ^~~~~~~~ idfetch.c: In function ‘Nlm_Main’: idfetch.c:1313:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 1313 | strncpy( buf, myargs[showfeatures].strvalue, 1024); | ^ In function ‘TryGetGi’, inlined from ‘Nlm_Main’ at idfetch.c:501:19: idfetch.c:661:15: warning: ‘type_int’ may be used uninitialized [-Wmaybe-uninitialized] 661 | sip->choice = choice; | ~~~~~~~~~~~~^~~~~~~~ idfetch.c: In function ‘Nlm_Main’: idfetch.c:140:7: note: ‘type_int’ was declared here 140 | int type_int; | ^~~~~~~~ x86_64-linux-gnu-gcc -g -o asn2gb -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asn2gb.c -lncbiid1 -lnetcli \ -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2gb.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords’: asn2gb.c:1748:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1748 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c: In function ‘CompareFlatFiles’: asn2gb.c:1185:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1185 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1192:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1192 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1217:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1217 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1243:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1243 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1246:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1246 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1251:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1251 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1254:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1254 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c: In function ‘ReportDiffs’: asn2gb.c:1072:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1072 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1075:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1075 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1078:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1078 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1081:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1081 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1084:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1084 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c:1097:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1097 | system (cmmd); | ^~~~~~~~~~~~~ asn2gb.c: At top level: asn2gb.c:1291:13: warning: ‘CheckOrder’ defined but not used [-Wunused-function] 1291 | static void CheckOrder ( | ^~~~~~~~~~ asn2gb.c:968:13: warning: ‘FreeUnpubAffil’ defined but not used [-Wunused-function] 968 | static void FreeUnpubAffil ( | ^~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1626:24: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1626 | sprintf (buf, "%s.before", accn); | ^~ asn2gb.c:1628:24: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1628 | sprintf (buf, "%s.gbff.before", accn); | ^~ asn2gb.c:1250:43: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 236 [-Wformat-overflow=] 1250 | sprintf (cmmd, "./oldasn2gb -f p -i %s -o %s", path3, path1); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1250:7, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 25 and 8215 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1253:43: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 236 [-Wformat-overflow=] 1253 | sprintf (cmmd, "./newasn2gb -f p -i %s -o %s", path3, path2); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1253:7, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 25 and 8215 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1242:38: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 241 [-Wformat-overflow=] 1242 | sprintf (cmmd, "./oldasn2gb -i %s -o %s", path3, path1); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1242:7, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 20 and 8210 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1245:38: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 241 [-Wformat-overflow=] 1245 | sprintf (cmmd, "./newasn2gb -i %s -o %s", path3, path2); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1245:7, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 20 and 8210 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1258:29: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 248 [-Wformat-overflow=] 1258 | sprintf (cmmd, "diff -b %s %s > %s", path1, path2, path3); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1258:5, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 12298 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1268:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 252 [-Wformat-overflow=] 1268 | sprintf (cmmd, "cat %s", path3); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1268:7, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 4100 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1216:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 1216 | sprintf (cmmd, "%s %s -i %s -o %s", asn2flat, arguments, path3, path2); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1216:5, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 8200) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1184:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 1184 | sprintf (cmmd, "%s %s -i %s -o %s", asn2flat, arguments, path3, path1); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1184:5, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 8200) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1191:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 1191 | sprintf (cmmd, "%s %s -i %s -o %s", asn2flat, arguments, path3, path2); | ^~ ...... 1661 | CompareFlatFiles (path1, path2, path3, sep, ofp, | ~~~~~ In function ‘sprintf’, inlined from ‘CompareFlatFiles’ at asn2gb.c:1191:5, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1661:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 8200) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2gb.c: In function ‘HandleMultipleRecords.constprop.0’: asn2gb.c:1747:22: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 253 [-Wformat-overflow=] 1747 | sprintf (cmmd, "rm %s; rm %s; rm %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘HandleMultipleRecords.constprop.0’ at asn2gb.c:1747:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 12299 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -o tbl2asn -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF tbl2asn.c -lncbitool -lblastcompadj \ -lncbiobj -lnetcli -lconnssl -lncbi -lm tbl2asn.c:45:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 45 | static char *date_of_compilation = __DATE__; | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from tbl2asn.c:47: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tbl2asn.c: In function ‘HasTaxon’: tbl2asn.c:872:11: warning: comparison between pointer and zero character constant [-Wpointer-compare] 872 | if (orp == FALSE) return FALSE; | ^~ tbl2asn.c:872:7: note: did you mean to dereference the pointer? 872 | if (orp == FALSE) return FALSE; | ^ tbl2asn.c: In function ‘ProcessOneAnnot’: tbl2asn.c:2566:15: warning: variable ‘sep’ set but not used [-Wunused-but-set-variable] 2566 | SeqEntryPtr sep; | ^~~ tbl2asn.c: In function ‘WarnAboutIncompleteFileRead’: tbl2asn.c:4297:16: warning: variable ‘str’ set but not used [-Wunused-but-set-variable] 4297 | CharPtr str; | ^~~ tbl2asn.c: In function ‘MakeOneRnaTitle’: tbl2asn.c:5536:22: warning: variable ‘cds’ set but not used [-Wunused-but-set-variable] 5536 | SeqFeatPtr cds; | ^~~ tbl2asn.c: In function ‘FindSingleNucleotideOrNucProtSetInBioseqInSet’: tbl2asn.c:6986:30: warning: variable ‘single_result’ set but not used [-Wunused-but-set-variable] 6986 | SeqEntryPtr single = NULL, single_result; | ^~~~~~~~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr.h:266, from ../include/aliparse.h:15, from tbl2asn.c:66: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ In file included from ../include/tax3api.h:51, from tbl2asn.c:69: ../include/objtax3.h:183:31: warning: ‘Value_valueFree’ declared ‘static’ but never defined [-Wunused-function] 183 | static Value_valuePtr LIBCALL Value_valueFree PROTO ((Value_valuePtr )); | ^~~~~~~~~~~~~~~ ../include/objtax3.h:184:31: warning: ‘Value_valueAsnRead’ declared ‘static’ but never defined [-Wunused-function] 184 | static Value_valuePtr LIBCALL Value_valueAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~ ../include/objtax3.h:185:24: warning: ‘Value_valueAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 185 | static Boolean LIBCALL Value_valueAsnWrite PROTO (( Value_valuePtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~~~~~ tbl2asn.c:6580:16: warning: ‘ValidateAssemblyGapFeat’ defined but not used [-Wunused-function] 6580 | static Boolean ValidateAssemblyGapFeat (SeqFeatPtr sfp, BioseqPtr bsp) | ^~~~~~~~~~~~~~~~~~~~~~~ tbl2asn.c:6005:20: warning: ‘GetDescriptorTypeAlreadyInList’ defined but not used [-Wunused-function] 6005 | static SeqDescrPtr GetDescriptorTypeAlreadyInList ( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tbl2asn.c:5901:13: warning: ‘ParseOneOrgLabel’ defined but not used [-Wunused-function] 5901 | static void ParseOneOrgLabel ( | ^~~~~~~~~~~~~~~~ tbl2asn.c:2654:16: warning: ‘ExceptionExplainsMismatch’ defined but not used [-Wunused-function] 2654 | static Boolean ExceptionExplainsMismatch (CharPtr except_text) | ^~~~~~~~~~~~~~~~~~~~~~~~~ tbl2asn.c: In function ‘MakeNucProtCDS’: tbl2asn.c:4960:28: warning: ‘%s’ directive writing up to 63 bytes into a region of size 60 [-Wformat-overflow=] 4960 | sprintf (lcl, "lcl|%s", id); | ^~ ~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘InRightNps’ at tbl2asn.c:4960:9, inlined from ‘MakeNucProtCDS’ at tbl2asn.c:5083:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 68 bytes into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ tbl2asn.c: In function ‘MakeNucProtCDS’: tbl2asn.c:4945:26: warning: ‘%s’ directive writing up to 63 bytes into a region of size 60 [-Wformat-overflow=] 4945 | sprintf (lcl, "lcl|%s", id); | ^~ ~~ In function ‘sprintf’, inlined from ‘InRightNps’ at tbl2asn.c:4945:7, inlined from ‘MakeNucProtCDS’ at tbl2asn.c:5083:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 5 and 68 bytes into a destination of size 64 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -o gene2xml -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF gene2xml.c -lnetcli -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from gene2xml.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gene2xml.c: In function ‘ProcessOneRecord’: gene2xml.c:364:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 364 | system (cmmd); | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -o entrez2 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF entrez2.c -lncbiid1 -lnetcli -lncbidesk \ -lblastapi -lblast -lncbimmdb -lncbitool -lblastcompadj \ -lncbiobj -lvibrant -lconnssl -lncbi \ -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from entrez2.c:49: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ entrez2.c: In function ‘Nlm_Main’: entrez2.c:868:12: warning: variable ‘server’ set but not used [-Wunused-but-set-variable] 868 | CharPtr server = "www.ncbi.nlm.nih.gov"; | ^~~~~~ entrez2.c:866:12: warning: variable ‘port’ set but not used [-Wunused-but-set-variable] 866 | Uint2 port = 2441; | ^~~~ entrez2.c:865:12: warning: variable ‘path’ set but not used [-Wunused-but-set-variable] 865 | CharPtr path = "/entrez/utils/entrez2server.fcgi"; | ^~~~ entrez2.c: At top level: entrez2.c:726:13: warning: ‘AboutProc’ defined but not used [-Wunused-function] 726 | static void AboutProc (IteM i) | ^~~~~~~~~ : entrez2 x86_64-linux-gnu-gcc -g -o gbseqget -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF gbseqget.c -lncbiid1 -lnetcli \ -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from gbseqget.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -g -o asn2all -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asn2all.c ncbithr.o -lncbiid1 \ -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm -lpthread In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2all.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2all.c: In function ‘DoLockFarComponents’: asn2all.c:68:27: warning: variable ‘stop_time’ set but not used [-Wunused-but-set-variable] 68 | time_t start_time, stop_time; | ^~~~~~~~~ asn2all.c:68:15: warning: variable ‘start_time’ set but not used [-Wunused-but-set-variable] 68 | time_t start_time, stop_time; | ^~~~~~~~~~ /usr/bin/ld: warning: size of symbol `structTls' changed from 24 in ncbithr.o (symbol from plugin) to 16 in /tmp/ccwJfpyE.ltrans0.ltrans.o /usr/bin/ld: warning: NOTE: size discrepancies can cause real problems. Investigation is advised. x86_64-linux-gnu-gcc -o asn2asn -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asn2asn.c -lncbiid1 -lnetcli -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/asn.h:54, from ../include/objsset.h:48, from ../include/sequtil.h:43, from ../include/seqport.h:47, from asn2asn.c:17: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -g -o asn2fsa -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asn2fsa.c ncbithr.o -lncbiid1 \ -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm -lpthread In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asn2fsa.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asn2fsa.c: In function ‘AddBspToList’: asn2fsa.c:217:15: warning: variable ‘vnp’ set but not used [-Wunused-but-set-variable] 217 | ValNodePtr vnp; | ^~~ asn2fsa.c: In function ‘DoLockFarComponents’: asn2fsa.c:408:27: warning: variable ‘stop_time’ set but not used [-Wunused-but-set-variable] 408 | time_t start_time, stop_time; | ^~~~~~~~~ asn2fsa.c:408:15: warning: variable ‘start_time’ set but not used [-Wunused-but-set-variable] 408 | time_t start_time, stop_time; | ^~~~~~~~~~ asn2fsa.c: In function ‘ProcessMultipleRecord’: asn2fsa.c:793:32: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 251 [-Wformat-overflow=] 793 | sprintf (cmmd, "zcat %s", path); | ^~ ~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘ProcessMultipleRecord’ at asn2fsa.c:793:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 6 and 4101 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2fsa.c: In function ‘ProcessMultipleRecord’: asn2fsa.c:786:31: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 250 [-Wformat-overflow=] 786 | sprintf (cmmd, "gzcat %s", path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘ProcessMultipleRecord’ at asn2fsa.c:786:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 4102 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ asn2fsa.c: In function ‘ProcessMultipleRecord’: asn2fsa.c:782:26: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 255 [-Wformat-overflow=] 782 | sprintf (cmmd, "%s %s", gzcatprog, path); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘ProcessMultipleRecord’ at asn2fsa.c:782:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 2 or more bytes (assuming 4097) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/bin/ld: warning: size of symbol `structTls' changed from 24 in ncbithr.o (symbol from plugin) to 16 in /tmp/ccaTUQYW.ltrans0.ltrans.o /usr/bin/ld: warning: NOTE: size discrepancies can cause real problems. Investigation is advised. x86_64-linux-gnu-gcc -g -o asndisc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asndisc.c ncbithr.o -lncbiid1 \ -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm -lpthread In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asndisc.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asndisc.c: In function ‘ProcessMultipleRecord’: asndisc.c:735:19: warning: variable ‘memory_usage’ set but not used [-Wunused-but-set-variable] 735 | Boolean memory_usage = FALSE; | ^~~~~~~~~~~~ asndisc.c:733:19: warning: variable ‘detailed_report’ set but not used [-Wunused-but-set-variable] 733 | Boolean detailed_report = FALSE; | ^~~~~~~~~~~~~~~ asndisc.c:729:19: warning: variable ‘subcit’ set but not used [-Wunused-but-set-variable] 729 | SeqDescrPtr subcit = NULL; | ^~~~~~ /usr/bin/ld: warning: size of symbol `structTls' changed from 24 in ncbithr.o (symbol from plugin) to 16 in /tmp/ccnfGusS.ltrans0.ltrans.o /usr/bin/ld: warning: NOTE: size discrepancies can cause real problems. Investigation is advised. x86_64-linux-gnu-gcc -o asnmacro -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asnmacro.c -lblastapi -lblast -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asnmacro.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from asnmacro.c:54: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ asnmacro.c:147:20: warning: ‘GlobalAlign2Seq’ defined but not used [-Wunused-function] 147 | static SeqAlignPtr GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp) | ^~~~~~~~~~~~~~~ In file included from asnmacro.c:57: ../include/asnmacro.h:1376:21: warning: ‘amp’ defined but not used [-Wunused-variable] 1376 | static AsnModulePtr amp = ampx; | ^~~ ../include/asnmacro.h:1375:19: warning: ‘at’ defined but not used [-Wunused-variable] 1375 | static AsnTypePtr at = atx; | ^~ ../include/asnmacro.h:1374:23: warning: ‘avn’ defined but not used [-Wunused-variable] 1374 | static AsnValxNodePtr avn = avnx; | ^~~ ../include/asnmacro.h:12:15: warning: ‘asnfilename’ defined but not used [-Wunused-variable] 12 | static char * asnfilename = "asnmacro.h11"; | ^~~~~~~~~~~ asnmacro.c: In function ‘AsnIoFromOutputStream’: asnmacro.c:233:14: warning: ‘aip’ may be used uninitialized [-Wmaybe-uninitialized] 233 | AsnIoPtr aip; | ^~~ x86_64-linux-gnu-gcc -g -o asnval -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF asnval.c ncbithr.o -lncbiid1 \ -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm -lpthread In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from asnval.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ asnval.c: In function ‘DoLockFarComponents’: asnval.c:558:27: warning: variable ‘stop_time’ set but not used [-Wunused-but-set-variable] 558 | time_t start_time, stop_time; | ^~~~~~~~~ asnval.c:558:15: warning: variable ‘start_time’ set but not used [-Wunused-but-set-variable] 558 | time_t start_time, stop_time; | ^~~~~~~~~~ /usr/bin/ld: warning: size of symbol `structTls' changed from 24 in ncbithr.o (symbol from plugin) to 16 in /tmp/cc8f4Hgz.ltrans0.ltrans.o /usr/bin/ld: warning: NOTE: size discrepancies can cause real problems. Investigation is advised. x86_64-linux-gnu-gcc -o cleanasn -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF cleanasn.c -lblastapi -lblast -lncbiid1 \ -lncbitool -lblastcompadj -lnetcli -lncbiobj -lconnssl -lncbi \ -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cleanasn.c:45: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cleanasn.c: In function ‘FindISOJTA’: cleanasn.c:2186:17: warning: variable ‘is_issn’ set but not used [-Wunused-but-set-variable] 2186 | Boolean is_issn = FALSE; | ^~~~~~~ cleanasn.c: In function ‘JournalIsPresent’: cleanasn.c:10641:14: warning: variable ‘is_issn’ set but not used [-Wunused-but-set-variable] 10641 | Boolean is_issn = FALSE; | ^~~~~~~ cleanasn.c: In function ‘RemoveGIProc’: cleanasn.c:10946:18: warning: variable ‘nextid’ set but not used [-Wunused-but-set-variable] 10946 | SeqIdPtr nextid, sip; | ^~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/actutils.h:105, from cleanasn.c:66: ../include/objalignloc.h: At top level: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ cleanasn.c: In function ‘ReportAsnDiffs’: cleanasn.c:3907:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3907 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8330:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8330 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8333:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8333 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8359:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8359 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8388:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8388 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8446:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8446 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8449:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8449 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c: In function ‘DoValidatorReport’: cleanasn.c:8505:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8505 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8508:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8508 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:8536:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8536 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c: In function ‘CppBasicCleanup’: cleanasn.c:11556:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11556 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11560:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11560 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11586:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11586 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11588:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11588 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11590:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11590 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11592:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11592 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11594:7: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11594 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c:11604:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11604 | system (cmmd); | ^~~~~~~~~~~~~ cleanasn.c: At top level: cleanasn.c:14106:13: warning: ‘AccessionToGi’ defined but not used [-Wunused-function] 14106 | static Int4 AccessionToGi (CharPtr string) | ^~~~~~~~~~~~~ cleanasn.c:14065:16: warning: ‘PvtStrToLong’ defined but not used [-Wunused-function] 14065 | static Boolean PvtStrToLong (CharPtr str, Int4Ptr longval) | ^~~~~~~~~~~~ cleanasn.c:12099:20: warning: ‘MakeVirtualProtein’ defined but not used [-Wunused-function] 12099 | static SeqEntryPtr MakeVirtualProtein (void) | ^~~~~~~~~~~~~~~~~~ cleanasn.c:10401:13: warning: ‘CheckPubmedSI’ defined but not used [-Wunused-function] 10401 | static void CheckPubmedSI ( | ^~~~~~~~~~~~~ cleanasn.c:10219:13: warning: ‘DoUnpublishedReport’ defined but not used [-Wunused-function] 10219 | static void DoUnpublishedReport ( | ^~~~~~~~~~~~~~~~~~~ cleanasn.c:9089:19: warning: ‘DuplicateStringList’ defined but not used [-Wunused-function] 9089 | static ValNodePtr DuplicateStringList ( | ^~~~~~~~~~~~~~~~~~~ cleanasn.c:6073:16: warning: ‘IsStopWord’ defined but not used [-Wunused-function] 6073 | static Boolean IsStopWord ( | ^~~~~~~~~~ cleanasn.c:5235:13: warning: ‘FindOneCds’ defined but not used [-Wunused-function] 5235 | static void FindOneCds ( | ^~~~~~~~~~ cleanasn.c:5214:13: warning: ‘PrintSegSeqTitleAfter’ defined but not used [-Wunused-function] 5214 | static void PrintSegSeqTitleAfter ( | ^~~~~~~~~~~~~~~~~~~~~ cleanasn.c:5193:13: warning: ‘PrintSegSeqTitleBefore’ defined but not used [-Wunused-function] 5193 | static void PrintSegSeqTitleBefore ( | ^~~~~~~~~~~~~~~~~~~~~~ cleanasn.c:5178:13: warning: ‘PrintPartsTitle’ defined but not used [-Wunused-function] 5178 | static void PrintPartsTitle ( | ^~~~~~~~~~~~~~~ cleanasn.c:4899:13: warning: ‘CountParts’ defined but not used [-Wunused-function] 4899 | static void CountParts ( | ^~~~~~~~~~ cleanasn.c:4848:13: warning: ‘NormalizeSegSetTitle’ defined but not used [-Wunused-function] 4848 | static void NormalizeSegSetTitle ( | ^~~~~~~~~~~~~~~~~~~~ cleanasn.c:1910:13: warning: ‘FindSegSeq’ defined but not used [-Wunused-function] 1910 | static void FindSegSeq ( | ^~~~~~~~~~ cleanasn.c: In function ‘DoValidatorReport’: cleanasn.c:8504:25: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 508 [-Wformat-overflow=] 8504 | sprintf (cmmd, "%s -i %s -o stdout -Q 1 -r -l | sort > %s", asnval, path3, path1); | ^~ ~~~~~ In file included from /usr/include/stdio.h:980, from ../include/ncbilcl.h:154: In function ‘sprintf’, inlined from ‘DoValidatorReport’ at cleanasn.c:8504:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 36 or more bytes (assuming 8226) into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoValidatorReport’: cleanasn.c:8507:25: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 508 [-Wformat-overflow=] 8507 | sprintf (cmmd, "%s -i %s -o stdout -Q 1 -r -l | sort > %s", asnval, path4, path2); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoValidatorReport’ at cleanasn.c:8507:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 36 or more bytes (assuming 8226) into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoValidatorReport’: cleanasn.c:8510:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 504 [-Wformat-overflow=] 8510 | sprintf (cmmd, "diff -h %s %s > %s", path1, path2, path5); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoValidatorReport’ at cleanasn.c:8510:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 12298 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoValidatorReport’: cleanasn.c:8535:22: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 8535 | sprintf (cmmd, "rm %s; rm %s; rm %s; rm %s; rm %s", path1, path2, path3, path4, path5); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoValidatorReport’ at cleanasn.c:8535:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 24 and 20499 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘CppBasicCleanup’: cleanasn.c:11553:25: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 447 [-Wformat-overflow=] 11553 | sprintf (cmmd, "%s -i %s | cleanasn -a e -o %s", | ^~ 11554 | "~/ncbi_cxx/compilers/xCode/build/bin/Debug/test_basic_cleanup", 11555 | path1, path2); | ~~~~~ In function ‘sprintf’, inlined from ‘CppBasicCleanup’ at cleanasn.c:11553:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 86 and 8276 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘CppBasicCleanup’: cleanasn.c:11558:31: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 500 [-Wformat-overflow=] 11558 | sprintf (cmmd, "cleanasn -i %s -o %s -K b", | ^~ 11559 | path1, path3); | ~~~~~ In function ‘sprintf’, inlined from ‘CppBasicCleanup’ at cleanasn.c:11558:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 22 and 8212 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘CppBasicCleanup’: cleanasn.c:11593:28: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 507 [-Wformat-overflow=] 11593 | sprintf (cmmd, "diff %s %s >> ~/Desktop/diffclean.txt", path3, path2); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘CppBasicCleanup’ at cleanasn.c:11593:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 34 and 8224 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘CppBasicCleanup’: cleanasn.c:11603:22: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 11603 | sprintf (cmmd, "rm %s; rm %s; rm %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘CppBasicCleanup’ at cleanasn.c:11603:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 12299 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8445:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 508 [-Wformat-overflow=] 8445 | sprintf (cmmd, "%s -o %s -n %s -d %s", cfp->ffdiff, path1, path2, rep); | ^~ ~~~~~ cleanasn.c:8445:20: note: assuming directive output of 7 bytes 8445 | sprintf (cmmd, "%s -o %s -n %s -d %s", cfp->ffdiff, path1, path2, rep); | ^~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8445:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 13 or more bytes (assuming 8210) into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8448:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 8448 | sprintf (cmmd, "rm %s; rm %s", path1, path2); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8448:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 8199 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8358:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 507 [-Wformat-overflow=] 8358 | sprintf (cmmd, "%s %s -i %s -o %s", cfp->asn2flat, arguments, path3, path2); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8358:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 8200) into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8361:29: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 504 [-Wformat-overflow=] 8361 | sprintf (cmmd, "diff -h %s %s > %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8361:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 13 and 12298 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8387:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 8387 | sprintf (cmmd, "rm %s; rm %s; rm %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8387:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 12299 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8329:27: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 508 [-Wformat-overflow=] 8329 | sprintf (cmmd, "%s -o %s -n %s -d %s", cfp->ffdiff, path1, path2, rep); | ^~ ~~~~~ cleanasn.c:8329:20: note: assuming directive output of 7 bytes 8329 | sprintf (cmmd, "%s -o %s -n %s -d %s", cfp->ffdiff, path1, path2, rep); | ^~~~~~~~~~~~~~~~~~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8329:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output 13 or more bytes (assuming 8210) into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘DoGBFFReport’: cleanasn.c:8332:24: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 8332 | sprintf (cmmd, "rm %s; rm %s", path1, path2); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘DoGBFFReport’ at cleanasn.c:8332:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 8199 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘ReportAsnDiffs’: cleanasn.c:3872:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 501 [-Wformat-overflow=] 3872 | sprintf (cmmd, "diff -b -h %s %s > %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘ReportAsnDiffs’ at cleanasn.c:3872:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 16 and 12301 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cleanasn.c: In function ‘ReportAsnDiffs’: cleanasn.c:3906:22: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 509 [-Wformat-overflow=] 3906 | sprintf (cmmd, "rm %s; rm %s; rm %s", path1, path2, path3); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘ReportAsnDiffs’ at cleanasn.c:3906:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 14 and 12299 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -o insdseqget -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF insdseqget.c -lncbiid1 -lnetcli \ -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi \ -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from insdseqget.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -g -o nps2gps -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF nps2gps.c -lncbitool -lblastcompadj \ -lncbiobj -lconnssl -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from nps2gps.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ nps2gps.c: In function ‘LclMakeOneRnaTitle’: nps2gps.c:422:22: warning: variable ‘cds’ set but not used [-Wunused-but-set-variable] 422 | SeqFeatPtr cds; | ^~~ nps2gps.c: In function ‘MakeIdFromLocation’: nps2gps.c:706:16: warning: variable ‘altid’ set but not used [-Wunused-but-set-variable] 706 | ValNodePtr altid; | ^~~~~ nps2gps.c: In function ‘LoopThroughCDSs’: nps2gps.c:1221:22: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 1221 | Int2 count; | ^~~~~ nps2gps.c: In function ‘NPStoGPS’: nps2gps.c:1891:39: warning: variable ‘lastmrna’ set but not used [-Wunused-but-set-variable] 1891 | SeqFeatPtr cds, gene, mrna, lastmrna, sfp, lastsfp; | ^~~~~~~~ nps2gps.c: At top level: nps2gps.c:589:17: warning: ‘MakeIdFromLocusTag’ defined but not used [-Wunused-function] 589 | static SeqIdPtr MakeIdFromLocusTag ( | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -o spidey -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF spideymain.c -lncbiid1 -lncbitool \ -lblastcompadj -lnetcli -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from spideymain.c:79: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from ../include/samutil.h:234, from ../include/alignmgr2.h:114, from ../include/spidey.h:103, from spideymain.c:80: ../include/objalignloc.h:80:27: warning: ‘Loc_locFree’ declared ‘static’ but never defined [-Wunused-function] 80 | static Loc_locPtr LIBCALL Loc_locFree PROTO ((Loc_locPtr )); | ^~~~~~~~~~~ ../include/objalignloc.h:81:27: warning: ‘Loc_locAsnRead’ declared ‘static’ but never defined [-Wunused-function] 81 | static Loc_locPtr LIBCALL Loc_locAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~ ../include/objalignloc.h:82:24: warning: ‘Loc_locAsnWrite’ declared ‘static’ but never defined [-Wunused-function] 82 | static Boolean LIBCALL Loc_locAsnWrite PROTO (( Loc_locPtr , AsnIoPtr, AsnTypePtr)); | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -o trna2sap -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF trna2sap.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from trna2sap.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ trna2sap.c: In function ‘ProcessOneRecord’: trna2sap.c:290:28: warning: unused variable ‘entityID’ [-Wunused-variable] 290 | Uint2 datatype, entityID = 0; | ^~~~~~~~ trna2sap.c: In function ‘Nlm_Main’: trna2sap.c:460:12: warning: variable ‘tsp’ set but not used [-Wunused-but-set-variable] 460 | T2SPtr tsp; | ^~~ x86_64-linux-gnu-gcc -g -o trna2tbl -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF trna2tbl.c -lncbitool -lblastcompadj \ -lncbiobj -lncbi -lm trna2tbl.c: In function ‘RunTrnaScan’: trna2tbl.c:142:13: warning: unused variable ‘str’ [-Wunused-variable] 142 | Char str [80]; | ^~~ trna2tbl.c:139:13: warning: unused variable ‘speed’ [-Wunused-variable] 139 | CharPtr speed; | ^~~~~ trna2tbl.c:127:13: warning: unused variable ‘cmmd’ [-Wunused-variable] 127 | Char cmmd [256]; | ^~~~ trna2tbl.c: At top level: trna2tbl.c:232:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 232 | main (int argc, char *argv[]) | ^~~~ /usr/bin/ld: ../shlib/libncbi.so: warning: the 're_max_failures' variable is obsolete and will go away. x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" cn3dmain.c In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from cn3dmain.c:210: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ cn3dmain.c: In function ‘OpenMimeFile’: cn3dmain.c:237:5: warning: "/*" within comment [-Wcomment] 237 | /* the Web browsers on other platforms get upset if you delete the file, */ | cn3dmain.c: In function ‘NetConfigureProc’: cn3dmain.c:267:13: warning: unused variable ‘netCurrentlyOn’ [-Wunused-variable] 267 | Boolean netCurrentlyOn = FALSE; | ^~~~~~~~~~~~~~ cn3dmain.c: In function ‘Cn3D_PrintImage’: cn3dmain.c:288:10: warning: variable ‘pmldVec’ set but not used [-Wunused-but-set-variable] 288 | PMLD pmldVec = NULL; | ^~~~~~~ cn3dmain.c:284:11: warning: unused variable ‘pdnmlFirst’ [-Wunused-variable] 284 | PDNML pdnmlFirst = NULL; | ^~~~~~~~~~ cn3dmain.c: In function ‘Nlm_Main’: cn3dmain.c:334:13: warning: unused variable ‘netCurrentlyOn’ [-Wunused-variable] 334 | Boolean netCurrentlyOn = FALSE; | ^~~~~~~~~~~~~~ cn3dmain.c: At top level: cn3dmain.c:246:25: warning: ‘seqedprocs’ defined but not used [-Wunused-variable] 246 | static SeqEditViewProcs seqedprocs; | ^~~~~~~~~~ x86_64-linux-gnu-gcc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -I../include -DWIN_MOTIF -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF netentcf.c -o netentcf In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25, from ../include/ncbilcl.h:150, from ../include/ncbi.h:57, from ../include/vibtypes.h:94, from ../include/vibrant.h:124, from netentcf.c:41: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ x86_64-linux-gnu-gcc -o Cn3D -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/ncbi-tools6-6.1.20170106+dfsg1-10.1 -Wall -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include -L../shlib -DWIN_MOTIF cn3dmain.o -lvibnet -lncbicn3dOGL -lncbidesk \ -lddvlib -lncbimmdb -lncbiNacc -lnetentr \ -lvibrantOGL -lncbiobj -lncbi /usr/bin/ld: ../shlib/libncbi.so: warning: the 're_max_failures' variable is obsolete and will go away. make[3]: Leaving directory '/<>/build' make[2]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp make[1]: Leaving directory '/<>' dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/<>' install -d debian/tmp/usr/lib/x86_64-linux-gnu install -m 644 lib/* shlib/*.so.6.1.20170106 debian/tmp/usr/lib/x86_64-linux-gnu for x in ncbiacc ncbiCacc netentr; do \ rm -f debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so.6.1.20170106 && \ ln -s libncbiNacc.so.6 \ debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so.6 && \ ln -s libncbiNacc.so debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so; \ done for x in ncbicn3d vibrant; do \ rm -f debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so.6.1.20170106 && \ ln -s lib${x}OGL.so.6 \ debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so.6 && \ ln -s lib${x}OGL.so debian/tmp/usr/lib/x86_64-linux-gnu/lib$x.so; \ done rm -f debian/tmp/usr/lib/x86_64-linux-gnu/libregexp.* cd debian/tmp/usr/lib/x86_64-linux-gnu && \ for f in *.so.6.1.20170106; do \ base=`basename $f .so.6.1.20170106` && \ ln -s $f $base.so.6 && \ ln -s $f $base.so; \ done install -d debian/tmp/usr/include/ncbi cp -LRp include/* debian/tmp/usr/include/ncbi cd debian/tmp/usr/include/ncbi && \ rm -f FSpCompat.h FullPath.h More*.h Optimization*.h pcre*.h find debian/tmp/usr/include -type f | xargs chmod 644 install -d debian/tmp/usr/bin install `find build -type f -perm /111 -print` debian/tmp/usr/bin rm -f debian/tmp/usr/bin/*test* rm -f debian/tmp/usr/bin/*demo* rm -f debian/tmp/usr/bin/dosimple rm -f debian/tmp/usr/bin/ncbisort rm -f debian/tmp/usr/bin/cdscan rm -f debian/tmp/usr/bin/entrcmd mv debian/tmp/usr/bin/Cn3D debian/tmp/usr/bin/Cn3D-3.0 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/<>' convert link/mswin/asntool.ico debian/asntool.xpm icotool -x -w 32 -b 32 -o - link/mswin/ncbilogo.ico | \ convert png:- debian/ncbilogo.xpm install -d debian/ncbi-data/etc/ncbi install -m 644 debian/.*rc debian/ncbi-data/etc/ncbi install -d debian/ncbi-data/usr/bin install debian/vibrate debian/ncbi-data/usr/bin install -d debian/ncbi-data/usr/share/ncbi/data install -m 644 data/* debian/ncbi-data/usr/share/ncbi/data install -d debian/ncbi-rrna-data/usr/share/ncbi/data mv debian/ncbi-data/usr/share/ncbi/data/*_[n9]*.n?? \ debian/ncbi-data/usr/share/ncbi/data/rRNA*.nal \ debian/ncbi-data/usr/share/ncbi/data/Combined16SrRNA.n?? \ debian/ncbi-rrna-data/usr/share/ncbi/data/ install -d debian/ncbi-data/usr/share/pixmaps install -m 644 debian/asntool.xpm debian/ncbilogo.xpm debian/ncbi-data/usr/share/pixmaps for w in 16 32 48 256; do \ d=${w}x${w} && \ install -d debian/ncbi-data/usr/share/icons/hicolor/$d && \ icotool -x -w $w -b 32 -o debian/ncbi-data/usr/share/icons/hicolor/$d/ncbilogo.png link/mswin/ncbilogo.ico \ || exit 1 ; \ done make[1]: Leaving directory '/<>' dh_install debian/rules override_dh_installdocs-arch make[1]: Entering directory '/<>' dh_installdocs install -m 644 config/README \ debian/libncbi6t64/usr/share/doc/libncbi6t64/README.config install -m 644 network/nsclilib/readme \ debian/libncbi6t64/usr/share/doc/libncbi6t64/README.net-cfg install -m 644 doc/fa2htgs/README \ debian/ncbi-tools-bin/usr/share/doc/ncbi-tools-bin/README.fa2htgs install -m 644 sequin/README \ debian/ncbi-tools-x11/usr/share/doc/ncbi-tools-x11/README.sequin make[1]: Leaving directory '/<>' dh_installdocs -Nlibncbi6t64 -Nlibncbi6-dev -Nncbi-tools-bin -Nncbi-tools-x11 -Nncbi-cn3d -Nlibvibrant6t64 -Nlibvibrant6-dev debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs -k README make[1]: Leaving directory '/<>' dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_link # otherwise runs too late to influence debian/installman chmod +x debian/installman debian/installman ncbi-cn3d debian/installman ncbi-tools-bin debian/installman ncbi-tools-x11 debian/installman ncbi-data dh_installman make[1]: Leaving directory '/<>' debian/rules override_dh_installmenu-arch make[1]: Entering directory '/<>' chmod +x debian/makemenu debian/makemenu debian/ncbi-cn3d.install debian/makemenu debian/ncbi-tools-x11.install dh_installmenu make[1]: Leaving directory '/<>' dh_installmime dh_lintian dh_icons dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/ncbi-tools-bin/usr/bin/checksub: Unknown DWARF DW_FORM_0x1f21 4a93310d0b6321e502cfd5a5473d46fa70b20a3b debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 e159e96915ee3d65142c0aa19aa6e4db7d043600 9122bab3f7d27783a5364103daf3095c302af3be debugedit: debian/ncbi-tools-bin/usr/bin/findspl: Unknown DWARF DW_FORM_0x1f21 999a979f7936d25569390caa50ceae02a6ae17d6 debugedit: debian/libvibrant6t64/usr/lib/x86_64-linux-gnu/libncbidesk.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/ncbi-tools-bin/usr/bin/asntool: Unknown DWARF DW_FORM_0x1f20 f22a8f92f7eff18ff42f0ecb02a837a7ca545cfb b8535af4d7a289375043c2c79e7054cb0b54e7b6 debugedit: debian/ncbi-tools-bin/usr/bin/asndisc: Unknown DWARF DW_FORM_0x1f20 9117443238d34c4e919f500a5c2de604aacd027a debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbitxc2.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 f7bf4dd70649fedd35677f4cc7c3c07b6fc6d3f3 debugedit: debian/ncbi-tools-bin/usr/bin/asnmacro: Unknown DWARF DW_FORM_0x1f21 eab73ad972ab0bc46bc667bc41da83e00cd4de5d debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 debugedit: debian/ncbi-tools-bin/usr/bin/spidey: Unknown DWARF DW_FORM_0x1f20 56cfde4ecae13d973f064b322f795d97d57b1201 debugedit: debian/ncbi-tools-bin/usr/bin/cleanasn: Unknown DWARF DW_FORM_0x1f20 b5c7b98979d8d5a050273c8150c5eb3baba062d8 a22378f2d3f2ce067bfaa4ba541a3fe97ee08c9f debugedit: debian/ncbi-tools-bin/usr/bin/fa2htgs: Unknown DWARF DW_FORM_0x1f20 699853ab50a730150175f3bdbe9a17df05185c97 debugedit: debian/ncbi-tools-bin/usr/bin/sortbyquote: Unknown DWARF DW_FORM_0x1f21 102a36a2757553ea41ed05b97620324a26aff075 debugedit: debian/ncbi-tools-bin/usr/bin/getpub: Unknown DWARF DW_FORM_0x1f21 23d98e0c6497c62030a491486786b3ff0225fb29 debugedit: debian/ncbi-tools-bin/usr/bin/asn2all: Unknown DWARF DW_FORM_0x1f21 92d25430fc50fdaf6160aff845f5ac823a16614a debugedit: debian/ncbi-tools-bin/usr/bin/debruijn: Unknown DWARF DW_FORM_0x1f21 933dc3d1efa385f079422cb29d5a73c6d27195e6 debugedit: debian/ncbi-tools-bin/usr/bin/asn2xml: Unknown DWARF DW_FORM_0x1f21 1e08b122ccc24954ddb71197eaa9997e2efb371c debugedit: debian/ncbi-tools-bin/usr/bin/idfetch: Unknown DWARF DW_FORM_0x1f20 8eed2596af7820c8f3e30aa2f02dfce24882ea2b debugedit: debian/ncbi-tools-bin/usr/bin/asn2asn: Unknown DWARF DW_FORM_0x1f21 74c4e44953fae85d6331109ab7e9cde5c75c850b debugedit: debian/ncbi-tools-bin/usr/bin/getmesh: Unknown DWARF DW_FORM_0x1f21 8f3775815ddad1deb5484a34471da25e8e7b34b5 debugedit: debian/ncbi-tools-bin/usr/bin/errhdr: Unknown DWARF DW_FORM_0x1f21 db7ca5a27128681b69f2a1c34a317ff9656bcec0 debugedit: debian/ncbi-tools-bin/usr/bin/nps2gps: Unknown DWARF DW_FORM_0x1f21 ce99985184b29289705bcc7f05f30d491e0210aa debugedit: debian/libvibrant6t64/usr/lib/x86_64-linux-gnu/libncbicn3dOGL.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 6ac18ebfd05787c72b6347839b5e84a3b344131a debugedit: debian/ncbi-tools-bin/usr/bin/asnval: Unknown DWARF DW_FORM_0x1f20 9f5621110bfa563b7cf532a023fdbc01b0dd6433 debugedit: debian/ncbi-tools-bin/usr/bin/indexpub: Unknown DWARF DW_FORM_0x1f21 6c8754c920dc9714146bb625218883c7e8e940a7 debugedit: debian/libvibrant6t64/usr/lib/x86_64-linux-gnu/libvibnet.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 a7c74ba6ca89d8068ebdab522900d066dc8f43c6 debugedit: debian/ncbi-tools-bin/usr/bin/asn2ff: Unknown DWARF DW_FORM_0x1f21 58b53ab9f186911fb6e1752ce21dd3c462ea2d9b debugedit: debian/ncbi-tools-bin/usr/bin/vecscreen: Unknown DWARF DW_FORM_0x1f21 37233b55ed0b58bb60656a6878bba3bd5361bb86 debugedit: debian/libvibrant6t64/usr/lib/x86_64-linux-gnu/libvibrantOGL.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 a90a265194f4120ffc5c7a54bed4f8c5dec29e94 debugedit: debian/ncbi-tools-bin/usr/bin/gbseqget: Unknown DWARF DW_FORM_0x1f21 5337ce35854e7d90dde0bdc97b15ed026f6e3acf debugedit: debian/ncbi-tools-bin/usr/bin/asn2fsa: Unknown DWARF DW_FORM_0x1f20 da1ad9e4f58e2308b0bdedcb6b2a9cc178398051 debugedit: debian/ncbi-tools-bin/usr/bin/trna2tbl: Unknown DWARF DW_FORM_0x1f20 65b377e8fc02f44522b02b8322f6cf4174c906db debugedit: debian/ncbi-tools-bin/usr/bin/trna2sap: Unknown DWARF DW_FORM_0x1f21 38ee9752204baf625d277eebc3bc21615e8d32ca debugedit: debian/ncbi-tools-bin/usr/bin/asn2gb: Unknown DWARF DW_FORM_0x1f20 ea53c6e288401294c8138bfdae4443caf0890de0 debugedit: debian/ncbi-tools-bin/usr/bin/asn2idx: Unknown DWARF DW_FORM_0x1f21 803c42fc2aa83a0c49c49c4bbc5fc17a5636f6f8 debugedit: debian/ncbi-tools-bin/usr/bin/gil2bin: Unknown DWARF DW_FORM_0x1f21 5681d3595ad0460456a14cbd3f4ea3103e7e07c0 debugedit: debian/libvibrant6t64/usr/lib/x86_64-linux-gnu/libddvlib.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 8536ccb1df44741a65eb6c0338527787d560f755 debugedit: debian/ncbi-tools-bin/usr/bin/makeset: Unknown DWARF DW_FORM_0x1f21 20b904e182ef28f894b204fa45494b50524fcec6 debugedit: debian/ncbi-tools-bin/usr/bin/tbl2asn: Unknown DWARF DW_FORM_0x1f20 6034f0d95e058d5c5cff1c34d2970eaa4b89507c debugedit: debian/ncbi-tools-bin/usr/bin/asndhuff: Unknown DWARF DW_FORM_0x1f21 2968d126f4a66825d82ffaa5314be4b258177736 debugedit: debian/ncbi-tools-bin/usr/bin/insdseqget: Unknown DWARF DW_FORM_0x1f21 ae6e64a06ba4c0ecaceac9203c23b5d213002739 debugedit: debian/ncbi-tools-bin/usr/bin/subfuse: Unknown DWARF DW_FORM_0x1f21 cb3e3dc8dc35f7900757ce981361661681accd48 debugedit: debian/ncbi-tools-bin/usr/bin/gene2xml: Unknown DWARF DW_FORM_0x1f21 aa007e94f5efb0738bd5f854b76ef37b91d81119 debugedit: debian/ncbi-tools-bin/usr/bin/taxblast: Unknown DWARF DW_FORM_0x1f21 39596fc5d06d8874cd66ee482350156c006a85c2 debugedit: debian/ncbi-tools-x11/usr/bin/ddv: Unknown DWARF DW_FORM_0x1f20 fd732c0263388e0d21ca787bf1abc8d77dc5219e debugedit: debian/ncbi-tools-x11/usr/bin/Psequin: Unknown DWARF DW_FORM_0x1f21 68846b0aa74b1f36dd00d701a2eab7ac1ba28eec debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbiNacc.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 72e5fc3c00ec324870b2e40cbe23f4e657b5abe9 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbitool.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 339e9a0fc2b4dcbf7265e93aa7bf9bf4ec44e032 debugedit: debian/ncbi-tools-x11/usr/bin/sbtedit: Unknown DWARF DW_FORM_0x1f20 c90656ab2a5a124cf667327748e4509923273ef9 debugedit: debian/ncbi-tools-x11/usr/bin/udv: Unknown DWARF DW_FORM_0x1f20 3a24da85fa95c98243237e19a14d6fcc23a107e5 debugedit: debian/ncbi-tools-x11/usr/bin/entrez2: Unknown DWARF DW_FORM_0x1f20 669d767ad74efc2c21716763e2902993117d1beb debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbimmdb.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 eed3fb34ae1aaa3f9f22424e5a0f1d7646eef5d1 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libconnssl.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 569e02ba0127945abd68f5aeee72cb903c26328b debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libblastapi.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 ac256b3c89bfd6fa388cb4307efbf2a3a9f6e8e8 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libnetblast.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 e0583cded082a40cc2a9a876f2d0c9431112d84c debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbimla.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 ef1b2d83e44c1c8a0556caa2b7a93327ab5ab2e3 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libblast.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 a230c15a7e90e7d24ddbb48b8df2343ac3b13088 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 89992a21b4d69e6b77d4c904b36e70b97b49a333 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libnetcli.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 2c68fa4e25059655e0e3664d45c8c37c63eab3e8 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libvibgif.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f21 4f4a1d334ab45c4f32357a1c35af0d0155746468 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbicdr.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 2db9ba3b6ae08775dd8cc98e59f05eb1a380d439 debugedit: debian/libncbi6t64/usr/lib/x86_64-linux-gnu/libncbiid1.so.6.1.20170106: Unknown DWARF DW_FORM_0x1f20 1d4020e28e8229b9d3adf603bd54418c7c734564 debian/rules override_dh_makeshlibs-arch make[1]: Entering directory '/<>' dh_makeshlibs -V make[1]: Leaving directory '/<>' dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol-arch make[1]: Entering directory '/<>' dh_gencontrol -pncbi-cn3d -- -v3.0.20170106+dfsg1-10.1 dh_gencontrol -Nncbi-cn3d make[1]: Leaving directory '/<>' dh_gencontrol -Nlibncbi6t64 -Nlibncbi6-dev -Nncbi-tools-bin -Nncbi-tools-x11 -Nncbi-cn3d -Nlibvibrant6t64 -Nlibvibrant6-dev dh_md5sums debian/rules override_dh_builddeb make[1]: Entering directory '/<>' dh_builddeb -pncbi-rrna-data -- -Zxz -z7 -Sextreme INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ncbi-rrna-data (in debian/ncbi-rrna-data); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ncbi-rrna-data/DEBIAN/control, package ncbi-rrna-data, directory debian/ncbi-rrna-data .. removing usr/share/doc/ncbi-rrna-data/changelog.gz Searching for duplicated docs in dependency ncbi-data... symlinking NEWS.Debian.gz in ncbi-rrna-data to file in ncbi-data symlinking changelog.Debian.gz in ncbi-rrna-data to file in ncbi-data pkgstripfiles: Running PNG optimization (using 4 cpus) for package ncbi-rrna-data ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ncbi-rrna-data' in '../ncbi-rrna-data_6.1.20170106+dfsg1-10.1_all.deb'. dh_builddeb -Nncbi-rrna-data INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ncbi-tools-bin (in debian/ncbi-tools-bin); do_strip: , oemstrip: pkgstriptranslations: processing libncbi6t64 (in debian/libncbi6t64); do_strip: , oemstrip: pkgstriptranslations: processing ncbi-cn3d (in debian/ncbi-cn3d); do_strip: , oemstrip: pkgstriptranslations: processing libvibrant6-dev (in debian/libvibrant6-dev); do_strip: , oemstrip: debian/ncbi-cn3d/usr/share/applications/Cn3D-3.0.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ncbi-tools-bin/DEBIAN/control, package ncbi-tools-bin, directory debian/ncbi-tools-bin pkgstripfiles: processing control file: debian/libncbi6t64/DEBIAN/control, package libncbi6t64, directory debian/libncbi6t64 .. removing usr/share/doc/ncbi-tools-bin/changelog.gz .. removing usr/share/doc/libncbi6t64/changelog.gz INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... Skipping arch: any to arch: all dependency to ncbi-data pkgstripfiles: Running PNG optimization (using 4 cpus) for package libncbi6t64 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libncbi6t64' in '../libncbi6t64_6.1.20170106+dfsg1-10.1_amd64.deb'. pkgstripfiles: processing control file: debian/ncbi-cn3d/DEBIAN/control, package ncbi-cn3d, directory debian/ncbi-cn3d .. removing usr/share/doc/ncbi-cn3d/changelog.gz INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libvibrant6-dev/DEBIAN/control, package libvibrant6-dev, directory debian/libvibrant6-dev .. removing usr/share/doc/libvibrant6-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstriptranslations version 154 INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... pkgstriptranslations: processing libncbi6t64-dbgsym (in debian/.debhelper/libncbi6t64/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libncbi6t64/dbgsym-root/DEBIAN/control, package libncbi6t64-dbgsym, directory debian/.debhelper/libncbi6t64/dbgsym-root dpkg-deb: building package 'libncbi6t64-dbgsym' in 'debian/.debhelper/scratch-space/build-libncbi6t64/libncbi6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... Renaming libncbi6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb to libncbi6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libncbi6-dev (in debian/libncbi6-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libncbi6-dev/DEBIAN/control, package libncbi6-dev, directory debian/libncbi6-dev .. removing usr/share/doc/libncbi6-dev/changelog.gz Searching for duplicated docs in dependency libncbi6t64... symlinking NEWS.Debian.gz in libncbi6-dev to file in libncbi6t64 symlinking changelog.Debian.gz in libncbi6-dev to file in libncbi6t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libncbi6-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libncbi6-dev' in '../libncbi6-dev_6.1.20170106+dfsg1-10.1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ncbi-data (in debian/ncbi-data); do_strip: , oemstrip: INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ncbi-data/DEBIAN/control, package ncbi-data, directory debian/ncbi-data .. removing usr/share/doc/ncbi-data/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package ncbi-data ... xargs: warning: options --max-lines and --replace/-I/-i are mutually exclusive, ignoring previous --max-lines value oooINFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstripfiles: waiting for lock (ncbi-tools-bin) ... INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... o pkgstripfiles: PNG optimization (4/0) for package ncbi-data took 1 s dpkg-deb: building package 'ncbi-data' in '../ncbi-data_6.1.20170106+dfsg1-10.1_all.deb'. INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... Searching for duplicated docs in dependency libncbi6t64... symlinking NEWS.Debian.gz in ncbi-tools-bin to file in libncbi6t64 symlinking changelog.Debian.gz in ncbi-tools-bin to file in libncbi6t64 Searching for duplicated docs in dependency libncbi6t64... pkgstripfiles: Running PNG optimization (using 4 cpus) for package ncbi-tools-bin ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ncbi-tools-bin' in '../ncbi-tools-bin_6.1.20170106+dfsg1-10.1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... INFO: pkgstriptranslations version 154 INFO: pkgstripfiles: waiting for lock (ncbi-cn3d) ... pkgstriptranslations: processing ncbi-tools-bin-dbgsym (in debian/.debhelper/ncbi-tools-bin/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ncbi-tools-bin/dbgsym-root/DEBIAN/control, package ncbi-tools-bin-dbgsym, directory debian/.debhelper/ncbi-tools-bin/dbgsym-root dpkg-deb: building package 'ncbi-tools-bin-dbgsym' in 'debian/.debhelper/scratch-space/build-ncbi-tools-bin/ncbi-tools-bin-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb'. Renaming ncbi-tools-bin-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb to ncbi-tools-bin-dbgsym_6.1.20170106+dfsg1-10.1_amd64.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ncbi-tools-x11 (in debian/ncbi-tools-x11); do_strip: , oemstrip: debian/ncbi-tools-x11/usr/share/applications/udv.desktop: does not have gettext domain, not stripping debian/ncbi-tools-x11/usr/share/applications/entrez2.desktop: does not have gettext domain, not stripping debian/ncbi-tools-x11/usr/share/applications/ddv.desktop: does not have gettext domain, not stripping debian/ncbi-tools-x11/usr/share/applications/sbtedit.desktop: does not have gettext domain, not stripping debian/ncbi-tools-x11/usr/share/applications/Psequin.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ncbi-tools-x11/DEBIAN/control, package ncbi-tools-x11, directory debian/ncbi-tools-x11 .. removing usr/share/doc/ncbi-tools-x11/changelog.gz INFO: pkgstripfiles: waiting for lock (libvibrant6-dev) ... 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INFO: pkgstriptranslations version 154 pkgstriptranslations: processing ncbi-cn3d-dbgsym (in debian/.debhelper/ncbi-cn3d/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ncbi-cn3d/dbgsym-root/DEBIAN/control, package ncbi-cn3d-dbgsym, directory debian/.debhelper/ncbi-cn3d/dbgsym-root dpkg-deb: building package 'ncbi-cn3d-dbgsym' in 'debian/.debhelper/scratch-space/build-ncbi-cn3d/ncbi-cn3d-dbgsym_3.0.20170106+dfsg1-10.1_amd64.deb'. 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INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libvibrant6t64-dbgsym (in debian/.debhelper/libvibrant6t64/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libvibrant6t64/dbgsym-root/DEBIAN/control, package libvibrant6t64-dbgsym, directory debian/.debhelper/libvibrant6t64/dbgsym-root dpkg-deb: building package 'libvibrant6t64-dbgsym' in 'debian/.debhelper/scratch-space/build-libvibrant6t64/libvibrant6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb'. Renaming libvibrant6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.deb to libvibrant6t64-dbgsym_6.1.20170106+dfsg1-10.1_amd64.ddeb make[1]: Leaving directory '/<>' dpkg-genbuildinfo --build=binary -O../ncbi-tools6_6.1.20170106+dfsg1-10.1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../ncbi-tools6_6.1.20170106+dfsg1-10.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from ncbi-tools6-6.1.20170106+dfsg1/debian/source/options: --single-debian-patch dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-03-01T17:57:49Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ncbi-tools6_6.1.20170106+dfsg1-10.1_amd64.changes: -------------------------------------------------- Format: 1.8 Date: Fri, 01 Mar 2024 10:43:06 +0000 Source: ncbi-tools6 Binary: libncbi6-dev libncbi6t64 libvibrant6-dev libvibrant6t64 ncbi-cn3d ncbi-data ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 Built-For-Profiles: noudeb Architecture: amd64 all Version: 6.1.20170106+dfsg1-10.1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: libncbi6-dev - NCBI libraries for biology applications (development files) libncbi6t64 - NCBI libraries for biology applications libvibrant6-dev - NCBI libraries for graphic biology applications (development file libvibrant6t64 - NCBI libraries for graphic biology applications ncbi-cn3d - 3-dimensional viewer for biological molecules ncbi-data - Platform-independent data for the NCBI toolkit ncbi-rrna-data - large rRNA BLAST databases distributed with the NCBI toolkit ncbi-tools-bin - NCBI libraries for biology applications (text-based utilities) ncbi-tools-x11 - NCBI libraries for biology applications (X-based utilities) Closes: 1064245 Changes: ncbi-tools6 (6.1.20170106+dfsg1-10.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. 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package, version 2.0. size 4359262 bytes: control archive=67105 bytes. 863 bytes, 19 lines control 2646 bytes, 33 lines md5sums 788 bytes, 16 lines shlibs 443525 bytes, 11665 lines symbols 75 bytes, 2 lines triggers Package: libncbi6t64 Source: ncbi-tools6 Version: 6.1.20170106+dfsg1-10.1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 13395 Depends: ncbi-data (= 6.1.20170106+dfsg1-10.1), libc6 (>= 2.38), libgnutls30 (>= 3.8.1) Breaks: libncbi6 (<< 6.1.20170106+dfsg1-10.1) Replaces: libncbi6 Provides: libncbi6 (= 6.1.20170106+dfsg1-10.1) Section: libs Priority: optional Multi-Arch: same Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: NCBI libraries for biology applications The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI. 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graphic biological applications. drwxr-xr-x root/root 0 2024-03-01 10:43 ./ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/include/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/include/ncbi/ -rw-r--r-- root/root 491 2019-07-29 01:01 ./usr/include/ncbi/aacomp.h -rw-r--r-- root/root 15032 2019-07-29 01:01 ./usr/include/ncbi/algorend.h -rw-r--r-- root/root 4028 2019-07-29 01:01 ./usr/include/ncbi/apparam.h -rw-r--r-- root/root 5272 2019-07-29 01:01 ./usr/include/ncbi/biosrc.h -rw-r--r-- root/root 15773 2019-07-29 01:01 ./usr/include/ncbi/bspview.h -rw-r--r-- root/root 6284 2019-07-29 01:01 ./usr/include/ncbi/cdrgn.h -rw-r--r-- root/root 16040 2019-07-29 01:01 ./usr/include/ncbi/cn3d.h -rw-r--r-- root/root 2819 2019-07-29 01:01 ./usr/include/ncbi/cn3dentr.h -rw-r--r-- root/root 7553 2019-07-29 01:01 ./usr/include/ncbi/cn3dmain.h -rw-r--r-- root/root 2391 2019-07-29 01:01 ./usr/include/ncbi/cn3dmesh.h -rw-r--r-- root/root 4737 2019-07-29 01:01 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(>= 2.38), libgl1, libglu1-mesa | libglu1, libpng16-16t64 (>= 1.6.2), libx11-6, libxm4 (>= 2.3.4), libxmu6 (>= 2:1.1.3), libxt6t64 Recommends: sensible-utils Conflicts: libvibrant6, libvibrant6a Breaks: libvibrant6b (<< 6.1.20170106+dfsg1-10.1) Replaces: libvibrant6, libvibrant6a, libvibrant6b Provides: libvibrant6b (= 6.1.20170106+dfsg1-10.1) Section: libs Priority: optional Multi-Arch: same Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: NCBI libraries for graphic biology applications This is the library for those who just want to run Vibrant applications. It also includes a wrapper (vibrate) that allows many NCBI applications to provide a GUI for selecting options. drwxr-xr-x root/root 0 2024-03-01 10:43 ./ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libddvlib.so.6 -> libddvlib.so.6.1.20170106 -rw-r--r-- root/root 121320 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libddvlib.so.6.1.20170106 lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libncbicn3d.so.6 -> libncbicn3dOGL.so.6 lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libncbicn3dOGL.so.6 -> libncbicn3dOGL.so.6.1.20170106 -rw-r--r-- root/root 184576 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libncbicn3dOGL.so.6.1.20170106 lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/lib/x86_64-linux-gnu/libncbidesk.so.6 -> libncbidesk.so.6.1.20170106 -rw-r--r-- root/root 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changelog.gz lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/share/doc/libvibrant6t64/changelog.Debian.gz -> ../libncbi6t64/changelog.Debian.gz -rw-r--r-- root/root 10310 2022-09-02 20:28 ./usr/share/doc/libvibrant6t64/copyright drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 113 2024-03-01 10:39 ./usr/share/lintian/overrides/libvibrant6t64 ncbi-cn3d_3.0.20170106+dfsg1-10.1_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 10088 bytes: control archive=933 bytes. 933 bytes, 18 lines control 326 bytes, 5 lines md5sums 198 bytes, 9 lines * postinst #!/bin/sh 72 bytes, 6 lines * prerm #!/bin/sh Package: ncbi-cn3d Source: ncbi-tools6 (6.1.20170106+dfsg1-10.1) Version: 3.0.20170106+dfsg1-10.1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 71 Depends: libncbi6t64 (<< 6.1.20170106+dfsg1.1), libncbi6t64 (>= 6.1.20170106+dfsg1), libvibrant6t64 (<< 6.1.20170106+dfsg1.1), libvibrant6t64 (>= 6.1.20170106+dfsg1), libc6 (>= 2.38) Suggests: ncbi-tools-bin, ncbi-tools-x11 Breaks: ncbi-tools-x11 (<< 6.1.20170106+dfsg1-5~) Replaces: ncbi-tools-x11 (<< 6.1.20170106+dfsg1-5~) Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: 3-dimensional viewer for biological molecules Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. drwxr-xr-x root/root 0 2024-03-01 10:43 ./ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/bin/ -rwxr-xr-x root/root 18584 2024-03-01 10:43 ./usr/bin/Cn3D-3.0 drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/lib/mime/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/lib/mime/packages/ -rw-r--r-- 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ncbi-data_6.1.20170106+dfsg1-10.1_all.deb ----------------------------------------- new Debian package, version 2.0. size 4394608 bytes: control archive=3387 bytes. 40 bytes, 2 lines conffiles 524 bytes, 14 lines control 7563 bytes, 108 lines md5sums Package: ncbi-data Source: ncbi-tools6 Version: 6.1.20170106+dfsg1-10.1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 24832 Section: libs Priority: optional Multi-Arch: foreign Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: Platform-independent data for the NCBI toolkit This package contains support files needed by the NCBI toolkit on all platforms. drwxr-xr-x root/root 0 2024-03-01 10:43 ./ drwxr-xr-x root/root 0 2024-03-01 10:43 ./etc/ lrwxrwxrwx root/root 0 2024-03-01 10:43 ./etc/.ncbirc -> ncbi/.ncbirc drwxr-xr-x root/root 0 2024-03-01 10:43 ./etc/ncbi/ -rw-r--r-- root/root 1268 2024-03-01 10:43 ./etc/ncbi/.ncbirc -rw-r--r-- root/root 10951 2024-03-01 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10:43 ./usr/share/pixmaps/ncbilogo.xpm ncbi-rrna-data_6.1.20170106+dfsg1-10.1_all.deb ---------------------------------------------- new Debian package, version 2.0. size 46272056 bytes: control archive=1272 bytes. 944 bytes, 21 lines control 1405 bytes, 18 lines md5sums Package: ncbi-rrna-data Source: ncbi-tools6 Version: 6.1.20170106+dfsg1-10.1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 351534 Depends: ncbi-data Recommends: ncbi-blast+ Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: large rRNA BLAST databases distributed with the NCBI toolkit This package contains some ribosomal RNA BLAST databases distributed as part of the NCBI C Toolkit that are too large and specialized to include in ncbi-data. Specifically, it contains the databases Combined16SrRNA, LSURef_93.fasta, LSU_nomito_nochloro_noplastid, SSURef_93.fasta, and SSU_nomito_nochloro_noplastid, along with alias files to facilitate searching some of them in conjunction with databases included in ncbi-data. drwxr-xr-x root/root 0 2024-03-01 10:43 ./ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/doc/ncbi-rrna-data/ lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/share/doc/ncbi-rrna-data/NEWS.Debian.gz -> ../ncbi-data/NEWS.Debian.gz lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/share/doc/ncbi-rrna-data/README.gz -> changelog.gz lrwxrwxrwx root/root 0 2024-03-01 10:43 ./usr/share/doc/ncbi-rrna-data/changelog.Debian.gz -> ../ncbi-data/changelog.Debian.gz -rw-r--r-- root/root 10310 2022-09-02 20:28 ./usr/share/doc/ncbi-rrna-data/copyright drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/ncbi/ drwxr-xr-x root/root 0 2024-03-01 10:43 ./usr/share/ncbi/data/ -rw-r--r-- root/root 35554937 2024-03-01 10:43 ./usr/share/ncbi/data/Combined16SrRNA.nhr -rw-r--r-- root/root 2642992 2024-03-01 10:43 ./usr/share/ncbi/data/Combined16SrRNA.nin -rw-r--r-- root/root 84038286 2024-03-01 10:43 ./usr/share/ncbi/data/Combined16SrRNA.nsq -rw-r--r-- root/root 1634928 2024-03-01 10:43 ./usr/share/ncbi/data/LSURef_93.fasta.nhr -rw-r--r-- root/root 121600 2024-03-01 10:43 ./usr/share/ncbi/data/LSURef_93.fasta.nin -rw-r--r-- root/root 7333878 2024-03-01 10:43 ./usr/share/ncbi/data/LSURef_93.fasta.nsq -rw-r--r-- root/root 1548626 2024-03-01 10:43 ./usr/share/ncbi/data/LSU_nomito-nochloro-noplastid.nhr -rw-r--r-- root/root 111712 2024-03-01 10:43 ./usr/share/ncbi/data/LSU_nomito-nochloro-noplastid.nin -rw-r--r-- root/root 6762870 2024-03-01 10:43 ./usr/share/ncbi/data/LSU_nomito-nochloro-noplastid.nsq -rw-r--r-- root/root 33050471 2024-03-01 10:43 ./usr/share/ncbi/data/SSURef_93.fasta.nhr -rw-r--r-- root/root 2448872 2024-03-01 10:43 ./usr/share/ncbi/data/SSURef_93.fasta.nin -rw-r--r-- root/root 75568499 2024-03-01 10:43 ./usr/share/ncbi/data/SSURef_93.fasta.nsq -rw-r--r-- root/root 31535519 2024-03-01 10:43 ./usr/share/ncbi/data/SSU_nomito_nochloro_noplastid.nhr -rw-r--r-- root/root 2435044 2024-03-01 10:43 ./usr/share/ncbi/data/SSU_nomito_nochloro_noplastid.nin -rw-r--r-- root/root 75130397 2024-03-01 10:43 ./usr/share/ncbi/data/SSU_nomito_nochloro_noplastid.nsq -rw-r--r-- root/root 248 2024-03-01 10:43 ./usr/share/ncbi/data/rRNA_blast.nal -rw-r--r-- root/root 99 2024-03-01 10:43 ./usr/share/ncbi/data/rRNAstrand.nal ncbi-tools-bin_6.1.20170106+dfsg1-10.1_amd64.deb ------------------------------------------------ new Debian package, version 2.0. size 1892792 bytes: control archive=3320 bytes. 1034 bytes, 20 lines control 6322 bytes, 97 lines md5sums Package: ncbi-tools-bin Source: ncbi-tools6 Version: 6.1.20170106+dfsg1-10.1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3702 Depends: libncbi6t64 (<< 6.1.20170106+dfsg1.1), libncbi6t64 (>= 6.1.20170106+dfsg1), libc6 (>= 2.38) Suggests: libvibrant6t64, ncbi-blast+, ncbi-cn3d, ncbi-tools-x11 Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: NCBI libraries for biology applications (text-based utilities) This package includes various utilities distributed with the NCBI C SDK, including the development tools asntool and errhdr (formerly of libncbi6-dev). None of the programs in this package require X; you can find the X-based utilities in the ncbi-tools-x11 package. 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Team Installed-Size: 2723 Depends: libncbi6t64 (<< 6.1.20170106+dfsg1.1), libncbi6t64 (>= 6.1.20170106+dfsg1), libvibrant6t64 (<< 6.1.20170106+dfsg1.1), libvibrant6t64 (>= 6.1.20170106+dfsg1), ncbi-cn3d, libc6 (>= 2.38) Suggests: ncbi-tools-bin Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/ Description: NCBI libraries for biology applications (X-based utilities) This package includes some X-based utilities distributed with the NCBI C SDK: Network Entrez, Sequin, ddv, and udv. 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./usr/share/man/man1/udv.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1927504 Build-Time: 979 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 13 Job: ncbi-tools6_6.1.20170106+dfsg1-10.1.dsc Machine Architecture: amd64 Package: ncbi-tools6 Package-Time: 996 Source-Version: 6.1.20170106+dfsg1-10.1 Space: 1927504 Status: successful Version: 6.1.20170106+dfsg1-10.1 -------------------------------------------------------------------------------- Finished at 2024-03-01T17:57:49Z Build needed 00:16:36, 1927504k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27858619 Scanning for processes to kill in build PACKAGEBUILD-27858619