https://launchpad.net/ubuntu/+source/wise/2.4.1-24build1/+build/28014854 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-009 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 Apr 16:48:53 ntpdate[1885]: adjust time server 10.211.37.1 offset 0.000109 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28014854 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-28014854 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28014854 Starting target for build PACKAGEBUILD-28014854 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28014854 '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-28014854 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28014854 Updating target for build PACKAGEBUILD-28014854 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1358 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6091 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main s390x Packages [675 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe s390x Packages [4414 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [526 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [187 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3215 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1382 kB] Fetched 35.4 MB in 21s (1680 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 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 bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 155 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 105 MB of archives. After this operation, 76.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6-dev s390x 2.39-0ubuntu8 [1629 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-dev-bin s390x 2.39-0ubuntu8 [20.2 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1.1build1 [197 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libnss-nisplus s390x 1.3-5build1 [23.8 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1build1 [85.9 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libacl1 s390x 2.3.2-1 [18.0 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu3 [50.8 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.4-2build2 [15.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit1 s390x 1:3.1.2-2.1build1 [48.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu4 [128 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libcap2 s390x 1:2.66-5ubuntu1 [31.7 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4 [102 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgcrypt20 s390x 1.10.3-2 [499 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.6.1+really5.4.5-1 [135 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu5 [56.3 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu4 [138 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-6build1 [763 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.38t64 s390x 5.38.2-3.2build1 [5008 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.38.2-3.2build1 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.38.2-3.2build1 [1968 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu5 [15.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6 s390x 2.39-0ubuntu8 [2847 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-bin s390x 2.39-0ubuntu8 [654 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu3 [1009 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255.4-1ubuntu6 [2131 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu3 [264 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu3 [1675 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255.4-1ubuntu6 [104 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255.4-1ubuntu6 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255.4-1ubuntu6 [3533 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255.4-1ubuntu6 [443 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu4 [57.2 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules s390x 1.5.3-5ubuntu4 [289 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu1 [318 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu3 [944 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0t64 s390x 2.7.14build2 [1014 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240330-1ubuntu2 [47.4 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240330-1ubuntu2 [35.9 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240330-1ubuntu2 [905 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255.4-1ubuntu6 [178 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.6-1 [23.0 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2 [67.2 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu2 [747 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu16 [589 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu1 [161 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu1 [117 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-agent s390x 2.4.4-2ubuntu16 [240 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 2.4.4-2ubuntu16 [111 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pinentry-curses s390x 1.2.1-3ubuntu5 [37.6 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu16 [165 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.14build2 [214 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.14build2 [1390 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x debconf-i18n all 1.5.86 [205 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x debconf all 1.5.86 [124 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam0g s390x 1.5.3-5ubuntu4 [69.7 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu3 [142 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu4 [35.8 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu4 [151 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu4 [119 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu3 [22.9 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3 [9448 B] Get:96 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-20.20 [1592 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x base-files s390x 13ubuntu9 [73.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bash s390x 5.2.21-2ubuntu4 [845 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu4 [96.3 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-3ubuntu5 [1482 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3 [269 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.6ubuntu6 [1278 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4 [189 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x gzip s390x 1.12-1ubuntu2 [106 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x hostname s390x 3.23+nmu2ubuntu1 [11.1 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-4ubuntu1 [202 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu1 [198 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2 [207 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu4 [1142 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-6ubuntu2 [34.7 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu3 [22.6 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu3 [234 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu3 [615 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu4 [68.1 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu4 [33.4 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x libattr1 s390x 1:2.5.2-1 [11.7 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2 [24.7 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build5 [96.8 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu1 [857 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu3 [17.2 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1 [133 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main s390x krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu4 [76.3 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu1 [24.2 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.6.1+really5.4.5-1 [269 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240330-1ubuntu2 [1186 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240330-1ubuntu2 [151 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240330-1ubuntu2 [31.1 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240330-1ubuntu2 [9386 B] Get:157 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240330-1ubuntu2 [2994 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++-13 s390x 13.2.0-23ubuntu3 [14.5 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13 s390x 13.2.0-23ubuntu3 [469 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libstdc++-13-dev s390x 13.2.0-23ubuntu3 [2494 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgcc-13-dev s390x 13.2.0-23ubuntu3 [1003 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240330-1ubuntu2 [49.8 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp-13 s390x 13.2.0-23ubuntu3 [1026 B] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13-base s390x 13.2.0-23ubuntu3 [48.6 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [19.1 MB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [11.3 MB] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [9936 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:172 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:173 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.33-1 [31.9 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.33-1 [67.5 kB] Preconfiguring packages ... Fetched 105 MB in 14s (7739 kB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../2-libc6-dev_2.39-0ubuntu8_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu8_s390x.deb ... Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../4-libtirpc-common_1.3.4+ds-1.1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../5-libtirpc-dev_1.3.4+ds-1.1build1_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libnss-nisplus_1.3-5build1_s390x.deb ... 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Unpacking systemd (255.4-1ubuntu6) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu6_s390x.deb ... Unpacking libsystemd0:s390x (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Setting up libsystemd0:s390x (255.4-1ubuntu6) ... (Reading database ... 15485 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu4_s390x.deb ... Unpacking libpam-modules-bin (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam-modules-bin (1.5.3-5ubuntu4) ... (Reading database ... 15484 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-5ubuntu4_s390x.deb ... Unpacking libpam-modules:s390x (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/s390x-linux-gnu/security': Directory not empty Setting up libpam-modules:s390x (1.5.3-5ubuntu4) ... Installing new version of config file /etc/security/namespace.init ... dpkg: libhogweed6:s390x: dependency problems, but removing anyway as you requested: libgnutls30:s390x depends on libhogweed6 (>= 3.6). 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(both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:s390x (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:s390x. (Reading database ... 15491 files and directories currently installed.) 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Setting up libctf-nobfd0:s390x (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu2) ... Setting up libgomp1:s390x (14-20240330-1ubuntu2) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:s390x (2.42-4ubuntu2) ... Setting up libfakeroot:s390x (1.33-1) ... Setting up libjansson4:s390x (2.14-2build2) ... Setting up libkrb5support0:s390x (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Apr 3 16:49:51 UTC 2024. Universal Time is now: Wed Apr 3 16:49:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:s390x (13.2.0-23ubuntu3) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.1+really5.4.5-1) ... Setting up perl-modules-5.38 (5.38.2-3.2build1) ... Setting up libproc2-0:s390x (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libatomic1:s390x (14-20240330-1ubuntu2) ... Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:s390x (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:s390x (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:s390x (5.3.28+dfsg2-6build1) ... Setting up libubsan1:s390x (14-20240330-1ubuntu2) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu4) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4) ... Setting up libasan8:s390x (14-20240330-1ubuntu2) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:s390x (1.20.1-6ubuntu2) ... Setting up libperl5.38t64:s390x (5.38.2-3.2build1) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:s390x (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libitm1:s390x (14-20240330-1ubuntu2) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu3) ... Setting up binutils (2.42-4ubuntu2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:s390x (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.1build1) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.1build1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15548 files and directories currently installed.) Purging configuration files for libssl3:s390x (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28014854 s390x noble-proposed -c chroot:build-PACKAGEBUILD-28014854 --arch=s390x --dist=noble-proposed --nolog wise_2.4.1-24build1.dsc Initiating build PACKAGEBUILD-28014854 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-009.buildd +==============================================================================+ | wise 2.4.1-24build1 (s390x) Wed, 03 Apr 2024 16:49:55 +0000 | +==============================================================================+ Package: wise Version: 2.4.1-24build1 Source Version: 2.4.1-24build1 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-28014854/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/wise-MVB6oG/resolver-1mEeje' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- wise_2.4.1-24build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/wise-MVB6oG/wise-2.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/wise-MVB6oG' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, 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 [416 B] Get:5 copy:/<>/apt_archive ./ Packages [498 B] Fetched 1871 B in 0s (177 kB/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 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev libbrotli1 libbsd0 libcairo2 libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libelf1t64 libexpat1 libffi-dev libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfontenc1 libfreetype6 libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libkpathsea6 liblcms2-2 liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmime-charset-perl libmount-dev libnetpbm11t64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpixman-1-0 libpkgconf3 libpotrace0 libptexenc1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libraw23t64 libselinux1-dev libsepol-dev libsharpyuv0 libsm6 libsombok3 libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtool libuchardet0 libunicode-linebreak-perl libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libyaml-tiny-perl libzzip-0-13t64 lmodern m4 man-db media-types netbase netpbm opensp pkgconf pkgconf-bin po-debconf poppler-data python3 python3-minimal python3-packaging python3.12 python3.12-minimal sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc texlive-latex-extra imagemagick-6-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin cups-common libfftw3-bin libfftw3-dev low-memory-monitor gir1.2-glib-2.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin libxml2-utils libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc liblcms2-utils libmagickcore-6.q16-7-extra libencode-eucjpascii-perl libencode-hanextra-perl libpod2-base-perl libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser doc-base libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support sgml-base-doc perlsgml w3-recs perl-tk xpdf | pdf-viewer xzdec hintview chktex default-jre-headless dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps xindy texlive-latex-base-doc wp2latex Recommended packages: curl | wget | lynx libmagickcore-6.q16-7-extra dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs fonts-droid-fallback libheif-plugin-aomenc libheif-plugin-x265 javascript-common libltdl-dev libmail-sendmail-perl dvisvgm liblog-log4perl-perl ruby texlive-latex-recommended libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev libbrotli1 libbsd0 libcairo2 libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libelf1t64 libexpat1 libffi-dev libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfontenc1 libfreetype6 libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libkpathsea6 liblcms2-2 liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmime-charset-perl libmount-dev libnetpbm11t64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpixman-1-0 libpkgconf3 libpotrace0 libptexenc1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libraw23t64 libselinux1-dev libsepol-dev libsharpyuv0 libsm6 libsombok3 libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtool libuchardet0 libunicode-linebreak-perl libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libyaml-tiny-perl libzzip-0-13t64 lmodern m4 man-db media-types netbase netpbm opensp pkgconf pkgconf-bin po-debconf poppler-data python3 python3-minimal python3-packaging python3.12 python3.12-minimal sbuild-build-depends-main-dummy sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 174 newly installed, 0 to remove and 0 not upgraded. Need to get 234 MB of archives. After this operation, 586 MB of additional disk space will be used. 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libpython3-stdlib s390x 3.12.2-0ubuntu2 [9854 B] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3 s390x 3.12.2-0ubuntu2 [24.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu3 [512 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2build2 [375 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfreetype6 s390x 2.13.2+dfsg-1build3 [437 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsharpyuv0 s390x 1.3.2-0.4build3 [14.9 kB] Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x libdav1d7 s390x 1.4.1-1build1 [316 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libheif-plugin-dav1d s390x 1.17.6-1ubuntu3 [10.2 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libde265-0 s390x 1.0.15-1build2 [175 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libheif-plugin-libde265 s390x 1.17.6-1ubuntu3 [8300 B] Get:29 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0.21.2-2.1build1 [418 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebp7 s390x 1.3.2-0.4build3 [207 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu2 [218 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebpdemux2 s390x 1.3.2-0.4build3 [12.5 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebpmux3 s390x 1.3.2-0.4build3 [25.4 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libxau6 s390x 1:1.0.9-1build5 [7522 B] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1build1 [46.8 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu5 [10.8 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libxcb1 s390x 1.15-1 [48.3 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libx11-data all 2:1.8.7-1 [115 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libx11-6 s390x 2:1.8.7-1 [672 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x libxext6 s390x 2:1.3.4-1build1 [30.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu1 [10.9 MB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu3 [818 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick-6-common all 8:6.9.12.98+dfsg1-5.2build2 [69.5 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmagickcore-6.q16-7t64 s390x 8:6.9.12.98+dfsg1-5.2build2 [1889 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmagickwand-6.q16-7t64 s390x 8:6.9.12.98+dfsg1-5.2build2 [347 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main s390x poppler-data all 0.4.12-1 [2060 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdbus-1-3 s390x 1.14.10-4ubuntu3 [214 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libelf1t64 s390x 0.190-1.1build3 [69.6 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.80.0-6ubuntu1 [48.1 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x ucf all 3.0043+nmu1 [56.5 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libmagic-mgc s390x 1:5.45-3build1 [305 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libmagic1t64 s390x 1:5.45-3build1 [93.2 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x file s390x 1:5.45-3build1 [22.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main s390x gettext-base s390x 0.21-14ubuntu1 [39.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1 [76.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x groff-base s390x 1.23.0-3build2 [1049 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main s390x libpipeline1 s390x 1.5.7-2 [25.0 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-4build1 [1253 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x m4 s390x 1.4.19-4 [255 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x autopoint all 0.21-14ubuntu1 [422 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libtool all 2.4.7-7 [166 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x dh-autoreconf all 20 [16.1 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libdw1t64 s390x 0.190-1.1build3 [286 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debugedit s390x 1:5.0-5build1 [50.5 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1build6 [122 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14ubuntu1 [917 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.14.1ubuntu5 [869 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x sgml-data all 2.0.11+nmu1 [171 kB] Get:91 http://ftpmaster.internal/ubuntu noble/universe s390x docbook all 4.5-10 [120 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libosp5 s390x 1.5.2-15ubuntu2 [708 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x opensp s390x 1.5.2-15ubuntu2 [152 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe s390x docbook-to-man s390x 1:2.0.0-45 [80.7 kB] Get:95 http://ftpmaster.internal/ubuntu noble/universe s390x fonts-lmodern all 2.005-1 [4799 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgs-common all 10.02.1~dfsg1-0ubuntu6 [174 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgs10-common all 10.02.1~dfsg1-0ubuntu6 [488 kB] Get:98 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2023.20230311.66589-9build3 [41.6 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsynctex2 s390x 2023.20230311.66589-9build3 [65.1 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtexlua53-5 s390x 2023.20230311.66589-9build3 [132 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x t1utils s390x 1.41-4build2 [61.5 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcairo2 s390x 1.18.0-3 [589 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2build2 [515 kB] Get:127 http://ftpmaster.internal/ubuntu noble/universe s390x libpotrace0 s390x 1.16-2 [16.4 kB] Get:128 http://ftpmaster.internal/ubuntu noble/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x libxmu6 s390x 2:1.1.3-3build2 [53.0 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x libxpm4 s390x 1:3.5.17-1build2 [41.2 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x libxaw7 s390x 2:1.0.14-1build2 [204 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x libxi6 s390x 2:1.8.1-1 [35.7 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libzzip-0-13t64 s390x 0.13.72+dfsg.1-1.2build1 [28.6 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x texlive-binaries s390x 2023.20230311.66589-9build3 [9354 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:136 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-base all 2023.20240207-1 [21.7 MB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x hicolor-icon-theme all 0.17-2 [9976 B] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick-6.q16 s390x 8:6.9.12.98+dfsg1-5.2build2 [254 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick s390x 8:6.9.12.98+dfsg1-5.2build2 [14.2 kB] Get:140 http://ftpmaster.internal/ubuntu noble/universe s390x hevea s390x 2.36-2 [2045 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x libfile-which-perl all 1.27-2 [12.5 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x libfile-homedir-perl all 1.006-2 [37.0 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgirepository-2.0-0 s390x 2.80.0-6ubuntu1 [75.6 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-bin s390x 2.80.0-6ubuntu1 [101 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x libffi-dev s390x 3.4.6-1 [58.8 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-packaging all 24.0-1 [41.1 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-dev-bin s390x 2.80.0-6ubuntu1 [139 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-dev s390x 2.39.3-9ubuntu4 [34.2 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid-dev s390x 2.39.3-9ubuntu4 [213 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x libsepol-dev s390x 3.5-2 [395 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-16-0 s390x 10.42-4ubuntu1 [229 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-32-0 s390x 10.42-4ubuntu1 [217 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-posix3 s390x 10.42-4ubuntu1 [6704 B] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-dev s390x 10.42-4ubuntu1 [805 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1-dev s390x 3.5-2ubuntu2 [168 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount-dev s390x 2.39.3-9ubuntu4 [14.9 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main s390x libpkgconf3 s390x 1.8.1-2 [30.4 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf-bin s390x 1.8.1-2 [20.8 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf s390x 1.8.1-2 [16.7 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu2 [904 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-dev s390x 2.80.0-6ubuntu1 [1906 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:164 http://ftpmaster.internal/ubuntu noble/universe s390x libmime-charset-perl all 1.013.1-2 [31.0 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] Get:167 http://ftpmaster.internal/ubuntu noble/universe s390x libsombok3 s390x 2.4.0-2 [25.2 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe s390x libunicode-linebreak-perl s390x 0.0.20190101-1build7 [94.5 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x libyaml-tiny-perl all 1.74-1 [25.3 kB] Get:170 http://ftpmaster.internal/ubuntu noble/universe s390x lmodern all 2.005-1 [9542 kB] Get:171 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-latex-base all 2023.20240207-1 [1238 kB] Get:172 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-luatex all 2023.20240207-1 [25.8 MB] Get:173 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-plain-generic all 2023.20240207-1 [29.0 MB] Get:174 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-extra-utils all 2023.20240207-1 [63.0 MB] Preconfiguring packages ... Fetched 234 MB in 9s (25.3 MB/s) Selecting previously unselected package libpython3.12-minimal:s390x. (Reading database ... 15548 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-5ubuntu3_s390x.deb ... Unpacking libpython3.12-minimal:s390x (3.12.2-5ubuntu3) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.6.1-2build1_s390x.deb ... Unpacking libexpat1:s390x (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-5ubuntu3_s390x.deb ... Unpacking python3.12-minimal (3.12.2-5ubuntu3) ... Setting up libpython3.12-minimal:s390x (3.12.2-5ubuntu3) ... Setting up libexpat1:s390x (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-5ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15866 files and directories currently installed.) 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Setting up imagemagick-6-common (8:6.9.12.98+dfsg1-5.2build2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libdatrie1:s390x (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libijs-0.35:s390x (0.35-15.1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libgs-common (10.02.1~dfsg1-0ubuntu6) ... Setting up libbrotli1:s390x (1.1.0-2build2) ... Setting up libmagic1t64:s390x (1:5.45-3build1) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:s390x (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3build1) ... Setting up libffi-dev:s390x (3.4.6-1) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... Setting up libnetpbm11t64:s390x (2:11.05.02-1.1build1) ... Setting up libpcre2-16-0:s390x (10.42-4ubuntu1) ... Setting up libelf1t64:s390x (0.190-1.1build3) ... Setting up poppler-data (0.4.12-1) ... Setting up libdw1t64:s390x (0.190-1.1build3) ... Setting up libosp5 (1.5.2-15ubuntu2) ... Setting up libfontenc1:s390x (1:1.1.8-1build1) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:s390x (10.42-4ubuntu1) ... Setting up libglib2.0-0t64:s390x (2.80.0-6ubuntu1) ... No schema files found: doing nothing. Setting up libglib2.0-data (2.80.0-6ubuntu1) ... Setting up libpkgconf3:s390x (1.8.1-2) ... Setting up libzzip-0-13t64:s390x (0.13.72+dfsg.1-1.2build1) ... Setting up libfreetype6:s390x (2.13.2+dfsg-1build3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:s390x (0.20-1build3) ... Setting up libteckit0:s390x (2.5.12+ds1-1) ... Setting up uuid-dev:s390x (2.39.3-9ubuntu4) ... Setting up libavahi-common-data:s390x (0.8-13ubuntu5) ... Setting up libdbus-1-3:s390x (1.14.10-4ubuntu3) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:s390x (2023.20230311.66589-9build3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libidn12:s390x (1.42-1) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsepol-dev:s390x (3.5-2) ... Setting up ucf (3.0043+nmu1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... Setting up libltdl7:s390x (2.4.7-7) ... Setting up libfftw3-double3:s390x (3.3.10-1ubuntu3) ... Setting up libkpathsea6:s390x (2023.20230311.66589-9build3) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:s390x (1.3.2-0.4build3) ... Setting up libicu74:s390x (74.2-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Setting up libpcre2-posix3:s390x (10.42-4ubuntu1) ... Setting up dwz (0.15-1build6) ... Setting up libdav1d7:s390x (1.4.1-1build1) ... Setting up liblqr-1-0:s390x (0.4.2-2.1build2) ... Setting up libmime-charset-perl (1.013.1-2) ... Setting up libuchardet0:s390x (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:s390x (2.5.0-2build3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libharfbuzz0b:s390x (8.3.0-2build2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:s390x (1.0.15-1build2) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libwebpmux3:s390x (1.3.2-0.4build3) ... Setting up libbsd0:s390x (0.12.1-1build1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu3) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:s390x (2023.20230311.66589-9build3) ... Setting up libpotrace0:s390x (1.16-2) ... Setting up libjpeg8:s390x (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libblkid-dev:s390x (2.39.3-9ubuntu4) ... Setting up libpaper1:s390x (1.1.29) ... Creating config file /etc/papersize with new version Setting up libice6:s390x (2:1.0.10-1build2) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu5) ... Setting up libxcb1:s390x (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:s390x (3.12.2-5ubuntu3) ... Setting up libpcre2-dev:s390x (10.42-4ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libgirepository-2.0-0:s390x (2.80.0-6ubuntu1) ... Setting up libxcb-render0:s390x (1.15-1) ... Setting up libselinux1-dev:s390x (3.5-2ubuntu2) ... Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... Setting up libwebpdemux2:s390x (1.3.2-0.4build3) ... Setting up python3.12 (3.12.2-5ubuntu3) ... Setting up libavahi-common3:s390x (0.8-13ubuntu5) ... Setting up libglib2.0-bin (2.80.0-6ubuntu1) ... Setting up libxcb-shm0:s390x (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up opensp (1.5.2-15ubuntu2) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up pkgconf:s390x (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:s390x (0.1.29-2) ... Setting up libptexenc1:s390x (2023.20230311.66589-9build3) ... Setting up libraw23t64:s390x (0.21.2-2.1build1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu2) ... Setting up lmodern (2.005-1) ... Setting up xml-core (0.19) ... Setting up libx11-6:s390x (2:1.8.7-1) ... Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... Setting up libsm6:s390x (2:1.2.3-1build2) ... Setting up libavahi-client3:s390x (0.8-13ubuntu5) ... Setting up libmount-dev:s390x (2.39.3-9ubuntu4) ... Setting up libpython3-stdlib:s390x (3.12.2-0ubuntu2) ... Setting up libxpm4:s390x (1:3.5.17-1build2) ... Setting up libxrender1:s390x (1:0.9.10-1.1) ... Setting up libsombok3:s390x (2.4.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:s390x (2:1.3.4-1build1) ... Setting up python3 (3.12.2-0ubuntu2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up man-db (2.12.0-4build1) ... 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 libcairo2:s390x (1.18.0-3) ... Setting up python3-packaging (24.0-1) ... Setting up libunicode-linebreak-perl (0.0.20190101-1build7) ... Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... Setting up netpbm (2:11.05.02-1.1build1) ... Setting up libcups2t64:s390x (2.4.7-1.2ubuntu3) ... Setting up libgs10-common (10.02.1~dfsg1-0ubuntu6) ... Setting up libglib2.0-dev-bin (2.80.0-6ubuntu1) ... Setting up libxmu6:s390x (2:1.1.3-3build2) ... Setting up libxi6:s390x (2:1.8.1-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libxaw7:s390x (2:1.0.14-1build2) ... Setting up libglib2.0-dev:s390x (2.80.0-6ubuntu1) ... Setting up texlive-binaries (2023.20230311.66589-9build3) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgs10:s390x (10.02.1~dfsg1-0ubuntu6) ... Setting up texlive-luatex (2023.20240207-1) ... Setting up texlive-plain-generic (2023.20240207-1) ... Setting up ghostscript (10.02.1~dfsg1-0ubuntu6) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-extra-utils (2023.20240207-1) ... Setting up libheif-plugin-dav1d:s390x (1.17.6-1ubuntu3) ... Setting up libheif-plugin-libde265:s390x (1.17.6-1ubuntu3) ... Setting up libheif1:s390x (1.17.6-1ubuntu3) ... Setting up libmagickcore-6.q16-7t64:s390x (8:6.9.12.98+dfsg1-5.2build2) ... Setting up libmagickwand-6.q16-7t64:s390x (8:6.9.12.98+dfsg1-5.2build2) ... Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5.2build2) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up hevea (2.36-2) ... Setting up imagemagick (8:6.9.12.98+dfsg1-5.2build2) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for systemd (255.4-1ubuntu6) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-10) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-45) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-s390x-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu4 bsdutils_1:2.39.3-9ubuntu4 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu5 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu3 cpp-13-s390x-linux-gnu_13.2.0-23ubuntu3 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docbook_4.5-10 docbook-to-man_1:2.0.0-45 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 fontconfig-config_2.15.0-1.1ubuntu2 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 g++-13-s390x-linux-gnu_13.2.0-23ubuntu3 g++-s390x-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu3 gcc-13-base_13.2.0-23ubuntu3 gcc-13-s390x-linux-gnu_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-s390x-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 ghostscript_10.02.1~dfsg1-0ubuntu6 gpg_2.4.4-2ubuntu16 gpg-agent_2.4.4-2ubuntu16 gpgconf_2.4.4-2ubuntu16 gpgv_2.4.4-2ubuntu16 grep_3.11-4 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu2 hevea_2.36-2 hicolor-icon-theme_0.17-2 hostname_3.23+nmu2ubuntu1 imagemagick_8:6.9.12.98+dfsg1-5.2build2 imagemagick-6-common_8:6.9.12.98+dfsg1-5.2build2 imagemagick-6.q16_8:6.9.12.98+dfsg1-5.2build2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240330-1ubuntu2 libassuan0_2.5.6-1 libatomic1_14-20240330-1ubuntu2 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libavahi-client3_0.8-13ubuntu5 libavahi-common-data_0.8-13ubuntu5 libavahi-common3_0.8-13ubuntu5 libbinutils_2.42-4ubuntu2 libblkid-dev_2.39.3-9ubuntu4 libblkid1_2.39.3-9ubuntu4 libbrotli1_1.1.0-2build2 libbsd0_0.12.1-1build1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcairo2_1.18.0-3 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240330-1ubuntu2 libcom-err2_1.47.0-2.4~exp1ubuntu3 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu3 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcups2t64_2.4.7-1.2ubuntu3 libdatrie1_0.2.13-3 libdav1d7_1.4.1-1build1 libdb5.3t64_5.3.28+dfsg2-6build1 libdbus-1-3_1.14.10-4ubuntu3 libde265-0_1.0.15-1build2 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdw1t64_0.190-1.1build3 libelf1t64_0.190-1.1build3 libexpat1_2.6.1-2build1 libext2fs2t64_1.47.0-2.4~exp1ubuntu3 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu4 libffi-dev_3.4.6-1 libffi8_3.4.6-1 libfftw3-double3_3.3.10-1ubuntu3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libfontconfig1_2.15.0-1.1ubuntu2 libfontenc1_1:1.1.8-1build1 libfreetype6_2.13.2+dfsg-1build3 libgcc-13-dev_13.2.0-23ubuntu3 libgcc-s1_14-20240330-1ubuntu2 libgcrypt20_1.10.3-2 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgirepository-2.0-0_2.80.0-6ubuntu1 libglib2.0-0t64_2.80.0-6ubuntu1 libglib2.0-bin_2.80.0-6ubuntu1 libglib2.0-data_2.80.0-6ubuntu1 libglib2.0-dev_2.80.0-6ubuntu1 libglib2.0-dev-bin_2.80.0-6ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240330-1ubuntu2 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-11 libgraphite2-3_1.3.14-2 libgs-common_10.02.1~dfsg1-0ubuntu6 libgs10_10.02.1~dfsg1-0ubuntu6 libgs10-common_10.02.1~dfsg1-0ubuntu6 libgssapi-krb5-2_1.20.1-6ubuntu2 libharfbuzz0b_8.3.0-2build2 libheif-plugin-dav1d_1.17.6-1ubuntu3 libheif-plugin-libde265_1.17.6-1ubuntu3 libheif1_1.17.6-1ubuntu3 libhogweed6t64_3.9.1-2.2build1 libice6_2:1.0.10-1build2 libicu74_74.2-1ubuntu1 libidn12_1.42-1 libidn2-0_2.3.7-2 libijs-0.35_0.35-15.1 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libitm1_14-20240330-1ubuntu2 libjansson4_2.14-2build2 libjbig0_2.1-6.1ubuntu1 libjbig2dec0_0.20-1build3 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjson-c5_0.17-1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3 libkmod2_31+20240202-2ubuntu5 libkpathsea6_2023.20230311.66589-9build3 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 liblcms2-2_2.14-2 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblqr-1-0_0.4.2-2.1build2 libltdl7_2.4.7-7 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libperl5.38t64_5.38.2-3.2build1 libpipeline1_1.5.7-2 libpixman-1-0_0.42.2-1 libpkgconf3_1.8.1-2 libpng16-16t64_1.6.43-5build1 libpotrace0_1.16-2 libproc2-0_2:4.0.4-4ubuntu3 libptexenc1_2023.20230311.66589-9build3 libpython3-stdlib_3.12.2-0ubuntu2 libpython3.12-minimal_3.12.2-5ubuntu3 libpython3.12-stdlib_3.12.2-5ubuntu3 libraw23t64_0.21.2-2.1build1 libreadline8t64_8.2-4build1 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libselinux1-dev_3.5-2ubuntu2 libsemanage-common_3.5-1build5 libsemanage2_3.5-1build5 libsepol-dev_3.5-2 libsepol2_3.5-2 libsframe1_2.42-4ubuntu2 libsharpyuv0_1.3.2-0.4build3 libsm6_2:1.2.3-1build2 libsmartcols1_2.39.3-9ubuntu4 libsombok3_2.4.0-2 libsqlite3-0_3.45.1-1ubuntu2 libss2_1.47.0-2.4~exp1ubuntu3 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 libsub-override-perl_0.10-1 libsynctex2_2023.20230311.66589-9build3 libsystemd-shared_255.4-1ubuntu6 libsystemd0_255.4-1ubuntu6 libtasn1-6_4.19.0-3 libteckit0_2.5.12+ds1-1 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libyaml-tiny-perl_1.74-1 libzstd1_1.5.5+dfsg2-2 libzzip-0-13t64_0.13.72+dfsg.1-1.2build1 linux-libc-dev_6.8.0-20.20 lmodern_2.005-1 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2.4~exp1ubuntu3 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-4build1 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.39.3-9ubuntu4 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 netbase_6.4 netpbm_2:11.05.02-1.1build1 opensp_1.5.2-15ubuntu2 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3.2build1 perl-base_5.38.2-3.2build1 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2build1 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 poppler-data_0.4.12-1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 python3_3.12.2-0ubuntu2 python3-minimal_3.12.2-0ubuntu2 python3-packaging_24.0-1 python3.12_3.12.2-5ubuntu3 python3.12-minimal_3.12.2-5ubuntu3 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sgml-base_1.31 sgml-data_2.0.11+nmu1 systemd_255.4-1ubuntu6 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu6 sysvinit-utils_3.08-6ubuntu2 t1utils_1.41-4build2 tar_1.35+dfsg-3 tex-common_6.18 texlive-base_2023.20240207-1 texlive-binaries_2023.20230311.66589-9build3 texlive-extra-utils_2023.20240207-1 texlive-latex-base_2023.20240207-1 texlive-luatex_2023.20240207-1 texlive-plain-generic_2023.20240207-1 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 ucf_3.0043+nmu1 util-linux_2.39.3-9ubuntu4 uuid-dev_2.39.3-9ubuntu4 uuid-runtime_2.39.3-9ubuntu4 x11-common_1:7.7+23ubuntu2 xdg-utils_1.1.3-4.1ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build2 xml-core_0.19 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wise Binary: wise, wise-doc, wise-data Architecture: any all Version: 2.4.1-24build1 Maintainer: Ubuntu Developers Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/wise Vcs-Git: https://salsa.debian.org/med-team/wise.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Package-List: wise deb science optional arch=any wise-data deb doc optional arch=all wise-doc deb doc optional arch=all Checksums-Sha1: 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz eb1e48355ab10c00357024e9ab0d9f295b5a6c01 38572 wise_2.4.1-24build1.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz 767f627e307ef48996e8c9b3f8155817cdbb725bfdb7da924fa06c5958d958eb 38572 wise_2.4.1-24build1.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz f9f63f48cc75c745e5c0ddc771446ccd 38572 wise_2.4.1-24build1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEoIn7Nqr72tWswTJQafeQFxohCYQFAmYKcWMACgkQafeQFxoh CYSVrBAAtRyTOh7AbGLXs2K9fPm0MkyvK8PzKsims0zL2/CdSkPOT4loaKsUDmL4 /TH9jaP6nX540YXiSad2owU99xHKAP36S71QHdSHQqgzCJp60w5YgwSpfy4t2lq6 AqHee4si779tMZB2bKXpMKB82ghWeixvM65rIWvuDgcM1LDzrWAmGDwZY06Y5VSB jOsXejqinX5kVua3iWNJw/QUrA+Vulr5i60eQzxvC6Vm+2FpAhzbkthc+dTVgdN+ ELdCZwBXU0xCNTwladaqfaZLdUK3BGzaRdKLb8S+jNqqEbvSwzHau6KuT3ADDjeM NT4/w1FG4wxfczj/SNf28BqNBLrwhtnuLITKokSpbxAZkEqH8j8OFP4+977zWvsS EB/xPg7LHAA2NY34NXdoLMlLrIxQ9hDQK5X2DUQhnGHbQJwF/tvJAd1MXllCTyOf uBRi1eIlHUNY+LPZocmwZ0adQLC1kadhQmy0RvKFCurIkWZe3VxiwyKhKnCJ1Wdt y6xO9XJaLuY0vZTBQSbco0WoVmQ4xw1JEwNzbbTSZaNhvT2eWRQEOyMHS1jLpwsm V9DVuoEjE52a3GhKLlX2ihoVbUF1Xi8QjB3MXN7nhgrNucekergRQafNXEgjzb5t dQ273KASLvE1gwiZj690fk9AAapim+BDSiLY8W7hoNFcH6tmaPA= =0nSN -----END PGP SIGNATURE----- gpgv: Signature made Mon Apr 1 08:33:39 2024 UTC gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-24build1.dsc: no acceptable signature found dpkg-source: info: extracting wise in /<> dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-24build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-source: info: applying 11_consistent_manual_dates.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying implicit-function-declaration.patch dpkg-source: info: applying executable-is-script.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-28014854 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28014854 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28014854 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 wise dpkg-buildpackage: info: source version 2.4.1-24build1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' /usr/bin/make -C src clean make[2]: Entering directory '/<>/src' cd external ; /usr/bin/make clean make[3]: Entering directory '/<>/src/external' (cd mott; make clean) make[4]: Entering directory '/<>/src/external/mott' rm -f *.[oa] make[4]: Leaving directory '/<>/src/external/mott' make[3]: Leaving directory '/<>/src/external' if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi if test -d socket; then cd socket ; rm -f *.[oa]; fi if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi if test -d network; then cd network ; rm -f *.[oa]; fi if test -d dyc; then cd dyc ; rm -f *.[oa]; fi if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi make[2]: Leaving directory '/<>/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory '/<>/debian/manpages.d' rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 make[2]: Leaving directory '/<>/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server rm -f docs/temp.tex rm -f docs/api.* rm -f docs/wise2.image.tex rm -f docs/*.pdf rm -f docs/*.aux rm -f docs/*.log rm -f docs/*.toc rm -f docs/*.pdf rm -f docs/*.dvi rm -f docs/*.ps rm -f docs/*.4ct rm -f docs/*.4tc rm -f docs/*.css rm -f docs/*.idv rm -f docs/*.lg rm -f docs/*.tmp rm -f docs/*.xref rm -f docs/*.haux rm -f docs/*.htoc rm -f docs/*.html rm -f -r docs/api rm -f -r docs/dynamite rm -f -r docs/wise2 dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars debian/files rm -fr -- debian/wise/ debian/tmp/ debian/wise-doc/ debian/wise-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedirectory=src -- all cd src && make -j4 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/<>/src' (cd base ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/<>/src/base' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wiseconfig.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wisestring.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wiseerror.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wisememman.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wisefile.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wiserandom.c wisefile.dy: In function ‘Wise2_myfclose’: wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wisetime.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wiseoverlay.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include wisestreaminterface.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include commandline.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[3]: Leaving directory '/<>/src/base' (cd HMMer2 ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/<>/src/HMMer2' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c alphabet.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c core_algorithms.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c debug.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c emit.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c emulation.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c histogram.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c hmmio.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c mathsupport.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c masks.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c misc.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c modelmakers.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c plan7.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c plan9.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c prior.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c tophits.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c trace.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c aligneval.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c alignio.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c cluster.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c dayhoff.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c file.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c getopt.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c gnuregex.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c interleaved.c gnuregex.c: In function ‘re_match_2’: gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c iupac.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c msf.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c revcomp.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c selex.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c sqerror.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c sqio.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c sre_ctype.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c sre_math.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c sre_string.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c stack.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c translate.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c types.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[3]: Leaving directory '/<>/src/HMMer2' (cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/<>/src/dynlibsrc' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ packaln.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ aln.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ probability.c packaln.dy: In function ‘Wise2_read_simple_PackAln’: packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ alnrange.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ alnconvert.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ basematrix.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’: matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ complexsequence.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ complexevalset.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ sequence.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ sequencestream.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ seqalign.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hitlist.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsp.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hspstream.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ codon.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ compmat.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ codonmapper.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ sequencedb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hscore.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ seqlookup.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ histogram.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ proteindb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ protein.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ pairbase.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ genomicdb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ randommodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ randomdb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ genomic.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ cdna.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ cdnadb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dna.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ embl.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ genomicregion.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ gene.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ transcript.c genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’: genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ translation.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ btcanvas.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[3]: Leaving directory '/<>/src/dynlibsrc' (cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/<>/src/dynlibsrc' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ subseqhash.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ intallocator.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ shadowseq.c subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’: subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’: subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function ‘Wise2_add_seq_subseqhash_ghash’: subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function ‘Wise2_add_direct_number_subseqhash_ghash’: subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsphandler.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[3]: Leaving directory '/<>/src/dynlibsrc' (cd external ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/external' (cd mott; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include " all) make[4]: Entering directory '/<>/src/external/mott' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=3 -c -o mott_api.o mott_api.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=3 -c -o gaplib.o gaplib.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[4]: Leaving directory '/<>/src/external/mott' make[3]: Leaving directory '/<>/src/external' (cd socket ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/<>/src/socket' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ functionserver.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ functionclient.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ anonobj.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ transferinterface.c functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’: functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ | | | struct sockaddr_in * In file included from functionclient.c:7: /usr/include/s390x-linux-gnu/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’ 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[3]: Leaving directory '/<>/src/socket' (cd dnaindex ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/dnaindex' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’: kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function ‘Wise2_remove_sequence_label_KmerAssemblyLink’: kmer_assembly.dy:365:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘KmerAssemblyLink *’ [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’: kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’: kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:82: warning: passing argument 4 of ‘Wise2_lift_backward_tangled_tail’ from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected ‘int *’ but argument is of type ‘long int *’ 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’: kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’: compressed_protein_index.dy:223:10: warning: returning ‘void *’ from a function with return type ‘boolean’ {aka ‘int’} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[3]: Leaving directory '/<>/src/dnaindex' (cd network ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/network' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c wise_proteinindex_server.c: In function ‘show_version’: wise_proteinindex_server.c:28:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 28 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread make[3]: Leaving directory '/<>/src/network' (cd models ; make CC="cc" CFLAGS="-g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory '/<>/src/models' cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c dnal.c: In function ‘show_version’: dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c pswdb.c: In function ‘show_version’: pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘make_SeqAlign_from_align’: dbac.c:413:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~^ ~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. estwise.c: In function ‘show_version’: estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’: phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c In file included from /usr/include/stdio.h:980, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function ‘fgets’, inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: /usr/include/s390x-linux-gnu/bits/stdio2.h:202:12: warning: call to ‘*__fgets_chk’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 202 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genedisplay.dy: In function ‘Wise2_write_intron_desc’: genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function ‘show_version’: genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function ‘show_version’: genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ estwisedb.c: In function ‘show_version’: estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’: est_evidence.dy:142:16: warning: assignment to ‘int (*)(void *)’ from incompatible pointer type ‘Wise2_EstEvidence * (*)(Wise2_EstEvidence *)’ [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function ‘show_version’: sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 14 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function ‘show_version’: pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 15 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c promoterwise.c: In function ‘show_version’: promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c transfactor.dy: In function ‘Wise2_read_ben_IUPAC_TransFactorSet’: transfactor.dy:680:21: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 494 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); | ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/include/stdio.h:980, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: In function ‘sprintf’, inlined from ‘Wise2_read_ben_IUPAC_TransFactorSet’ at transfactor.dy:680:5: /usr/include/s390x-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 9 and 530 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c cc -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c scanwisep.c: In function ‘show_version’: scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 423 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libmodel.a cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` In function ‘Wise2_GeneWiseCodonModel_from_GeneFrequencies’, inlined from ‘Wise2_GeneParameter21_from_GeneFrequency21’ at geneparameter.dy:205:15: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm In function ‘Wise2_GeneWiseCodonModel_from_GeneFrequencies’, inlined from ‘Wise2_GeneParameter21_from_GeneFrequency21’ at geneparameter.dy:205:15, inlined from ‘Wise2_GeneParameter21_wrap’ at gwrap.dy:76:9, inlined from ‘build_db_objects’ at genewisedb.c:554:11: geneparameter.dy:115:34: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 115 | out->in_acceptor[perm] = acceptor->gsc[l]->number / 64.0; | ^ geneparameter.dy:108:14: note: within this loop 108 | for(i=0;i<4;i++) | ^ geneparameter.dy:97:24: warning: iteration 2 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ cc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` make[3]: Leaving directory '/<>/src/models' make bin make[3]: Entering directory '/<>/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /<>/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' /usr/bin/make -C debian/manpages.d make[2]: Entering directory '/<>/debian/manpages.d' docbook-to-man dba.sgml > dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make[2]: Leaving directory '/<>/debian/manpages.d' find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 198. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 9. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 205 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 6. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 207 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 208 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 209 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 210. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 215 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 5. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 16. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 17. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 218 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 219. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 8. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 229 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 23 0. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 231 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 233. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 234. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 235. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 239. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 389. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 39 1. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 3. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 395. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 397. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 399. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 400. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 401. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 402. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 03. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 10. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 411. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 2. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 413. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 4. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 415. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 416. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 417 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 423. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 424. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 5. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 26. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 427. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 433 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 434. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 435 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 441. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 2. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 443. LaTeX Warning: Reference `object_AlnBlock' on page 12 undefined on input line 4 51. LaTeX Warning: Reference `object_AlnColumn' on page 12 undefined on input line 453. LaTeX Warning: Reference `object_AlnUnit' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `object_AlnSequence' on page 12 undefined on input lin e 457. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 464. Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [12] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) LaTeX Warning: Reference `accessing_fields' on page 13 undefined on input line 513. [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 555. [14] LaTeX Warning: Reference `accessing_fields' on page 15 undefined on input line 623. [15] LaTeX Warning: Reference `object_AlnRange' on page 16 undefined on input line 6 52. LaTeX Warning: Reference `object_AlnRangeSet' on page 16 undefined on input lin e 654. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 661. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 688. [16] LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 741. LaTeX Warning: Reference `accessing_fields' on page 17 undefined on input line 748. [17] [18] [19] LaTeX Warning: Reference `object_cDNADB' on page 20 undefined on input line 884 . LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 924. [20] LaTeX Warning: Reference `object_CodonTable' on page 21 undefined on input line 1005. [21] [22] [23] [24] LaTeX Warning: Reference `accessing_fields' on page 25 undefined on input line 1213. [25] [26] [27] LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin e 1363. LaTeX Warning: Reference `accessing_fields' on page 28 undefined on input line 1391. [28] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input line 1442. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 29 undefined o n input line 1444. LaTeX Warning: Reference `accessing_fields' on page 29 undefined on input line 1451. [29] LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1482. LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15 17. LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1524. [30] [31] LaTeX Warning: Reference `object_DBSearchImpl' on page 32 undefined on input li ne 1624. [32] LaTeX Warning: Reference `accessing_fields' on page 33 undefined on input line 1671. [33] LaTeX Warning: Reference `object_DnaMatrix' on page 34 undefined on input line 1736. LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l ine 1738. [34] LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1799. LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1812. [35] LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1844. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1851. [36] [37] LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19 48. LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l ine 1950. [38] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 2038. [39] [40] LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line 2150. [41] LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 2168. Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2213. [43] LaTeX Warning: Reference `object_GenomicRegion' on page 44 undefined on input l ine 2298. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2305. [44] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [45] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [46] [47] LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 2505. [48] LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line 2553. Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [49] [50] [51] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [52] [53] [54] LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 293 0. LaTeX Warning: Reference `object_DataScore' on page 55 undefined on input line 2932. LaTeX Warning: Reference `object_DataEntry' on page 55 undefined on input line 2934. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2961. Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [55] [56] [57] LaTeX Warning: Reference `accessing_fields' on page 58 undefined on input line 3162. [58] LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line 3188. LaTeX Warning: Reference `object_PackAln' on page 59 undefined on input line 32 29. [59] LaTeX Warning: Reference `object_PackAlnUnit' on page 60 undefined on input lin e 3231. LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3238. [60] LaTeX Warning: Reference `accessing_fields' on page 61 undefined on input line 3308. [61] [62] LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34 31. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3438. [63] LaTeX Warning: Reference `object_ProteinDB' on page 64 undefined on input line 3488. LaTeX Warning: Reference `accessing_fields' on page 64 undefined on input line 3545. [64] LaTeX Warning: Reference `object_RandomProteinDB' on page 65 undefined on input line 3590. LaTeX Warning: Reference `object_RandomDNADB' on page 65 undefined on input lin e 3592. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3599. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3620. [65] LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input line 3642. LaTeX Warning: Reference `object_RandomModel' on page 66 undefined on input lin e 3644. LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3682. [66] LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line 3697. LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3 713. LaTeX Warning: Reference `object_SequenceSet' on page 67 undefined on input lin e 3715. [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3779. [68] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [69] [70] [71] [72] [73] [74] LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 4176. [75] [76] LaTeX Warning: Reference `object_SequenceDB' on page 77 undefined on input line 4265. LaTeX Warning: Reference `object_FileSource' on page 77 undefined on input line 4267. LaTeX Warning: Reference `accessing_fields' on page 77 undefined on input line 4294. [77] LaTeX Warning: Reference `accessing_fields' on page 78 undefined on input line 4355. LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4381. LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line 4383. [78] LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4390. LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4413. [79] LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin e 4482. LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 4489. Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [80] LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line 4549. [81] LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4579. LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin e 4602. Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [82] LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 4655. Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [83] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [84] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [85] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [86] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input line 4830. LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l ine 4832. LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input line 4834. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4879. Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4906. [88] LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4921. LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input line 4937. LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4944. [89] LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input line 4990. LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li ne 4992. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4999. Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [90] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 5065. [91] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 92 undefined on input li ne 5107. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 92 undefined on input line 5109. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5116. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5152. [92] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [93] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in put line 5243. LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input line 5245. LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line 5247. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5254. Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [95] LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5307. LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5320. Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [96] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [97] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [98] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [99] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [100] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l ine 5552. LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line 5559. [101] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [103] [104] LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu t line 5732. LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input line 5734. LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5775. [105] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [106] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5890. [107] [108] (./api.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tctt1000.tfm. Output written on tctt1000.600gf (128 characters, 19540 bytes). Transcript written on tctt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. Output written on api.pdf (108 pages, 304186 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib /texmf/fonts/map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 233. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 239. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 389. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 26. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 435 . Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [20] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [47] [48] [49] Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [50] [51] [52] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [53] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [54] [55] [56] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [57] [58] [59] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [60] [61] [62] Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [88] [89] Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [90] Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [91] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [92] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [93] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [94] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [95] Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [96] [97] Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [98] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) [99] [100] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [101] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [103] Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [104] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [105] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [106] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [107] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [108] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) [109] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [110] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [111] [112] [113] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [114] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [115] [116] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (116 pages, 318788 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 77. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [7] [8] [9] [10] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [11] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [12] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [13] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [14] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [15] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [16] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [17] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [19] [20] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [22] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [23] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [24] [25] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [26] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [27] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [28] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [29] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [30] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [34] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [36] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [37] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [40] [41] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [42] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [43] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [44] [45] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [46] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [47] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [48] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [49] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] [51] [52] [53] [54] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [55] [56] [57] [58] [59] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [60] [61] [62] (./dynamite.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (62 pages, 221231 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [9] [10] [11] [12] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [13] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [14] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [16] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [17] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [18] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [19] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [21] [22] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [24] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [25] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [26] [27] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [28] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [29] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [30] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [31] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [32] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [36] [37] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] [40] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [41] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [42] [43] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [44] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [45] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [46] [47] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [48] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [49] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [51] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [52] [53] [54] [55] [56] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [57] [58] [59] [60] [61] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [62] [63] [64] (./dynamite.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (64 pages, 224793 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 110 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 113. Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [5] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 297. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 6. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 455 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 66. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 3. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 3. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 13. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 708. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 900. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [22] [23] [24] [25] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [26] LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11 81. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 121 0. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1276. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [30] [31] LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137 7. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 9. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 561. [37] [38] [39] [40] [41] [42] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (42 pages, 213100 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [6] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 708. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [23] [24] [25] [26] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [27] [28] [29] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (43 pages, 215391 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory '/<>' rm -f debian/wise.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/wise.substvars rm -fr -- debian/.debhelper/generated/wise/ debian/wise/ debian/tmp/ dh_installdirs -a install -m0755 -d debian/wise/usr/bin dh_install -a install -m0755 -d debian/wise/usr/bin cp --reflink=auto -a ./src/bin/dba ./src/bin/dnal ./src/bin/estwise ./src/bin/estwisedb ./src/bin/genewise ./src/bin/genewisedb ./src/bin/promoterwise ./src/bin/psw ./src/bin/pswdb ./src/bin/scanwise ./src/bin/scanwise_server ./src/models/genomewise debian/wise/usr/bin/ dh_installdocs -a install -m0755 -d debian/wise/usr/share/doc/wise install -m0755 -d debian/wise/usr/share/doc/wise cp --reflink=auto -a ./README debian/wise/usr/share/doc/wise cp --reflink=auto -a ./debian/tests/run-unit-test debian/wise/usr/share/doc/wise chmod -R u\+rw,go=rX debian/wise/usr/share/doc install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright dh_installchangelogs -a install -m0755 -d debian/wise/usr/share/doc/wise install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian dh_installexamples -a dh_installman -a install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 debian/wise/usr/share/man/man1/estwise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 debian/wise/usr/share/man/man1/psw.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/pswdb.1 debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwisedb.1 debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1 mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1 mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1 chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1 debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1 mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1 mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1 chmod 0644 -- debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 debian/wise/usr/share/man/man1/estwise.1 mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1 mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1 mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1 chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 debian/wise/usr/share/man/man1/psw.1 mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1 mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.1 mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1 chmod 0644 -- debian/wise/usr/share/man/man1/pswdb.1 debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/wise chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 cd '/<>' debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/wise ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f -a -true -a ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -iname "*.hmm" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a install -m0755 -d debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu dwz -mdebian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug -- debian/wise/usr/bin/dba debian/wise/usr/bin/dnal debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug dh_strip -a debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/genewise debugedit: debian/wise/usr/bin/genewise: Unknown DWARF DW_FORM_0x1f20 d0a19d461d51aab1f76500d610f135ec348973d9 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d0 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d0/a19d461d51aab1f76500d610f135ec348973d9.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d0/a19d461d51aab1f76500d610f135ec348973d9.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripxo4G9I debian/wise/usr/bin/genewise chmod --reference debian/wise/usr/bin/genewise /tmp/t2hjk_vDZC/stripxo4G9I cat '/tmp/t2hjk_vDZC/stripxo4G9I' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/t2hjk_vDZC/stripxo4G9I debian/wise/usr/bin/genewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d0/a19d461d51aab1f76500d610f135ec348973d9.debug debian/wise/usr/bin/genewise /tmp/t2hjk_vDZC/objcopyLfr3So chmod --reference debian/wise/usr/bin/genewise /tmp/t2hjk_vDZC/objcopyLfr3So cat '/tmp/t2hjk_vDZC/objcopyLfr3So' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/t2hjk_vDZC/objcopyLfr3So debian/wise/usr/bin/genewise debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/estwisedb debugedit: debian/wise/usr/bin/estwisedb: Unknown DWARF DW_FORM_0x1f20 e562751554f6a888afdcb07e731cd1a44dd1f3ba install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/62751554f6a888afdcb07e731cd1a44dd1f3ba.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/62751554f6a888afdcb07e731cd1a44dd1f3ba.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripXfnbKb debian/wise/usr/bin/estwisedb chmod --reference debian/wise/usr/bin/estwisedb /tmp/t2hjk_vDZC/stripXfnbKb cat '/tmp/t2hjk_vDZC/stripXfnbKb' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/t2hjk_vDZC/stripXfnbKb debian/wise/usr/bin/estwisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/62751554f6a888afdcb07e731cd1a44dd1f3ba.debug debian/wise/usr/bin/estwisedb /tmp/t2hjk_vDZC/objcopy8mTYww chmod --reference debian/wise/usr/bin/estwisedb /tmp/t2hjk_vDZC/objcopy8mTYww cat '/tmp/t2hjk_vDZC/objcopy8mTYww' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/t2hjk_vDZC/objcopy8mTYww debian/wise/usr/bin/estwisedb debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/scanwise debugedit: debian/wise/usr/bin/scanwise: Unknown DWARF DW_FORM_0x1f21 4fce470b9f0e7b180647667f15b9b1d9c0129967 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4f objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4f/ce470b9f0e7b180647667f15b9b1d9c0129967.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4f/ce470b9f0e7b180647667f15b9b1d9c0129967.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripp36Ip5 debian/wise/usr/bin/scanwise chmod --reference debian/wise/usr/bin/scanwise /tmp/t2hjk_vDZC/stripp36Ip5 cat '/tmp/t2hjk_vDZC/stripp36Ip5' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/t2hjk_vDZC/stripp36Ip5 debian/wise/usr/bin/scanwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4f/ce470b9f0e7b180647667f15b9b1d9c0129967.debug debian/wise/usr/bin/scanwise /tmp/t2hjk_vDZC/objcopy2Upuob chmod --reference debian/wise/usr/bin/scanwise /tmp/t2hjk_vDZC/objcopy2Upuob cat '/tmp/t2hjk_vDZC/objcopy2Upuob' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/t2hjk_vDZC/objcopy2Upuob debian/wise/usr/bin/scanwise debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/scanwise_server debugedit: debian/wise/usr/bin/scanwise_server: Unknown DWARF DW_FORM_0x1f20 e1bf4fed13cd6e7cb58e3acb031ae97cdcbab449 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/bf4fed13cd6e7cb58e3acb031ae97cdcbab449.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/bf4fed13cd6e7cb58e3acb031ae97cdcbab449.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripLMpWFf debian/wise/usr/bin/scanwise_server chmod --reference debian/wise/usr/bin/scanwise_server /tmp/t2hjk_vDZC/stripLMpWFf cat '/tmp/t2hjk_vDZC/stripLMpWFf' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/t2hjk_vDZC/stripLMpWFf debian/wise/usr/bin/scanwise_server objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/bf4fed13cd6e7cb58e3acb031ae97cdcbab449.debug debian/wise/usr/bin/scanwise_server /tmp/t2hjk_vDZC/objcopyJ5ReDc chmod --reference debian/wise/usr/bin/scanwise_server /tmp/t2hjk_vDZC/objcopyJ5ReDc cat '/tmp/t2hjk_vDZC/objcopyJ5ReDc' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/t2hjk_vDZC/objcopyJ5ReDc debian/wise/usr/bin/scanwise_server debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/estwise debugedit: debian/wise/usr/bin/estwise: Unknown DWARF DW_FORM_0x1f21 b4044657bec13913451a61b921d3f486759241fa install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b4 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b4/044657bec13913451a61b921d3f486759241fa.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b4/044657bec13913451a61b921d3f486759241fa.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripa7v4pS debian/wise/usr/bin/estwise chmod --reference debian/wise/usr/bin/estwise /tmp/t2hjk_vDZC/stripa7v4pS cat '/tmp/t2hjk_vDZC/stripa7v4pS' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/t2hjk_vDZC/stripa7v4pS debian/wise/usr/bin/estwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b4/044657bec13913451a61b921d3f486759241fa.debug debian/wise/usr/bin/estwise /tmp/t2hjk_vDZC/objcopyLSFhvT chmod --reference debian/wise/usr/bin/estwise /tmp/t2hjk_vDZC/objcopyLSFhvT cat '/tmp/t2hjk_vDZC/objcopyLSFhvT' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/t2hjk_vDZC/objcopyLSFhvT debian/wise/usr/bin/estwise debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/promoterwise debugedit: debian/wise/usr/bin/promoterwise: Unknown DWARF DW_FORM_0x1f20 e7b18737bbd8823149256292697c2c2a31dd7dbd install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/b18737bbd8823149256292697c2c2a31dd7dbd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/b18737bbd8823149256292697c2c2a31dd7dbd.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripAkzWmm debian/wise/usr/bin/promoterwise chmod --reference debian/wise/usr/bin/promoterwise /tmp/t2hjk_vDZC/stripAkzWmm cat '/tmp/t2hjk_vDZC/stripAkzWmm' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/t2hjk_vDZC/stripAkzWmm debian/wise/usr/bin/promoterwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/b18737bbd8823149256292697c2c2a31dd7dbd.debug debian/wise/usr/bin/promoterwise /tmp/t2hjk_vDZC/objcopydCOZ9P chmod --reference debian/wise/usr/bin/promoterwise /tmp/t2hjk_vDZC/objcopydCOZ9P cat '/tmp/t2hjk_vDZC/objcopydCOZ9P' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/t2hjk_vDZC/objcopydCOZ9P debian/wise/usr/bin/promoterwise debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/dnal debugedit: debian/wise/usr/bin/dnal: Unknown DWARF DW_FORM_0x1f21 d7d0bf7ff6674493995da4c556d6be6ccbd568a3 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d7 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d7/d0bf7ff6674493995da4c556d6be6ccbd568a3.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d7/d0bf7ff6674493995da4c556d6be6ccbd568a3.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripgZz1rN debian/wise/usr/bin/dnal chmod --reference debian/wise/usr/bin/dnal /tmp/t2hjk_vDZC/stripgZz1rN cat '/tmp/t2hjk_vDZC/stripgZz1rN' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/t2hjk_vDZC/stripgZz1rN debian/wise/usr/bin/dnal objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d7/d0bf7ff6674493995da4c556d6be6ccbd568a3.debug debian/wise/usr/bin/dnal /tmp/t2hjk_vDZC/objcopyraJWdf chmod --reference debian/wise/usr/bin/dnal /tmp/t2hjk_vDZC/objcopyraJWdf cat '/tmp/t2hjk_vDZC/objcopyraJWdf' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/t2hjk_vDZC/objcopyraJWdf debian/wise/usr/bin/dnal debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/genomewise debugedit: debian/wise/usr/bin/genomewise: Unknown DWARF DW_FORM_0x1f21 799915f30ae2e2c39830b5132aad8e2ac09328b3 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/79 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/79/9915f30ae2e2c39830b5132aad8e2ac09328b3.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/79/9915f30ae2e2c39830b5132aad8e2ac09328b3.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripIEHw_9 debian/wise/usr/bin/genomewise chmod --reference debian/wise/usr/bin/genomewise /tmp/t2hjk_vDZC/stripIEHw_9 cat '/tmp/t2hjk_vDZC/stripIEHw_9' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/t2hjk_vDZC/stripIEHw_9 debian/wise/usr/bin/genomewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/79/9915f30ae2e2c39830b5132aad8e2ac09328b3.debug debian/wise/usr/bin/genomewise /tmp/t2hjk_vDZC/objcopygk0mLf chmod --reference debian/wise/usr/bin/genomewise /tmp/t2hjk_vDZC/objcopygk0mLf cat '/tmp/t2hjk_vDZC/objcopygk0mLf' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/t2hjk_vDZC/objcopygk0mLf debian/wise/usr/bin/genomewise debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/psw debugedit: debian/wise/usr/bin/psw: Unknown DWARF DW_FORM_0x1f20 93bf16b9fb788bfe448fec6598cfc4a4e8968534 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/93 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/93/bf16b9fb788bfe448fec6598cfc4a4e8968534.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/93/bf16b9fb788bfe448fec6598cfc4a4e8968534.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripOR4MtO debian/wise/usr/bin/psw chmod --reference debian/wise/usr/bin/psw /tmp/t2hjk_vDZC/stripOR4MtO cat '/tmp/t2hjk_vDZC/stripOR4MtO' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/t2hjk_vDZC/stripOR4MtO debian/wise/usr/bin/psw objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/93/bf16b9fb788bfe448fec6598cfc4a4e8968534.debug debian/wise/usr/bin/psw /tmp/t2hjk_vDZC/objcopyhkYzka chmod --reference debian/wise/usr/bin/psw /tmp/t2hjk_vDZC/objcopyhkYzka cat '/tmp/t2hjk_vDZC/objcopyhkYzka' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/t2hjk_vDZC/objcopyhkYzka debian/wise/usr/bin/psw debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/dba debugedit: debian/wise/usr/bin/dba: Unknown DWARF DW_FORM_0x1f21 705c575c9a0756d610a10ec331481f3e812b93fa install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/70 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/70/5c575c9a0756d610a10ec331481f3e812b93fa.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/70/5c575c9a0756d610a10ec331481f3e812b93fa.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripTRnPr4 debian/wise/usr/bin/dba chmod --reference debian/wise/usr/bin/dba /tmp/t2hjk_vDZC/stripTRnPr4 cat '/tmp/t2hjk_vDZC/stripTRnPr4' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/t2hjk_vDZC/stripTRnPr4 debian/wise/usr/bin/dba objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/70/5c575c9a0756d610a10ec331481f3e812b93fa.debug debian/wise/usr/bin/dba /tmp/t2hjk_vDZC/objcopyC5HDpW chmod --reference debian/wise/usr/bin/dba /tmp/t2hjk_vDZC/objcopyC5HDpW cat '/tmp/t2hjk_vDZC/objcopyC5HDpW' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/t2hjk_vDZC/objcopyC5HDpW debian/wise/usr/bin/dba debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/genewisedb debugedit: debian/wise/usr/bin/genewisedb: Unknown DWARF DW_FORM_0x1f20 13f1f9645bcfff8adc0f8c8e8e0ffeef4cdcddcd install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/f1f9645bcfff8adc0f8c8e8e0ffeef4cdcddcd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/f1f9645bcfff8adc0f8c8e8e0ffeef4cdcddcd.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripTcgPUP debian/wise/usr/bin/genewisedb chmod --reference debian/wise/usr/bin/genewisedb /tmp/t2hjk_vDZC/stripTcgPUP cat '/tmp/t2hjk_vDZC/stripTcgPUP' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/t2hjk_vDZC/stripTcgPUP debian/wise/usr/bin/genewisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/f1f9645bcfff8adc0f8c8e8e0ffeef4cdcddcd.debug debian/wise/usr/bin/genewisedb /tmp/t2hjk_vDZC/objcopyxsWkWx chmod --reference debian/wise/usr/bin/genewisedb /tmp/t2hjk_vDZC/objcopyxsWkWx cat '/tmp/t2hjk_vDZC/objcopyxsWkWx' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/t2hjk_vDZC/objcopyxsWkWx debian/wise/usr/bin/genewisedb debugedit --build-id --build-id-seed=wise/2.4.1-24build1 debian/wise/usr/bin/pswdb debugedit: debian/wise/usr/bin/pswdb: Unknown DWARF DW_FORM_0x1f20 c086a60a7d88aefcac0942551d9719ed54d846e0 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0/86a60a7d88aefcac0942551d9719ed54d846e0.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0/86a60a7d88aefcac0942551d9719ed54d846e0.debug strip --remove-section=.comment --remove-section=.note -o /tmp/t2hjk_vDZC/stripz4ripk debian/wise/usr/bin/pswdb chmod --reference debian/wise/usr/bin/pswdb /tmp/t2hjk_vDZC/stripz4ripk cat '/tmp/t2hjk_vDZC/stripz4ripk' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/t2hjk_vDZC/stripz4ripk debian/wise/usr/bin/pswdb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0/86a60a7d88aefcac0942551d9719ed54d846e0.debug debian/wise/usr/bin/pswdb /tmp/t2hjk_vDZC/objcopySK5NS8 chmod --reference debian/wise/usr/bin/pswdb /tmp/t2hjk_vDZC/objcopySK5NS8 cat '/tmp/t2hjk_vDZC/objcopySK5NS8' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/t2hjk_vDZC/objcopySK5NS8 debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wise/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wise/usr/lib/debug install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/share/doc ln -s wise debian/.debhelper/wise/dbgsym-root/usr/share/doc/wise-dbgsym install -m0755 -d debian/.debhelper/wise dh_makeshlibs -a rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wise/DEBIAN dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/estwise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/dnal debian/wise/usr/bin/genomewise debian/wise/usr/bin/psw debian/wise/usr/bin/dba debian/wise/usr/bin/genewisedb debian/wise/usr/bin/pswdb dh_installdeb -a install -m0755 -d debian/wise/DEBIAN dh_gencontrol -a install -m0755 -d debian/wise/DEBIAN echo misc:Depends= >> debian/wise.substvars echo misc:Pre-Depends= >> debian/wise.substvars install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=13f1f9645bcfff8adc0f8c8e8e0ffeef4cdcddcd 4fce470b9f0e7b180647667f15b9b1d9c0129967 705c575c9a0756d610a10ec331481f3e812b93fa 799915f30ae2e2c39830b5132aad8e2ac09328b3 93bf16b9fb788bfe448fec6598cfc4a4e8968534 b4044657bec13913451a61b921d3f486759241fa c086a60a7d88aefcac0942551d9719ed54d846e0 d0a19d461d51aab1f76500d610f135ec348973d9 d7d0bf7ff6674493995da4c556d6be6ccbd568a3 e1bf4fed13cd6e7cb58e3acb031ae97cdcbab449 e562751554f6a888afdcb07e731cd1a44dd1f3ba e7b18737bbd8823149256292697c2c2a31dd7dbd" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise chmod 0644 -- debian/wise/DEBIAN/control dh_md5sums -a install -m0755 -d debian/wise/DEBIAN cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wise/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/wise .. dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root debian/.debhelper/scratch-space/build-wise INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing wise (in debian/wise); do_strip: , oemstrip: pkgstriptranslations: processing wise-dbgsym (in debian/.debhelper/wise/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/wise/DEBIAN/control, package wise, directory debian/wise pkgstripfiles: Running PNG optimization (using 4 cpus) for package wise ... pkgstripfiles: No PNG files. dpkg-deb: building package 'wise' in '../wise_2.4.1-24build1_s390x.deb'. pkgstripfiles: processing control file: debian/.debhelper/wise/dbgsym-root/DEBIAN/control, package wise-dbgsym, directory debian/.debhelper/wise/dbgsym-root dpkg-deb: building package 'wise-dbgsym' in 'debian/.debhelper/scratch-space/build-wise/wise-dbgsym_2.4.1-24build1_s390x.deb'. Renaming wise-dbgsym_2.4.1-24build1_s390x.deb to wise-dbgsym_2.4.1-24build1_s390x.ddeb mv debian/.debhelper/scratch-space/build-wise/wise-dbgsym_2.4.1-24build1_s390x.deb ../wise-dbgsym_2.4.1-24build1_s390x.ddeb dpkg-genbuildinfo --build=any -O../wise_2.4.1-24build1_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../wise_2.4.1-24build1_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 2024-04-03T16:53:29Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ wise_2.4.1-24build1_s390x.changes: ---------------------------------- Format: 1.8 Date: Mon, 01 Apr 2024 19:33:38 +1100 Source: wise Binary: wise Built-For-Profiles: noudeb Architecture: s390x Version: 2.4.1-24build1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William Grant Description: wise - comparison of biopolymers, like DNA and protein sequences Changes: wise (2.4.1-24build1) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 090a7ec6cac8f85b14feaf9a970afd07e6289ffc 3289698 wise-dbgsym_2.4.1-24build1_s390x.ddeb e0f3c52bdd15ea35ee104f7c7b99de63265b3d13 11134 wise_2.4.1-24build1_s390x.buildinfo 221a021e729a78792fb6c08146931c5f085d35e4 938566 wise_2.4.1-24build1_s390x.deb Checksums-Sha256: ce4d7041c7f7ccbe3ff965a3c681607f78c2c8f4c43ae7f62b5991efd4dbc884 3289698 wise-dbgsym_2.4.1-24build1_s390x.ddeb ebeeb0d4c3323cc667f1625461698e1ce418e31606658821a73c4d7bb3964c0a 11134 wise_2.4.1-24build1_s390x.buildinfo c29a5614c7b01beebf61837074bafa3737badab6d9574ad08986077e1ae033a9 938566 wise_2.4.1-24build1_s390x.deb Files: 5c08c071efbfc8e843da085f34122b9e 3289698 debug optional wise-dbgsym_2.4.1-24build1_s390x.ddeb 21a1c5f46e338682cb01c939f42430cc 11134 science optional wise_2.4.1-24build1_s390x.buildinfo 88cd1b231a54fd29951ed14db6c20f5b 938566 science optional wise_2.4.1-24build1_s390x.deb Original-Maintainer: Debian Med Packaging Team /<>/wise_2.4.1-24build1_s390x.changes.new could not be renamed to /<>/wise_2.4.1-24build1_s390x.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: wise Binary: wise wise-dbgsym Architecture: s390x Version: 2.4.1-24build1 Checksums-Md5: 5c08c071efbfc8e843da085f34122b9e 3289698 wise-dbgsym_2.4.1-24build1_s390x.ddeb 88cd1b231a54fd29951ed14db6c20f5b 938566 wise_2.4.1-24build1_s390x.deb Checksums-Sha1: 090a7ec6cac8f85b14feaf9a970afd07e6289ffc 3289698 wise-dbgsym_2.4.1-24build1_s390x.ddeb 221a021e729a78792fb6c08146931c5f085d35e4 938566 wise_2.4.1-24build1_s390x.deb Checksums-Sha256: ce4d7041c7f7ccbe3ff965a3c681607f78c2c8f4c43ae7f62b5991efd4dbc884 3289698 wise-dbgsym_2.4.1-24build1_s390x.ddeb c29a5614c7b01beebf61837074bafa3737badab6d9574ad08986077e1ae033a9 938566 wise_2.4.1-24build1_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Wed, 03 Apr 2024 16:53:29 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-s390x-linux-gnu (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu4), bsdutils (= 1:2.39.3-9ubuntu4), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-s390x-linux-gnu (= 13.2.0-23ubuntu3), cpp-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docbook (= 4.5-10), docbook-to-man (= 1:2.0.0-45), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5), fontconfig-config (= 2.15.0-1.1ubuntu2), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), fonts-urw-base35 (= 20200910-8), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-s390x-linux-gnu (= 13.2.0-23ubuntu3), g++-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-13-s390x-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), ghostscript (= 10.02.1~dfsg1-0ubuntu6), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), hevea (= 2.36-2), hicolor-icon-theme (= 0.17-2), hostname (= 3.23+nmu2ubuntu1), imagemagick (= 8:6.9.12.98+dfsg1-5.2build2), imagemagick-6-common (= 8:6.9.12.98+dfsg1-5.2build2), imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-5.2build2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libavahi-client3 (= 0.8-13ubuntu5), libavahi-common-data (= 0.8-13ubuntu5), libavahi-common3 (= 0.8-13ubuntu5), libbinutils (= 2.42-4ubuntu2), libblkid-dev (= 2.39.3-9ubuntu4), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build2), libbsd0 (= 0.12.1-1build1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcairo2 (= 1.18.0-3), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240330-1ubuntu2), libcom-err2 (= 1.47.0-2.4~exp1ubuntu3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcups2t64 (= 2.4.7-1.2ubuntu3), libdatrie1 (= 0.2.13-3), libdav1d7 (= 1.4.1-1build1), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdbus-1-3 (= 1.14.10-4ubuntu3), libde265-0 (= 1.0.15-1build2), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build3), libelf1t64 (= 0.190-1.1build3), libexpat1 (= 2.6.1-2build1), libffi-dev (= 3.4.6-1), libffi8 (= 3.4.6-1), libfftw3-double3 (= 3.3.10-1ubuntu3), libfile-homedir-perl (= 1.006-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfile-which-perl (= 1.27-2), libfontconfig1 (= 2.15.0-1.1ubuntu2), libfontenc1 (= 1:1.1.8-1build1), libfreetype6 (= 2.13.2+dfsg-1build3), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgirepository-2.0-0 (= 2.80.0-6ubuntu1), libglib2.0-0t64 (= 2.80.0-6ubuntu1), libglib2.0-bin (= 2.80.0-6ubuntu1), libglib2.0-data (= 2.80.0-6ubuntu1), libglib2.0-dev (= 2.80.0-6ubuntu1), libglib2.0-dev-bin (= 2.80.0-6ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240330-1ubuntu2), libgpg-error0 (= 1.47-3build1), libgraphite2-3 (= 1.3.14-2), libgs-common (= 10.02.1~dfsg1-0ubuntu6), libgs10 (= 10.02.1~dfsg1-0ubuntu6), libgs10-common (= 10.02.1~dfsg1-0ubuntu6), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libharfbuzz0b (= 8.3.0-2build2), libheif-plugin-dav1d (= 1.17.6-1ubuntu3), libheif-plugin-libde265 (= 1.17.6-1ubuntu3), libheif1 (= 1.17.6-1ubuntu3), libhogweed6t64 (= 3.9.1-2.2build1), libice6 (= 2:1.0.10-1build2), libicu74 (= 74.2-1ubuntu1), libidn12 (= 1.42-1), libidn2-0 (= 2.3.7-2), libijs-0.35 (= 0.35-15.1), libisl23 (= 0.26-3), libitm1 (= 14-20240330-1ubuntu2), libjansson4 (= 2.14-2build2), libjbig0 (= 2.1-6.1ubuntu1), libjbig2dec0 (= 0.20-1build3), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libkpathsea6 (= 2023.20230311.66589-9build3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblcms2-2 (= 2.14-2), liblqr-1-0 (= 0.4.2-2.1build2), libltdl7 (= 2.4.7-7), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmagickcore-6.q16-7t64 (= 8:6.9.12.98+dfsg1-5.2build2), libmagickwand-6.q16-7t64 (= 8:6.9.12.98+dfsg1-5.2build2), libmd0 (= 1.1.0-2), libmime-charset-perl (= 1.013.1-2), libmount-dev (= 2.39.3-9ubuntu4), libmount1 (= 2.39.3-9ubuntu4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnetpbm11t64 (= 2:11.05.02-1.1build1), libnettle8t64 (= 3.9.1-2.2build1), libopenjp2-7 (= 2.5.0-2build3), libosp5 (= 1.5.2-15ubuntu2), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.3-5ubuntu4), libpam-modules-bin (= 1.5.3-5ubuntu4), libpam-runtime (= 1.5.3-5ubuntu4), libpam0g (= 1.5.3-5ubuntu4), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), 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), libperl5.38t64 (= 5.38.2-3.2build1), libpipeline1 (= 1.5.7-2), libpixman-1-0 (= 0.42.2-1), libpkgconf3 (= 1.8.1-2), libpng16-16t64 (= 1.6.43-5build1), libpotrace0 (= 1.16-2), libptexenc1 (= 2023.20230311.66589-9build3), libpython3-stdlib (= 3.12.2-0ubuntu2), libpython3.12-minimal (= 3.12.2-5ubuntu3), libpython3.12-stdlib (= 3.12.2-5ubuntu3), libraw23t64 (= 0.21.2-2.1build1), libreadline8t64 (= 8.2-4build1), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libselinux1-dev (= 3.5-2ubuntu2), libsepol-dev (= 3.5-2), libsepol2 (= 3.5-2), libsframe1 (= 2.42-4ubuntu2), libsharpyuv0 (= 1.3.2-0.4build3), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.39.3-9ubuntu4), libsombok3 (= 2.4.0-2), libsqlite3-0 (= 3.45.1-1ubuntu2), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240330-1ubuntu2), libsub-override-perl (= 0.10-1), libsynctex2 (= 2023.20230311.66589-9build3), libsystemd0 (= 255.4-1ubuntu6), libtasn1-6 (= 4.19.0-3), libteckit0 (= 2.5.12+ds1-1), libtexlua53-5 (= 2023.20230311.66589-9build3), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtiff6 (= 4.5.1+git230720-4ubuntu2), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu6), libunicode-linebreak-perl (= 0.0.20190101-1build7), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu4), libwebp7 (= 1.3.2-0.4build3), libwebpdemux2 (= 1.3.2-0.4build3), libwebpmux3 (= 1.3.2-0.4build3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxaw7 (= 2:1.0.14-1build2), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxi6 (= 2:1.8.1-1), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxmu6 (= 2:1.1.3-3build2), libxpm4 (= 1:3.5.17-1build2), libxrender1 (= 1:0.9.10-1.1), libxt6t64 (= 1:1.2.1-1.2build1), libyaml-tiny-perl (= 1.74-1), libzstd1 (= 1.5.5+dfsg2-2), libzzip-0-13t64 (= 0.13.72+dfsg.1-1.2build1), linux-libc-dev (= 6.8.0-20.20), lmodern (= 2.005-1), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), netpbm (= 2:11.05.02-1.1build1), opensp (= 1.5.2-15ubuntu2), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), python3 (= 3.12.2-0ubuntu2), python3-minimal (= 3.12.2-0ubuntu2), python3-packaging (= 24.0-1), python3.12 (= 3.12.2-5ubuntu3), python3.12-minimal (= 3.12.2-5ubuntu3), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sgml-base (= 1.31), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.08-6ubuntu2), t1utils (= 1.41-4build2), tar (= 1.35+dfsg-3), tex-common (= 6.18), texlive-base (= 2023.20240207-1), texlive-binaries (= 2023.20230311.66589-9build3), texlive-extra-utils (= 2023.20240207-1), texlive-latex-base (= 2023.20240207-1), texlive-luatex (= 2023.20240207-1), texlive-plain-generic (= 2023.20240207-1), tzdata (= 2024a-1ubuntu1), ucf (= 3.0043+nmu1), util-linux (= 2.39.3-9ubuntu4), uuid-dev (= 2.39.3-9ubuntu4), x11-common (= 1:7.7+23ubuntu2), xdg-utils (= 1.1.3-4.1ubuntu3), xfonts-encodings (= 1:1.0.5-0ubuntu2), xfonts-utils (= 1:7.7+6build2), xml-core (= 0.19), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711960418" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ wise_2.4.1-24build1_s390x.deb ----------------------------- new Debian package, version 2.0. size 938566 bytes: control archive=1950 bytes. 1820 bytes, 34 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-24build1 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 3748 Depends: libc6 (>= 2.34), libglib2.0-0t64 (>= 2.12.0), wise-data (= 2.4.1-24build1) Suggests: wise-doc (= 2.4.1-24build1) Section: science Priority: optional Homepage: https://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, like DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-04-01 08:33 ./ drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/ drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/bin/ -rwxr-xr-x root/root 141488 2024-04-01 08:33 ./usr/bin/dba -rwxr-xr-x root/root 67680 2024-04-01 08:33 ./usr/bin/dnal -rwxr-xr-x root/root 358720 2024-04-01 08:33 ./usr/bin/estwise -rwxr-xr-x root/root 440696 2024-04-01 08:33 ./usr/bin/estwisedb -rwxr-xr-x root/root 1055072 2024-04-01 08:33 ./usr/bin/genewise -rwxr-xr-x root/root 907680 2024-04-01 08:33 ./usr/bin/genewisedb -rwxr-xr-x root/root 153696 2024-04-01 08:33 ./usr/bin/genomewise -rwxr-xr-x root/root 157792 2024-04-01 08:33 ./usr/bin/promoterwise -rwxr-xr-x root/root 96352 2024-04-01 08:33 ./usr/bin/psw -rwxr-xr-x root/root 129176 2024-04-01 08:33 ./usr/bin/pswdb -rwxr-xr-x root/root 178272 2024-04-01 08:33 ./usr/bin/scanwise -rwxr-xr-x root/root 108640 2024-04-01 08:33 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/share/ drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/share/doc/wise/ -rw-r--r-- root/root 1973 2007-07-01 20:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 320 2024-03-14 14:39 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 1026 2024-04-01 08:33 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4297 2024-03-14 14:42 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 312 2024-03-14 14:39 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-01 08:33 ./usr/share/man/man1/ -rw-r--r-- root/root 846 2024-04-01 08:33 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2024-04-01 08:33 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2024-04-01 08:33 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2024-04-01 08:33 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2024-04-01 08:33 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2024-04-01 08:33 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2024-04-01 08:33 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2024-04-01 08:33 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2024-04-01 08:33 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2024-04-01 08:33 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2024-04-01 08:33 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2024-04-01 08:33 ./usr/share/man/man1/scanwise_server.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 157220 Build-Time: 126 Distribution: noble-proposed Host Architecture: s390x Install-Time: 87 Job: wise_2.4.1-24build1.dsc Machine Architecture: s390x Package: wise Package-Time: 214 Source-Version: 2.4.1-24build1 Space: 157220 Status: successful Version: 2.4.1-24build1 -------------------------------------------------------------------------------- Finished at 2024-04-03T16:53:29Z Build needed 00:03:34, 157220k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-28014854 Scanning for processes to kill in build PACKAGEBUILD-28014854