https://launchpad.net/ubuntu/+source/phast/1.6+dfsg-4/+build/27585349 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-s390x-017 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~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... 22 Dec 23:45:01 ntpdate[1895]: adjust time server 10.211.37.1 offset -0.000450 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27585349 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27585349 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27585349 Starting target for build PACKAGEBUILD-27585349 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27585349 '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-27585349 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27585349 Updating target for build PACKAGEBUILD-27585349 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [240 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1337 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.7 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6040 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [56.7 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [29.4 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [219 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [114 kB] Fetched 23.5 MB in 4s (6385 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils coreutils cpp cpp-13 debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblzma5 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps readline-common systemd systemd-dev systemd-sysv sysvinit-utils tar ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 130 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 95.5 MB of archives. After this operation, 7373 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.38-3ubuntu1 [1626 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.38-3ubuntu1 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-dev s390x 1.3.4+ds-1build1 [225 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgssapi-krb5-2 s390x 1.20.1-5build1 [146 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5-3 s390x 1.20.1-5build1 [354 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libk5crypto3 s390x 1.20.1-5build1 [89.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5support0 s390x 1.20.1-5build1 [34.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libssl3 s390x 3.0.10-1ubuntu3 [1625 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc3 s390x 1.3.4+ds-1build1 [100 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3 [44.4 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-libc-dev s390x 6.6.0-14.14 [1576 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 13.2.0-9ubuntu1 [50.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.41.50.20231214-1ubuntu1 [84.0 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.41.50.20231214-1ubuntu1 [88.1 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.41.50.20231214-1ubuntu1 [2387 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.41.50.20231214-1ubuntu1 [421 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.41.50.20231214-1ubuntu1 [230 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.41.50.20231214-1ubuntu1 [3062 B] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-9ubuntu1 [45.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 13.2.0-9ubuntu1 [35.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 13.2.0-9ubuntu1 [146 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 13.2.0-9ubuntu1 [31.3 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 13.2.0-9ubuntu1 [9382 B] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 13.2.0-9ubuntu1 [2852 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 13.2.0-9ubuntu1 [1112 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-9ubuntu1 [10.2 MB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-9ubuntu1 [2426 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-9ubuntu1 [1003 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-9ubuntu1 [17.6 MB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-9ubuntu1 [8794 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 13.2.0-9ubuntu1 [875 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g s390x 1:1.3.dfsg-3ubuntu1 [75.3 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.41.50.20231214-1ubuntu1 [13.1 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.38-3ubuntu1 [2839 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu5 [73.6 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.14 [89.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu1 [855 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x bsdutils s390x 1:2.39.2-6ubuntu1 [95.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x coreutils s390x 9.4-2ubuntu1 [1501 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.4.5-0.1 [133 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0~alpha2-0ubuntu7 [49.6 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-1 [5512 B] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.3-3 [15.7 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libaudit1 s390x 1:3.1.2-1 [48.7 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libblkid1 s390x 2.39.2-6ubuntu1 [126 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x libkmod2 s390x 30+20230601-2ubuntu1 [54.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libselinux1 s390x 3.5-1build2 [83.5 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libmount1 s390x 2.39.2-6ubuntu1 [137 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.2-9.1ubuntu1 [66.0 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libseccomp2 s390x 2.5.4-2ubuntu1 [52.2 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255-1ubuntu1 [11.7 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255-1ubuntu1 [98.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255-1ubuntu1 [3581 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255-1ubuntu1 [2129 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libuuid1 s390x 2.39.2-6ubuntu1 [34.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libcryptsetup12 s390x 2:2.6.1-5ubuntu1 [239 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libfdisk1 s390x 2.39.2-6ubuntu1 [149 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x mount s390x 2.39.2-6ubuntu1 [118 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255-1ubuntu1 [440 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255-1ubuntu1 [174 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0 s390x 2.7.7 [962 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.34+dfsg-1.4 [357 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.2ubuntu1 [1309 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-3 [172 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-3ubuntu1 [202 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20231209-1 [196 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.36 s390x 5.36.0-10ubuntu1 [4899 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.36.0-10ubuntu1 [235 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.36.0-10ubuntu1 [1881 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3 s390x 5.3.28+dfsg2-4 [752 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6 s390x 1.23-5 [35.5 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4 s390x 1.23-5 [6538 B] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x util-linux s390x 2.39.2-6ubuntu1 [1137 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libdebconfclient0 s390x 0.271ubuntu1 [11.3 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.38-3ubuntu1 [659 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20231209-1 [25.2 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-3ubuntu1 [34.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.7 [1377 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.7 [213 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.4-1build1 [65.1 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.4-2 [22.6 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-2ubuntu2 [313 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libgnutls30 s390x 3.8.1-4ubuntu6 [937 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.2-9.1ubuntu1 [51.9 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.2-9.1ubuntu1 [291 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x init s390x 1.66ubuntu1 [6188 B] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libsmartcols1 s390x 2.39.2-6ubuntu1 [66.3 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main s390x uuid-runtime s390x 2.39.2-6ubuntu1 [33.2 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build1 [9982 B] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build1 [95.1 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20231209-1 [158 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20231209-1 [115 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-3ubuntu1 [855 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-2ubuntu1 [58.6 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20231126-1 [132 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-2ubuntu1 [722 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-5build1 [13.7 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-3 [56.2 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8 s390x 8.2-3 [167 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main s390x libsqlite3-0 s390x 3.44.2-1 [727 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main s390x openssl s390x 3.0.10-1ubuntu3 [1189 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x bsdextrautils s390x 2.39.2-6ubuntu1 [75.7 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16 s390x 1.6.40-2 [197 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.4.5-0.1 [269 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-2ubuntu1 [1118 B] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-2ubuntu1 [5172 B] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-2ubuntu1 [29.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.2ubuntu1 [1147 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.2ubuntu1 [285 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 44 [12.4 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.32.2-1 [31.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.32.2-1 [67.3 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x optipng s390x 0.7.7-3 [87.0 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu1 [37.1 kB] Preconfiguring packages ... Fetched 95.5 MB in 4s (23.8 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../00-libnsl-dev_1.3.0-3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3) over (1.3.0-2build2) ... Preparing to unpack .../01-libc6-dev_2.38-3ubuntu1_s390x.deb ... Unpacking libc6-dev:s390x (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../02-libc-dev-bin_2.38-3ubuntu1_s390x.deb ... Unpacking libc-dev-bin (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../03-libtirpc-common_1.3.4+ds-1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1build1) over (1.3.3+ds-1) ... Preparing to unpack .../04-libtirpc-dev_1.3.4+ds-1build1_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1build1) over (1.3.3+ds-1) ... Preparing to unpack .../05-libgssapi-krb5-2_1.20.1-5build1_s390x.deb ... Unpacking libgssapi-krb5-2:s390x (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../06-libkrb5-3_1.20.1-5build1_s390x.deb ... 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Setting up libproc2-0:s390x (2:4.0.4-2ubuntu1) ... Setting up libpng16-16:s390x (1.6.40-2) ... Setting up libatomic1:s390x (13.2.0-9ubuntu1) ... Setting up libncursesw6:s390x (6.4+20231209-1) ... Setting up libk5crypto3:s390x (1.20.1-5build1) ... Setting up libubsan1:s390x (13.2.0-9ubuntu1) ... Setting up uuid-runtime (2.39.2-6ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up cpp (4:13.2.0-2ubuntu1) ... Setting up libasan8:s390x (13.2.0-9ubuntu1) ... Setting up procps (2:4.0.4-2ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20231126-1) ... Setting up libkrb5-3:s390x (1.20.1-5build1) ... Setting up libbinutils:s390x (2.41.50.20231214-1ubuntu1) ... Setting up libc-dev-bin (2.38-3ubuntu1) ... Setting up openssl (3.0.10-1ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3) ... Setting up libcc1-0:s390x (13.2.0-9ubuntu1) ... Setting up libitm1:s390x (13.2.0-9ubuntu1) ... Setting up libgdbm6:s390x (1.23-5) ... Setting up libctf0:s390x (2.41.50.20231214-1ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.41.50.20231214-1ubuntu1) ... Setting up libreadline8:s390x (8.2-3) ... Setting up binutils (2.41.50.20231214-1ubuntu1) ... Setting up optipng (0.7.7-3) ... Setting up libgssapi-krb5-2:s390x (1.20.1-5build1) ... Setting up libgdbm-compat4:s390x (1.23-5) ... Setting up libgcc-13-dev:s390x (13.2.0-9ubuntu1) ... Setting up libperl5.36:s390x (5.36.0-10ubuntu1) ... Setting up libtirpc3:s390x (1.3.4+ds-1build1) ... Setting up perl (5.36.0-10ubuntu1) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-9ubuntu1) ... Setting up libdpkg-perl (1.22.2ubuntu1) ... Setting up libnsl2:s390x (1.3.0-3) ... Setting up gcc (4:13.2.0-2ubuntu1) ... Setting up dpkg-dev (1.22.2ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3) ... Setting up libc6-dev:s390x (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:s390x (13.2.0-9ubuntu1) ... Setting up g++-13 (13.2.0-9ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.14) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27585349 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27585349 --arch=s390x --dist=noble-proposed --nolog phast_1.6+dfsg-4.dsc Initiating build PACKAGEBUILD-27585349 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-s390x-017.buildd +==============================================================================+ | phast 1.6+dfsg-4 (s390x) Fri, 22 Dec 2023 23:45:26 +0000 | +==============================================================================+ Package: phast Version: 1.6+dfsg-4 Source Version: 1.6+dfsg-4 Distribution: noble-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27585349/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/phast-OSOa0C/resolver-SvyhGi' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phast_1.6+dfsg-4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phast-OSOa0C/phast-1.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-OSOa0C' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man, build-essential, fakeroot 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 [410 B] Get:5 copy:/<>/apt_archive ./ Packages [495 B] Fetched 1862 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 ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After this operation, 111 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [736 B] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libelf1 s390x 0.190-1 [68.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu1 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3build3 [819 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libmagic-mgc s390x 1:5.45-2 [305 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libmagic1 s390x 1:5.45-2 [91.6 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x file s390x 1:5.45-2 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x gettext-base s390x 0.21-14 [39.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1 [76.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x groff-base s390x 1.23.0-3 [1047 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libpipeline1 s390x 1.5.7-1 [23.4 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x man-db s390x 2.12.0-1 [1242 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x m4 s390x 1.4.19-4 [255 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x automake all 1:1.16.5-1.3 [558 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x autopoint all 0.21-14 [422 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libdebhelper-perl all 13.11.9ubuntu1 [97.7 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libtool all 2.4.7-7 [166 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x dh-autoreconf all 20 [16.1 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libdw1 s390x 0.190-1 [282 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x debugedit s390x 1:5.0-5 [47.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1 [108 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14 [911 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.11.9ubuntu1 [968 kB] Get:32 http://ftpmaster.internal/ubuntu noble/universe s390x help2man s390x 1.49.3 [201 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.11.0-2build1 [243 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libblas-dev s390x 3.11.0-2build1 [237 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 13.2.0-9ubuntu1 [565 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.11.0-2build1 [2840 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x liblapack-dev s390x 3.11.0-2build1 [5660 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-16-0 s390x 10.42-4ubuntu1 [229 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-32-0 s390x 10.42-4ubuntu1 [217 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-posix3 s390x 10.42-4ubuntu1 [6704 B] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-dev s390x 10.42-4ubuntu1 [805 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libtmglib3 s390x 3.11.0-2build1 [154 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libtmglib-dev s390x 3.11.0-2build1 [157 kB] Preconfiguring packages ... Fetched 30.6 MB in 2s (18.6 MB/s) Selecting previously unselected package libelf1:s390x. (Reading database ... 13567 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.190-1_s390x.deb ... Unpacking libelf1:s390x (0.190-1) ... Selecting previously unselected package libicu74:s390x. Preparing to unpack .../01-libicu74_74.2-1ubuntu1_s390x.deb ... Unpacking libicu74:s390x (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3build3_s390x.deb ... Unpacking libxml2:s390x (2.9.14+dfsg-1.3build3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2_s390x.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../04-libmagic1_1%3a5.45-2_s390x.deb ... Unpacking libmagic1:s390x (1:5.45-2) ... Selecting previously unselected package file. 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Setting up libblas3:s390x (3.11.0-2build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up autopoint (0.21-14) ... Setting up libgfortran5:s390x (13.2.0-9ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libicu74:s390x (74.2-1ubuntu1) ... Setting up libpcre2-posix3:s390x (10.42-4ubuntu1) ... Setting up libuchardet0:s390x (0.0.8-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:s390x (0.190-1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3build3) ... Setting up libblas-dev:s390x (3.11.0-2build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:s390x (0.190-1) ... Setting up liblapack3:s390x (3.11.0-2build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up gettext (0.21-14) ... Setting up libpcre2-dev:s390x (10.42-4ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:s390x (3.11.0-2build1) ... Setting up liblapack-dev:s390x (3.11.0-2build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libtmglib-dev:s390x (3.11.0-2build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-1) ... 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 debhelper (13.11.9ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x (s390x) Toolchain package versions: binutils_2.41.50.20231214-1ubuntu1 dpkg-dev_1.22.2ubuntu1 g++-13_13.2.0-9ubuntu1 gcc-13_13.2.0-9ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-9ubuntu1 libstdc++6_13.2.0-9ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.7 apt-utils_2.7.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu5 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.50.20231214-1ubuntu1 binutils-common_2.41.50.20231214-1ubuntu1 binutils-s390x-linux-gnu_2.41.50.20231214-1ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.4-2ubuntu1 cpp_4:13.2.0-2ubuntu1 cpp-13_13.2.0-9ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.9ubuntu1 debianutils_5.14 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.2ubuntu1 dpkg-dev_1.22.2ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-2ubuntu1 g++-13_13.2.0-9ubuntu1 gcc_4:13.2.0-2ubuntu1 gcc-13_13.2.0-9ubuntu1 gcc-13-base_13.2.0-9ubuntu1 gettext_0.21-14 gettext-base_0.21-14 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 help2man_1.49.3 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-3 libapparmor1_4.0.0~alpha2-0ubuntu7 libapt-pkg6.0_2.7.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_13.2.0-9ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-9ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41.50.20231214-1ubuntu1 libblas-dev_3.11.0-2build1 libblas3_3.11.0-2build1 libblkid1_2.39.2-6ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcap-ng0_0.8.3-3 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-9ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-5ubuntu1 libctf-nobfd0_2.41.50.20231214-1ubuntu1 libctf0_2.41.50.20231214-1ubuntu1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.11.9ubuntu1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.2ubuntu1 libdw1_0.190-1 libelf1_0.190-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.32.2-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-9ubuntu1 libgcc-s1_13.2.0-9ubuntu1 libgcrypt20_1.10.2-3ubuntu1 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-9ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu6 libgomp1_13.2.0-9ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgssapi-krb5-2_1.20.1-5build1 libhogweed6_3.9.1-2 libicu74_74.2-1ubuntu1 libidn2-0_2.3.4-1build1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libitm1_13.2.0-9ubuntu1 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-2 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 liblapack-dev_3.11.0-2build1 liblapack3_3.11.0-2build1 liblocale-gettext-perl_1.07-6 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.3-2ubuntu2 libpam-modules_1.5.2-9.1ubuntu1 libpam-modules-bin_1.5.2-9.1ubuntu1 libpam-runtime_1.5.2-9.1ubuntu1 libpam0g_1.5.2-9.1ubuntu1 libpcre2-16-0_10.42-4ubuntu1 libpcre2-32-0_10.42-4ubuntu1 libpcre2-8-0_10.42-4ubuntu1 libpcre2-dev_10.42-4ubuntu1 libpcre2-posix3_10.42-4ubuntu1 libperl5.36_5.36.0-10ubuntu1 libpipeline1_1.5.7-1 libpng16-16_1.6.40-2 libproc2-0_2:4.0.4-2ubuntu1 libreadline8_8.2-3 libseccomp2_2.5.4-2ubuntu1 libselinux1_3.5-1build2 libsemanage-common_3.5-1build1 libsemanage2_3.5-1build1 libsepol2_3.5-2 libsframe1_2.41.50.20231214-1ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.44.2-1 libss2_1.47.0-2ubuntu1 libssl3_3.0.10-1ubuntu3 libstdc++-13-dev_13.2.0-9ubuntu1 libstdc++6_13.2.0-9ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255-1ubuntu1 libsystemd0_255-1ubuntu1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtmglib-dev_3.11.0-2build1 libtmglib3_3.11.0-2build1 libtool_2.4.7-7 libubsan1_13.2.0-9ubuntu1 libuchardet0_0.0.8-1 libudev1_255-1ubuntu1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libxml2_2.9.14+dfsg-1.3build3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.0-14.14 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_44 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 mount_2.39.2-6ubuntu1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 openssl_3.0.10-1ubuntu3 optipng_0.7.7-3 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.36.0-10ubuntu1 perl-base_5.36.0-10ubuntu1 perl-modules-5.36_5.36.0-10ubuntu1 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-1 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_255-1ubuntu1 systemd-dev_255-1ubuntu1 systemd-sysv_255-1ubuntu1 sysvinit-utils_3.08-3ubuntu1 tar_1.34+dfsg-1.4 tzdata_2023c-9ubuntu1 ubuntu-keyring_2023.11.28.1 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phast Vcs-Git: https://salsa.debian.org/med-team/phast.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz c0f74aa42bbb46eebe231f0adcb642694330bedf 57936 phast_1.6+dfsg-4.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz 7f5b1adf0df0a8290be8f07117762b2bea42720e2e9b2752e54f680b187f0678 57936 phast_1.6+dfsg-4.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz 2a268ec20d4b5b60d354fae365dc5c3e 57936 phast_1.6+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWFuT0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHOIA//eyCfPTB2qbw4E7fYvodojc5OvGnTMOR2 6nI+MSWImaD5neTkVstxYQENwrQ4npV9J8jbYn2RgnIqobH22HGP4d7RBAP86mq6 543imwc1jaDZBvYB8cxR6wG+mSjZT1OnfSZ+K/2ITLvlY6v2Fu9kjAzLADLqVf4a k9+JnI0dFAjdMsP4bws+G2yAwdyIKfaiYxlZH7padlKzLWXKT0OtW37Ircy1ARMJ 8IJIKtw7iBq3Dou/sqA8OR4D271shnsw3wMZJGS+OjdMo/13J7rEOyLKd/S9weyJ T6gerJHYXoxZ2UhAFFRfmNleG93S8pCn/FDoN+THv03U1FBb0Uj7WNapgkqe1GH0 fq7o69yU7OnHAtOM58WKgxTDSbBtNfGV9jcQekWcn7kkH2dvex0xno0iFqlb7Tyy fFpmueyHVb9mWfT5FPgSKJEFqYpqKsLDJn9PDgoeyf/zGk0fE0IybVCgcbZ1NGQC oOS9QJaNT6Qs51iDk9HRQKWx0iSOsDCnXCtjThNiUuOLBCFaA+0PrAXrc+gm7GGk hu5P8NgbK6AGrOXwSh+LezURWSwbGbnN6YcjqYawNyVQ3wwWP3qsXJofRr5A28/W u1C9T0KAw9/hslivACVzYXWGIIK4XBR7hYAqnojwsVBWAAsSPVLnf6GkXoaYNMhx 2XWe92QzcyI= =iVmf -----END PGP SIGNATURE----- gpgv: Signature made Fri Dec 22 16:28:45 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting phast in /<> dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying pcre2.patch 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-27585349 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27585349 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27585349 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 phast dpkg-buildpackage: info: source version 1.6+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean cd src && make clean make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make clean ; done make[4]: Entering directory '/<>/src/lib/base' rm -f *.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' rm -f *.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' rm -f *.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' rm -f *.o make[4]: Leaving directory '/<>/src/lib/motif' rm -f /<>/src/lib/../../lib/* make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' rm -f *.o dless.help dlessP.help /<>/src/dless/../../bin/dless /<>/src/dless/../../bin/dlessP make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' rm -f *.o *.help /<>/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' rm -f *.o /<>/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' rm -f *.o *.help /<>/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' rm -f *.o /<>/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' rm -f *.o /<>/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' rm -f *.o *.help /<>/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' rm -f *.o /<>/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' rm -f *.o /<>/src/prequel/../../bin/pbsDecode /<>/src/prequel/../../bin/pbsEncode /<>/src/prequel/../../bin/pbsScoreMatrix /<>/src/prequel/../../bin/pbsTrain /<>/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' rm -f *.o *.help /<>/src/util/../../bin/all_dists /<>/src/util/../../bin/base_evolve /<>/src/util/../../bin/chooseLines /<>/src/util/../../bin/clean_genes /<>/src/util/../../bin/consEntropy /<>/src/util/../../bin/convert_coords /<>/src/util/../../bin/display_rate_matrix /<>/src/util/../../bin/draw_tree /<>/src/util/../../bin/eval_predictions /<>/src/util/../../bin/hmm_train /<>/src/util/../../bin/hmm_tweak /<>/src/util/../../bin/hmm_view /<>/src/util/../../bin/indelFit /<>/src/util/../../bin/indelHistory /<>/src/util/../../bin/maf_parse /<>/src/util/../../bin/makeHKY /<>/src/util/../../bin/modFreqs /<>/src/util/../../bin/msa_diff /<>/src/util/../../bin/msa_split /<>/src/util/../../bin/msa_view /<>/src/util/../../bin/phast /<>/src/util/../../bin/phastBias /<>/src/util/../../bin/refeature /<>/src/util/../../bin/stringiphy /<>/src/util/../../bin/treeGen /<>/src/util/../../bin/tree_doctor make[3]: Leaving directory '/<>/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/<>/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<>/src/$dir && make ; done make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make ; done make[4]: Entering directory '/<>/src/lib/base' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_eigen.c: In function ‘mat_diagonalize’: phast_eigen.c:62:3: warning: implicit declaration of function ‘dgeev_’ [-Wimplicit-function-declaration] 62 | dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl, | ^~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_markov_matrix.c: In function ‘mm_exp_higham’: phast_markov_matrix.c:288:5: warning: implicit declaration of function ‘dgebal_’ [-Wimplicit-function-declaration] 288 | dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info); | ^~~~~~~ phast_markov_matrix.c:403:3: warning: implicit declaration of function ‘dgesv_’ [-Wimplicit-function-declaration] 403 | dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info); | ^~~~~~ phast_markov_matrix.c:428:5: warning: implicit declaration of function ‘dgebak_’ [-Wimplicit-function-declaration] 428 | dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info); | ^~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_matrix.c: In function ‘mat_invert’: phast_matrix.c:263:3: warning: implicit declaration of function ‘dgetrf_’ [-Wimplicit-function-declaration] 263 | dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info); | ^~~~~~~ phast_matrix.c:273:3: warning: implicit declaration of function ‘dgetri_’ [-Wimplicit-function-declaration] 273 | dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info); | ^~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_misc.c: In function ‘make_name_hash’: phast_misc.c:672:46: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c:672:35: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~ phast_misc.c: In function ‘phast_fclose’: phast_misc.c:301:5: warning: pointer ‘f_5(D)’ used after ‘fclose’ [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to ‘fclose’ here 300 | fclose(f); | ^~~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of ‘pcre2_match_8’ differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:935:1: note: expected ‘PCRE2_SPTR8’ {aka ‘const unsigned char *’} but argument is of type ‘char *’ 935 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c: In function ‘str_re_match’: phast_stringsplus.c:532:30: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_search’: phast_stringsplus.c:538:28: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:504:52: warning: ‘ovector’ may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ phast_stringsplus.c:491:15: note: ‘ovector’ was declared here 491 | PCRE2_SIZE *ovector; | ^~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /<>/src/lib/base/../../../lib/libphast.a ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_local_alignment.c: In function ‘la_read_lav’: phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_local_alignment.c:50:44: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_maf.c: In function ‘maf_read_cats_subset’: phast_maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_msa.c: In function ‘msa_read_fasta’: phast_msa.c:264:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_msa.c:39: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:264:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^ phast_msa.c:257:40: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function ‘msa_read_seq_fasta’: phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:1929:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^ phast_msa.c: In function ‘msa_format_for_content’: phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2590:9: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2592 | fasta_re = str_re_new("^>.*"); | ^ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2593 | lav_re = str_re_new("^#:lav.*"); | ^ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2594 | maf_re = str_re_new("^##maf"); | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_multi_msa.c: In function ‘multimsa_new_from_files’: phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:54:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:36: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_sufficient_stats.c: In function ‘ss_from_msas’: phast_sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function ‘ss_read’: phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from /<>/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:661:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^ ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_bed.c: In function ‘gff_print_bed’: phast_bed.c:143:52: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_bed.c:15: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_bed.c:143:41: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_category_map.c: In function ‘cm_read’: phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:39:18: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:15: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_gff.c: In function ‘gff_read_set’: phast_gff.c:56:38: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_gff.c:13: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:56:25: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^ phast_gff.c: In function ‘gff_new_feature_genomic_pos’: phast_gff.c:272:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:272:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^ phast_gff.c: In function ‘gff_group’: phast_gff.c:688:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:688:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 688 | tag_re = str_re_new(tmpstr); | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_phylo_p_print.c: In function ‘print_feats_generic’: phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_phylo_p_print.c:752:39: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_motif.c: In function ‘mtf_print’: phast_motif.c:1411:21: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function ‘mtf_print_html’: phast_motif.c:1604:23: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_tfbs.c: In function ‘pwm_read’: phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:147:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^ phast_tfbs.c: In function ‘ms_read’: phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:229:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^ phast_tfbs.c:219:32: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/<>/src/lib/motif' make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/<>/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/exoniphy/../../lib -o /<>/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_leaves’ at ../lib/phylo/phast_trees.c:1285:3, inlined from ‘gp_set_patterns’ at ../lib/phylo_hmm/phast_gap_patterns.c:419:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘gp_set_patterns’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phastCons/../../lib -o /<>/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phastOdds/../../lib -o /<>/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/<>/src/phastMotif/../../lib -o /<>/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5, inlined from ‘mtf_free’ at ../lib/motif/phast_motif.c:1262:7: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘mtf_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloFit/../../lib -o /<>/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloBoot/../../lib -o /<>/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:405:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_create_copy’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:521:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloP/../../lib -o /<>/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:521:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/<>/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:405:3, inlined from ‘main’ at all_dists.c:101:17: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:408:3, inlined from ‘main’ at all_dists.c:101:17: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5, inlined from ‘main’ at all_dists.c:102:7: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:438:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_postorder’ at ../lib/phylo/phast_trees.c:630:5, inlined from ‘tl_compute_log_likelihood.constprop.isra’ at ../lib/phylo/phast_tree_likelihoods.c:192:23: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tl_compute_log_likelihood.constprop.isra’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tr_new_from_file’ at ../lib/phylo/phast_trees.c:55:12, inlined from ‘main’ at hmm_tweak.c:117:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tr_new_from_file’ at ../lib/phylo/phast_trees.c:55:12, inlined from ‘main’ at hmm_view.c:63:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes’ at ../lib/phylo/phast_trees.c:1318:3, inlined from ‘ih_expand’ at ../lib/phylo/phast_indel_history.c:82:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘ih_expand’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tm_new_from_file’ at ../lib/phylo/phast_tree_model.c:438:14, inlined from ‘main’ at modFreqs.c:44:9: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition msa_view.c: In function ‘fill_with_Ns’: msa_view.c:361:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from msa_view.c:14: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ msa_view.c:361:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:433:3, inlined from ‘main’ at treeGen.c:135:16: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-4 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition tree_doctor.c: In function ‘main’: tree_doctor.c:348:19: warning: the comparison will always evaluate as ‘true’ for the address of ‘name’ will never be NULL [-Waddress] 348 | if (n->name != NULL && n->name[0] != '\0' && | ^~ In file included from /<>/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /<>/src/../include/phast/trees.h:47:8: note: ‘name’ declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-4/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd test && PATH=/<>/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/<>/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi -e Passed all tests. make[2]: Leaving directory '/<>/test' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j4 install DESTDIR=/<>/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' (cd src; make install DESTDIR=/<>/debian/phast ) make[2]: Entering directory '/<>/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /<>/debian/phast/usr/bin/ mkdir -p /<>/debian/phast/usr/share/phast/data/ mkdir -p /<>/debian/phast/usr/share/man/man1/ cp ../bin/* /<>/debian/phast/usr/bin/ cp -R ../data/* /<>/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /<>/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/phast/usr/bin/convert_coords: Unknown DWARF DW_FORM_0x1f20 cff6311829b5e2ade171f13de5728f21705ddb3c debugedit: debian/phast/usr/bin/phastOdds: Unknown DWARF DW_FORM_0x1f20 fc48b8bd718c025ac57bf419b3ea22a2685f71ec debugedit: debian/phast/usr/bin/hmm_view: Unknown DWARF DW_FORM_0x1f20 bffb2152521463384c1f3e7170c191ff2ce5cd90 debugedit: debian/phast/usr/bin/base_evolve: Unknown DWARF DW_FORM_0x1f20 526567386a1d1e946f2c99638ce238d563e1421c debugedit: debian/phast/usr/bin/stringiphy: Unknown DWARF DW_FORM_0x1f20 8d006d8dd9de2e44c5b98bf5e68270d5f9cc080d debugedit: debian/phast/usr/bin/hmm_tweak: Unknown DWARF DW_FORM_0x1f20 bddff034352b7c546125a9e77a75ed7c2605d114 debugedit: debian/phast/usr/bin/eval_predictions: Unknown DWARF DW_FORM_0x1f20 cce963e35a3f9eb6d0bd79f1e37b6ccd5e3718fc debugedit: debian/phast/usr/bin/makeHKY: Unknown DWARF DW_FORM_0x1f20 52ef058e4da2116ba6f663682a9cc5929b609ea2 debugedit: debian/phast/usr/bin/refeature: Unknown DWARF DW_FORM_0x1f21 1e845a2db38b977c5aa6dd72681c4dc37a387418 debugedit: debian/phast/usr/bin/maf_parse: Unknown DWARF DW_FORM_0x1f20 63022057a64f89437c0ef365fdecf725a2ba2876 debugedit: debian/phast/usr/bin/hmm_train: Unknown DWARF DW_FORM_0x1f21 79609dcf451c0f1eef244f7cf2d13821507de2c2 debugedit: debian/phast/usr/bin/treeGen: Unknown DWARF DW_FORM_0x1f20 b53459c9dadb4db70eb1571b6c518e11679badff debugedit: debian/phast/usr/bin/chooseLines: Unknown DWARF DW_FORM_0x1f20 883603b9f1cdbf26aaebe8416d539e2a03c32427 debugedit: debian/phast/usr/bin/indelFit: Unknown DWARF DW_FORM_0x1f20 2c800f09ef3657eca6e173c1c975e7d65d0a0291 debugedit: debian/phast/usr/bin/consEntropy: Unknown DWARF DW_FORM_0x1f21 42a0621233b3fad15ef8c07e28b63632db06cee1 debugedit: debian/phast/usr/bin/exoniphy: Unknown DWARF DW_FORM_0x1f21 cf115257b7c00bb41282b7a9b10084888471347a debugedit: debian/phast/usr/bin/msa_diff: Unknown DWARF DW_FORM_0x1f20 a895834f1582fec1482c45f49275407cfcc07040 debugedit: debian/phast/usr/bin/msa_split: Unknown DWARF DW_FORM_0x1f20 972e0f0f62305c0067a9f81b0f27229af1605fed debugedit: debian/phast/usr/bin/tree_doctor: Unknown DWARF DW_FORM_0x1f20 36e13b77c07d38201c23e471553c678ac8097a46 debugedit: debian/phast/usr/bin/phastMotif: Unknown DWARF DW_FORM_0x1f20 e0f9c04b94dad9b9ef21de39377929ae2e200732 debugedit: debian/phast/usr/bin/phyloBoot: Unknown DWARF DW_FORM_0x1f20 481027f06b35d7d7e35840adf1a07155f85b97d5 debugedit: debian/phast/usr/bin/clean_genes: Unknown DWARF DW_FORM_0x1f20 24a55579568e3b929e3fc7d9dbe07fb067f5dada debugedit: debian/phast/usr/bin/phastCons: Unknown DWARF DW_FORM_0x1f20 dd8ab874e26cbed5f0c18d1381165475517ae5f7 debugedit: debian/phast/usr/bin/phyloFit: Unknown DWARF DW_FORM_0x1f21 dce8c73fa4fa4aa032c0b885b7cfe92a52924dc6 debugedit: debian/phast/usr/bin/phyloP: Unknown DWARF DW_FORM_0x1f21 b418432e529310389bf8df44cde16ee816fa935d debugedit: debian/phast/usr/bin/indelHistory: Unknown DWARF DW_FORM_0x1f21 0293dfc5b779e990026d0fd39bc18d6e6b8f1d45 debugedit: debian/phast/usr/bin/all_dists: Unknown DWARF DW_FORM_0x1f20 2dfe4b99dd9d819ffd779d5b5596e1edae49c071 debugedit: debian/phast/usr/bin/msa_view: Unknown DWARF DW_FORM_0x1f20 463c1664b5511d8c1c848a6a3b2d8aafa3a54091 debugedit: debian/phast/usr/bin/display_rate_matrix: Unknown DWARF DW_FORM_0x1f20 16b22f345523ca0e0fb2533c4d39b372d4a6ed98 debugedit: debian/phast/usr/bin/phast: Unknown DWARF DW_FORM_0x1f20 0ec0e47589cac85fa36531b84124c86bd5dd26f0 debugedit: debian/phast/usr/bin/draw_tree: Unknown DWARF DW_FORM_0x1f20 84193d7162a012551a683581fd1a99820e362b30 debugedit: debian/phast/usr/bin/phastBias: Unknown DWARF DW_FORM_0x1f20 723db11b2e7d5467dfad5f1b1a0e85d47d424914 debugedit: debian/phast/usr/bin/modFreqs: Unknown DWARF DW_FORM_0x1f20 3ed86c11b08c729f024472e78b31bfd3a47f560f dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing phast (in debian/phast); do_strip: , oemstrip: pkgstriptranslations: processing phast-dbgsym (in debian/.debhelper/phast/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/phast/DEBIAN/control, package phast, directory debian/phast pkgstripfiles: Running PNG optimization (using 4 cpus) for package phast ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-4_s390x.deb'. pkgstripfiles: processing control file: debian/.debhelper/phast/dbgsym-root/DEBIAN/control, package phast-dbgsym, directory debian/.debhelper/phast/dbgsym-root dpkg-deb: building package 'phast-dbgsym' in 'debian/.debhelper/scratch-space/build-phast/phast-dbgsym_1.6+dfsg-4_s390x.deb'. Renaming phast-dbgsym_1.6+dfsg-4_s390x.deb to phast-dbgsym_1.6+dfsg-4_s390x.ddeb dpkg-genbuildinfo --build=any -O../phast_1.6+dfsg-4_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../phast_1.6+dfsg-4_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-12-22T23:48:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.6+dfsg-4_s390x.changes: ------------------------------- Format: 1.8 Date: Wed, 29 Nov 2023 10:25:18 +0100 Source: phast Binary: phast Built-For-Profiles: noudeb Architecture: s390x Version: 1.6+dfsg-4 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: phast - phylogenetic analysis with space/time models Closes: 1056681 Changes: phast (1.6+dfsg-4) unstable; urgency=medium . [ Andreas Tille ] * s/libatlas-base-dev/liblapacke-dev/ in Build-Depends to use LAPACKE instead of clapack * Provide alternative Build-Depends to liblapack-dev and libblas-dev * Standards-Version: 4.6.2 (routine-update) * Upstream email removed from d/copyright since its bouncing . [ Sébastien Villemot ] * Complete migration away from ATLAS Closes: #1056681 Checksums-Sha1: b6364bc13c8df3496f4328e4f40d6e9a5054777b 7013738 phast-dbgsym_1.6+dfsg-4_s390x.ddeb e91ae5825e7386a7b67c049be8c780b49cfa4e6d 5970 phast_1.6+dfsg-4_s390x.buildinfo 386dbb8bc2aaf9dc32d44ec8dc5ee2a6ca9ab95d 3554568 phast_1.6+dfsg-4_s390x.deb Checksums-Sha256: 301c7c3ab7dd0c60e0bfe3e5439f483f696420c9842c7623fd99383730573c28 7013738 phast-dbgsym_1.6+dfsg-4_s390x.ddeb f82f2375c2c8f7727e621fdabfd4c0a2f9b97a0f1db4ffb0a23071f5da198265 5970 phast_1.6+dfsg-4_s390x.buildinfo fc4ac9bfae5af2cf37e3ecd0d7dc417bea507370e67b819c90fa7cd0cf21dd7c 3554568 phast_1.6+dfsg-4_s390x.deb Files: c944798d60e0ee6dc7d7175b20a972dd 7013738 debug optional phast-dbgsym_1.6+dfsg-4_s390x.ddeb 61a69ebd0847b5f843361dfded19288b 5970 science optional phast_1.6+dfsg-4_s390x.buildinfo 11e7169e5434b421cd51e935407652ca 3554568 science optional phast_1.6+dfsg-4_s390x.deb /<>/phast_1.6+dfsg-4_s390x.changes.new could not be renamed to /<>/phast_1.6+dfsg-4_s390x.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: s390x Version: 1.6+dfsg-4 Checksums-Md5: c944798d60e0ee6dc7d7175b20a972dd 7013738 phast-dbgsym_1.6+dfsg-4_s390x.ddeb 11e7169e5434b421cd51e935407652ca 3554568 phast_1.6+dfsg-4_s390x.deb Checksums-Sha1: b6364bc13c8df3496f4328e4f40d6e9a5054777b 7013738 phast-dbgsym_1.6+dfsg-4_s390x.ddeb 386dbb8bc2aaf9dc32d44ec8dc5ee2a6ca9ab95d 3554568 phast_1.6+dfsg-4_s390x.deb Checksums-Sha256: 301c7c3ab7dd0c60e0bfe3e5439f483f696420c9842c7623fd99383730573c28 7013738 phast-dbgsym_1.6+dfsg-4_s390x.ddeb fc4ac9bfae5af2cf37e3ecd0d7dc417bea507370e67b819c90fa7cd0cf21dd7c 3554568 phast_1.6+dfsg-4_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Fri, 22 Dec 2023 23:48:15 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13ubuntu5), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.50.20231214-1ubuntu1), binutils-common (= 2.41.50.20231214-1ubuntu1), binutils-s390x-linux-gnu (= 2.41.50.20231214-1ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), coreutils (= 9.4-2ubuntu1), cpp (= 4:13.2.0-2ubuntu1), cpp-13 (= 13.2.0-9ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.9ubuntu1), debianutils (= 5.14), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.2ubuntu1), dpkg-dev (= 1.22.2ubuntu1), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-2ubuntu1), g++-13 (= 13.2.0-9ubuntu1), gcc (= 4:13.2.0-2ubuntu1), gcc-13 (= 13.2.0-9ubuntu1), gcc-13-base (= 13.2.0-9ubuntu1), gettext (= 0.21-14), gettext-base (= 0.21-14), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), help2man (= 1.49.3), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-9ubuntu1), libatomic1 (= 13.2.0-9ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libbinutils (= 2.41.50.20231214-1ubuntu1), libblas-dev (= 3.11.0-2build1), libblas3 (= 3.11.0-2build1), libblkid1 (= 2.39.2-6ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.3-3), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-9ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41.50.20231214-1ubuntu1), libctf0 (= 2.41.50.20231214-1ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.9ubuntu1), libdpkg-perl (= 1.22.2ubuntu1), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-9ubuntu1), libgcc-s1 (= 13.2.0-9ubuntu1), libgcrypt20 (= 1.10.2-3ubuntu1), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 13.2.0-9ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgomp1 (= 13.2.0-9ubuntu1), libgpg-error0 (= 1.47-3build1), libgssapi-krb5-2 (= 1.20.1-5build1), libicu74 (= 74.2-1ubuntu1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-9ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack-dev (= 3.11.0-2build1), liblapack3 (= 3.11.0-2build1), liblocale-gettext-perl (= 1.07-6), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.1), 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libtmglib-dev (= 3.11.0-2build1), libtmglib3 (= 3.11.0-2build1), libtool (= 2.4.7-7), libubsan1 (= 13.2.0-9ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255-1ubuntu1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libxml2 (= 2.9.14+dfsg-1.3build3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 44), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231126-1), ncurses-base (= 6.4+20231209-1), ncurses-bin (= 6.4+20231209-1), patch (= 2.7.6-7build2), perl (= 5.36.0-10ubuntu1), perl-base (= 5.36.0-10ubuntu1), perl-modules-5.36 (= 5.36.0-10ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.34+dfsg-1.4), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.1), zlib1g (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1701249918" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast_1.6+dfsg-4_s390x.deb -------------------------- new Debian package, version 2.0. size 3554568 bytes: control archive=5856 bytes. 1190 bytes, 23 lines control 14785 bytes, 195 lines md5sums Package: phast Version: 1.6+dfsg-4 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9840 Depends: libc6 (>= 2.34), liblapack3 | liblapack.so.3, libpcre2-8-0 (>= 10.22) Section: science Priority: optional Homepage: http://compgen.cshl.edu/phast/ Description: phylogenetic analysis with space/time models PHAST is a software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. . PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison). drwxr-xr-x root/root 0 2023-11-29 09:25 ./ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/bin/ -rwxr-xr-x root/root 71960 2023-11-29 09:25 ./usr/bin/all_dists -rwxr-xr-x root/root 122896 2023-11-29 09:25 ./usr/bin/base_evolve -rwxr-xr-x root/root 10320 2023-11-29 09:25 ./usr/bin/chooseLines -rwxr-xr-x root/root 152512 2023-11-29 09:25 ./usr/bin/clean_genes -rwxr-xr-x root/root 106440 2023-11-29 09:25 ./usr/bin/consEntropy -rwxr-xr-x root/root 84048 2023-11-29 09:25 ./usr/bin/convert_coords -rwxr-xr-x root/root 108704 2023-11-29 09:25 ./usr/bin/display_rate_matrix -rwxr-xr-x root/root 63640 2023-11-29 09:25 ./usr/bin/draw_tree -rwxr-xr-x root/root 63568 2023-11-29 09:25 ./usr/bin/eval_predictions -rwxr-xr-x root/root 254520 2023-11-29 09:25 ./usr/bin/exoniphy -rwxr-xr-x root/root 129104 2023-11-29 09:25 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./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2023-11-29 09:25 ./usr/share/phast/data/phastCons/simple-coding.hmm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 106664 Build-Time: 164 Distribution: noble-proposed Host Architecture: s390x Install-Time: 6 Job: phast_1.6+dfsg-4.dsc Machine Architecture: s390x Package: phast Package-Time: 170 Source-Version: 1.6+dfsg-4 Space: 106664 Status: successful Version: 1.6+dfsg-4 -------------------------------------------------------------------------------- Finished at 2023-12-22T23:48:16Z Build needed 00:02:50, 106664k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27585349 Scanning for processes to kill in build PACKAGEBUILD-27585349