https://launchpad.net/ubuntu/+source/wise/2.4.1-23build2/+build/27904284 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-012 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... 12 Mar 05:26:54 ntpdate[1879]: adjust time server 10.211.37.1 offset -0.000039 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27904284 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27904284 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27904284 Starting target for build PACKAGEBUILD-27904284 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27904284 '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-27904284 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27904284 Updating target for build PACKAGEBUILD-27904284 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1367 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.9 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6039 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [584 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [210 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [2972 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1166 kB] Fetched 28.3 MB in 6s (4576 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* libcom-err2* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libreadline8* libss2* 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 libcom-err2t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libreadline8t64 libss2t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: optipng The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-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 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 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 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 libpng16-16 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 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 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 151 upgraded, 24 newly installed, 15 to remove and 1 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-proposed/main s390x libnsl-dev s390x 1.3.0-3build2 [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 2.39-0ubuntu5 [1629 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-dev-bin s390x 2.39-0ubuntu5 [20.2 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-dev s390x 1.3.4+ds-1.1 [197 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnss-nisplus s390x 1.3-5 [23.6 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1 [85.8 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgssapi-krb5-2 s390x 1.20.1-5.1build2 [149 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5-3 s390x 1.20.1-5.1build2 [360 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libk5crypto3 s390x 1.20.1-5.1build2 [90.2 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5support0 s390x 1.20.1-5.1build2 [34.6 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2t64 s390x 1.47.0-2.3ubuntu1 [22.8 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.3ubuntu1 [222 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.3ubuntu1 [22.3 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2t64 s390x 1.47.0-2.3ubuntu1 [17.4 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.3ubuntu1 [616 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libacl1 s390x 2.3.2-1 [18.0 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0~alpha4-0ubuntu1 [50.2 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit-common all 1:3.1.2-2.1 [5674 B] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.4-2 [15.7 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit1 s390x 1:3.1.2-2.1 [48.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu2 [128 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libcap2 s390x 1:2.66-5ubuntu1 [31.7 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4 [102 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libgcrypt20 s390x 1.10.3-2 [499 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblzma5 s390x 5.6.0-0.2 [137 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu4 [56.3 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1 s390x 3.5-2build2 [84.3 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu2 [138 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2 [3110 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-5 [763 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1 [36.4 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1 [6880 B] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2 [5007 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2 [231 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2 [1961 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu3 [15.7 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-iconv-perl s390x 1.7-8build2 [13.8 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-charwidth-perl s390x 0.04-11build2 [9484 B] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6 s390x 2.39-0ubuntu5 [2847 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-bin s390x 2.39-0ubuntu5 [654 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu1 [1006 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255.4-1ubuntu4 [2131 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu2 [264 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu1 [1652 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255.4-1ubuntu4 [103 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255.4-1ubuntu4 [11.9 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255.4-1ubuntu4 [3534 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255.4-1ubuntu4 [443 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu3 [57.4 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules s390x 1.5.3-5ubuntu3 [289 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnettle8t64 s390x 3.9.1-2.2 [210 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libhogweed6t64 s390x 3.9.1-2.2 [204 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu1 [318 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu2 [1044 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0t64 s390x 2.7.13ubuntu1 [1013 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x bzip2 s390x 1.0.8-5ubuntu1 [35.5 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-1.0 s390x 1.0.8-5ubuntu1 [40.1 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240303-1ubuntu1 [46.9 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240303-1ubuntu1 [35.9 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240303-1ubuntu1 [908 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255.4-1ubuntu4 [178 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu1 [75.7 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.6-1 [23.0 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2 [67.2 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdebconfclient0 s390x 0.271ubuntu2 [11.4 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu15 [589 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libreadline8t64 s390x 8.2-3.1 [171 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-3.1 [56.4 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu1 [161 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu1 [117 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-agent s390x 2.4.4-2ubuntu15 [240 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 2.4.4-2ubuntu15 [111 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pinentry-curses s390x 1.2.1-3ubuntu3 [37.6 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1 [8148 B] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu15 [165 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x libseccomp2 s390x 2.5.5-1ubuntu1 [53.3 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.13ubuntu1 [214 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.13ubuntu1 [1390 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x debconf-i18n all 1.5.86 [205 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x debconf all 1.5.86 [124 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam0g s390x 1.5.3-5ubuntu3 [69.8 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu2 [142 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu2 [35.6 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu2 [151 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu2 [119 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3 [9448 B] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnsl2 s390x 1.3.0-3build2 [44.1 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu7 [74.2 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debianutils s390x 5.17 [90.1 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu2 [845 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu2 [96.1 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-3ubuntu3 [1482 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3 [269 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.5ubuntu4 [1279 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x dash s390x 0.5.12-6ubuntu4 [94.9 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4 [189 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x gzip s390x 1.12-1ubuntu2 [106 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main s390x hostname s390x 3.23+nmu2ubuntu1 [11.1 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-4ubuntu1 [202 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu1 [198 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2 [207 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu2 [1143 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-6ubuntu2 [34.7 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu2 [67.9 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu2 [33.4 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x libattr1 s390x 1:2.5.2-1 [11.7 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2 [24.7 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage-common all 3.5-1build3 [10.1 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage2 s390x 3.5-1build3 [96.7 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu1 [857 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-17ubuntu2 [14.4 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-17ubuntu2 [467 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-17ubuntu2 [1026 B] Get:133 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [9929 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240303-1ubuntu1 [49.9 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-3ubuntu1 [98.4 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-3ubuntu1 [100 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-3ubuntu1 [14.3 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-3ubuntu1 [2270 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-3ubuntu1 [477 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-3ubuntu1 [3058 B] Get:141 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-3ubuntu1 [217 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-17ubuntu2 [2430 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240303-1ubuntu1 [31.1 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240303-1ubuntu1 [2998 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240303-1ubuntu1 [1186 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-17ubuntu2 [1003 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [19.1 MB] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [11.3 MB] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-17ubuntu2 [47.4 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu1 [60.0 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1 [133 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-4ubuntu1 [724 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x krb5-locales all 1.20.1-5.1build2 [13.8 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu1 [24.2 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main s390x tzdata all 2024a-1ubuntu1 [273 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu2 [76.3 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16 s390x 1.6.43-1 [200 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x psmisc s390x 23.7-1 [178 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xz-utils s390x 5.6.0-0.2 [274 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:166 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:167 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.5ubuntu4 [1060 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.5ubuntu4 [269 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.33-1 [31.9 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.33-1 [67.5 kB] Preconfiguring packages ... Fetched 105 MB in 5s (20.0 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build2_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build2) 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_2.39-0ubuntu5_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu5) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu5_s390x.deb ... Unpacking libc-dev-bin (2.39-0ubuntu5) over (2.38-1ubuntu6) ... Preparing to unpack .../4-libtirpc-common_1.3.4+ds-1.1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.3+ds-1) ... Preparing to unpack .../5-libtirpc-dev_1.3.4+ds-1.1_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libnss-nisplus_1.3-5_s390x.deb ... 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(Reading database ... 14821 files and directories currently installed.) Removing libdb5.3:s390x (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:s390x. (Reading database ... 14815 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_s390x.deb ... Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-5) ... dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm6 (>= 1.21). libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). (Reading database ... 14821 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. (Reading database ... 14816 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1_s390x.deb ... 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Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu4_s390x.deb ... Unpacking libsystemd-shared:s390x (255.4-1ubuntu4) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu2_s390x.deb ... Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu2) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15349 files and directories currently installed.) Removing libssl3:s390x (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:s390x. (Reading database ... 15338 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_s390x.deb ... Unpacking libssl3t64:s390x (3.0.13-0ubuntu1) ... Setting up libssl3t64:s390x (3.0.13-0ubuntu1) ... (Reading database ... 15351 files and directories currently installed.) 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Unpacking systemd (255.4-1ubuntu4) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty 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_255.4-1ubuntu4_s390x.deb ... 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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_1.0.8-5ubuntu1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.8-5ubuntu1) over (1.0.8-5build1) ... Setting up libbz2-1.0:s390x (1.0.8-5ubuntu1) ... Selecting previously unselected package gcc-14-base:s390x. (Reading database ... 15514 files and directories currently installed.) 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Setting up libgdbm6t64:s390x (1.23-5.1) ... Setting up bsdextrautils (2.39.3-9ubuntu2) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... Setting up psmisc (23.7-1) ... Setting up libtirpc-common (1.3.4+ds-1.1) ... Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ... Setting up binutils-common:s390x (2.42-3ubuntu1) ... Setting up linux-libc-dev:s390x (6.8.0-11.11) ... Setting up libctf-nobfd0:s390x (2.42-3ubuntu1) ... Setting up krb5-locales (1.20.1-5.1build2) ... Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... Setting up bzip2 (1.0.8-5ubuntu1) ... Setting up libsframe1:s390x (2.42-3ubuntu1) ... Setting up libfakeroot:s390x (1.33-1) ... Setting up libkrb5support0:s390x (1.20.1-5.1build2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Mar 12 05:27:44 UTC 2024. Universal Time is now: Tue Mar 12 05:27:44 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:s390x (13.2.0-17ubuntu2) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.0-0.2) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libproc2-0:s390x (2:4.0.4-4ubuntu1) ... Setting up libpng16-16:s390x (1.6.43-1) ... Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... Setting up libncursesw6:s390x (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:s390x (1.20.1-5.1build2) ... Setting up logsave (1.47.0-2.3ubuntu1) ... Setting up libdb5.3t64:s390x (5.3.28+dfsg2-5) ... Setting up libubsan1:s390x (14-20240303-1ubuntu1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu2) ... 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 (14-20240303-1ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:s390x (1.20.1-5.1build2) ... Setting up libperl5.38t64:s390x (5.38.2-3.2) ... Setting up libbinutils:s390x (2.42-3ubuntu1) ... Setting up libc-dev-bin (2.39-0ubuntu5) ... Setting up openssl (3.0.13-0ubuntu1) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3.1) ... Setting up libcc1-0:s390x (14-20240303-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu3) ... Setting up libitm1:s390x (14-20240303-1ubuntu1) ... Setting up libctf0:s390x (2.42-3ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu3) ... Setting up apt-utils (2.7.13ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.42-3ubuntu1) ... Setting up cpp-13 (13.2.0-17ubuntu2) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.3ubuntu1) ... Setting up binutils (2.42-3ubuntu1) ... 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 (5.38.2-3.2) ... Setting up libgssapi-krb5-2:s390x (1.20.1-5.1build2) ... Setting up libdpkg-perl (1.22.5ubuntu4) ... Setting up libreadline8t64:s390x (8.2-3.1) ... Setting up libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu15) ... Setting up libc6-dev:s390x (2.39-0ubuntu5) ... Setting up gpg (2.4.4-2ubuntu15) ... Setting up libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... Setting up gpg-agent (2.4.4-2ubuntu15) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.1) ... Setting up dpkg-dev (1.22.5ubuntu4) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... Setting up gcc-13 (13.2.0-17ubuntu2) ... Setting up libnsl2:s390x (1.3.0-3build2) ... Setting up g++-13 (13.2.0-17ubuntu2) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build2) ... Processing triggers for libc-bin (2.39-0ubuntu5) ... Processing triggers for debianutils (5.17) ... (Reading database ... 15497 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-27904284 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27904284 --arch=s390x --dist=noble-proposed --nolog wise_2.4.1-23build2.dsc Initiating build PACKAGEBUILD-27904284 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-012.buildd +==============================================================================+ | wise 2.4.1-23build2 (s390x) Tue, 12 Mar 2024 05:27:50 +0000 | +==============================================================================+ Package: wise Version: 2.4.1-23build2 Source Version: 2.4.1-23build2 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-27904284/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/wise-qmo8bD/resolver-BGKojb' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- wise_2.4.1-23build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/wise-qmo8bD/wise-2.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/wise-qmo8bD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), 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 [418 B] Get:5 copy:/<>/apt_archive ./ Packages [496 B] Fetched 1871 B in 0s (164 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 libcups2 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.q16-7 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 libpng16-16t64 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-0-13 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 packages will be REMOVED: libpng16-16* 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 libcups2 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.q16-7 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 libpng16-16t64 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-0-13 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, 175 newly installed, 1 to remove and 1 not upgraded. Need to get 234 MB of archives. After this operation, 586 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [716 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpng16-16t64 s390x 1.6.43-3 [200 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-minimal s390x 3.12.2-4build2 [829 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libexpat1 s390x 2.6.1-2 [94.8 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12-minimal s390x 3.12.2-4build2 [2437 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-minimal s390x 3.12.2-0ubuntu1 [27.1 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x media-types all 10.1.0 [27.5 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x netbase all 6.4 [13.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-stdlib s390x 3.12.2-4build2 [2046 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12 s390x 3.12.2-4build2 [645 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3-stdlib s390x 3.12.2-0ubuntu1 [9804 B] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3 s390x 3.12.2-0ubuntu1 [24.1 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu1 [465 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2 [374 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfreetype6 s390x 2.13.2+dfsg-1build1 [437 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.4-1build3 [14.2 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu1 [37.4 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu1 [150 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsharpyuv0 s390x 1.3.2-0.4build1 [14.9 kB] Get:26 http://ftpmaster.internal/ubuntu noble/universe s390x libdav1d7 s390x 1.4.0-1 [316 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libheif-plugin-dav1d s390x 1.17.6-1ubuntu2 [10.2 kB] Get:28 http://ftpmaster.internal/ubuntu noble/universe s390x libde265-0 s390x 1.0.15-1 [201 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libheif-plugin-libde265 s390x 1.17.6-1ubuntu2 [8306 B] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libheif1 s390x 1.17.6-1ubuntu2 [299 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x liblqr-1-0 s390x 0.4.2-2.1build1 [32.7 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libltdl7 s390x 2.4.7-7 [41.6 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libopenjp2-7 s390x 2.5.0-2build1 [192 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libraw23t64 s390x 0.21.2-2.1 [418 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebp7 s390x 1.3.2-0.4build1 [207 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu1 [218 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebpdemux2 s390x 1.3.2-0.4build1 [12.5 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebpmux3 s390x 1.3.2-0.4build1 [25.4 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libxau6 s390x 1:1.0.9-1build5 [7522 B] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu5 [10.8 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libxcb1 s390x 1.15-1 [48.3 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libx11-data all 2:1.8.7-1 [115 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x libx11-6 s390x 2:1.8.7-1 [672 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libxext6 s390x 2:1.3.4-1build1 [30.5 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu1 [10.9 MB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu1 [818 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick-6-common all 8:6.9.12.98+dfsg1-5.1build2 [69.4 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmagickcore-6.q16-7 s390x 8:6.9.12.98+dfsg1-5build1 [1889 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmagickwand-6.q16-7t64 s390x 8:6.9.12.98+dfsg1-5.1build2 [352 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main s390x poppler-data all 0.4.12-1 [2060 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdbus-1-3 s390x 1.14.10-4ubuntu2 [213 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 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-proposed/main s390x libmagic-mgc s390x 1:5.45-3 [305 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic1t64 s390x 1:5.45-3 [93.1 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main s390x file s390x 1:5.45-3 [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-proposed/main s390x groff-base s390x 1.23.0-3build1 [1049 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main s390x libpipeline1 s390x 1.5.7-1 [23.4 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-3build4 [1246 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-proposed/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-proposed/main s390x libelf1t64 s390x 0.190-1.1build1 [69.7 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdw1t64 s390x 0.190-1.1build1 [286 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debugedit s390x 1:5.0-5build1 [50.5 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dwz s390x 0.15-1build5 [122 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14ubuntu1 [917 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debhelper all 13.14.1ubuntu5 [869 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x sgml-data all 2.0.11+nmu1 [171 kB] Get:92 http://ftpmaster.internal/ubuntu noble/universe s390x docbook all 4.5-10 [120 kB] Get:93 http://ftpmaster.internal/ubuntu noble/universe s390x libosp5 s390x 1.5.2-15ubuntu1 [708 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe s390x opensp s390x 1.5.2-15ubuntu1 [152 kB] Get:95 http://ftpmaster.internal/ubuntu noble/universe s390x docbook-to-man s390x 1:2.0.0-45 [80.7 kB] Get:96 http://ftpmaster.internal/ubuntu noble/universe s390x fonts-lmodern all 2.005-1 [4799 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgs-common all 10.02.1~dfsg1-0ubuntu4 [174 kB] Get:98 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s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxt6t64 s390x 1:1.2.1-1.2 [184 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgs10 s390x 10.02.1~dfsg1-0ubuntu4 [4249 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ghostscript s390x 10.02.1~dfsg1-0ubuntu4 [43.5 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libnetpbm11t64 s390x 2:11.05.02-1.1 [124 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x netpbm s390x 2:11.05.02-1.1 [2188 kB] Get:114 http://ftpmaster.internal/ubuntu noble/universe s390x tex-common all 6.18 [32.8 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkpathsea6 s390x 2023.20230311.66589-9build1 [66.5 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libptexenc1 s390x 2023.20230311.66589-9build1 [41.6 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsynctex2 s390x 2023.20230311.66589-9build1 [65.0 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtexlua53-5 s390x 2023.20230311.66589-9build1 [132 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x t1utils s390x 1.41-4build2 [61.5 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcairo2 s390x 1.18.0-1ubuntu1 [589 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libharfbuzz0b s390x 8.3.0-2build1 [515 kB] Get:128 http://ftpmaster.internal/ubuntu noble/universe s390x libpotrace0 s390x 1.16-2 [16.4 kB] Get:129 http://ftpmaster.internal/ubuntu noble/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxmu6 s390x 2:1.1.3-3build1 [52.9 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxpm4 s390x 1:3.5.17-1build1 [41.4 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxaw7 s390x 2:1.0.14-1build1 [204 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main s390x libxi6 s390x 2:1.8.1-1 [35.7 kB] Get:134 http://ftpmaster.internal/ubuntu noble/universe s390x libzzip-0-13 s390x 0.13.72+dfsg.1-1.1 [26.1 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x texlive-binaries s390x 2023.20230311.66589-9build1 [9351 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:137 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-base all 2023.20240207-1 [21.7 MB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x hicolor-icon-theme all 0.17-2 [9976 B] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick-6.q16 s390x 8:6.9.12.98+dfsg1-5.1build2 [254 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x imagemagick s390x 8:6.9.12.98+dfsg1-5.1build2 [14.2 kB] Get:141 http://ftpmaster.internal/ubuntu noble/universe s390x hevea s390x 2.36-2 [2045 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x libfile-which-perl all 1.27-2 [12.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main s390x libfile-homedir-perl all 1.006-2 [37.0 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgirepository-2.0-0 s390x 2.79.3-3ubuntu5 [75.4 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-bin s390x 2.79.3-3ubuntu5 [101 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x libffi-dev s390x 3.4.6-1 [58.8 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x python3-packaging all 23.2-1 [40.6 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-dev-bin s390x 2.79.3-3ubuntu5 [225 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-dev s390x 2.39.3-9ubuntu2 [34.2 kB] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid-dev s390x 2.39.3-9ubuntu2 [213 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x libsepol-dev s390x 3.5-2 [395 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-16-0 s390x 10.42-4ubuntu1 [229 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-32-0 s390x 10.42-4ubuntu1 [217 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-posix3 s390x 10.42-4ubuntu1 [6704 B] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-dev s390x 10.42-4ubuntu1 [805 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1-dev s390x 3.5-2build2 [168 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount-dev s390x 2.39.3-9ubuntu2 [14.9 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main s390x libpkgconf3 s390x 1.8.1-2 [30.4 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf-bin s390x 1.8.1-2 [20.8 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf s390x 1.8.1-2 [16.7 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu1 [904 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-dev s390x 2.79.3-3ubuntu5 [1820 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe s390x libmime-charset-perl all 1.013.1-2 [31.0 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe s390x libsombok3 s390x 2.4.0-2 [25.2 kB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libunicode-linebreak-perl s390x 0.0.20190101-1build6 [94.4 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x libyaml-tiny-perl all 1.74-1 [25.3 kB] Get:171 http://ftpmaster.internal/ubuntu noble/universe s390x lmodern all 2.005-1 [9542 kB] Get:172 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-latex-base all 2023.20240207-1 [1238 kB] Get:173 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-luatex all 2023.20240207-1 [25.8 MB] Get:174 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-plain-generic all 2023.20240207-1 [29.0 MB] Get:175 http://ftpmaster.internal/ubuntu noble/universe s390x texlive-extra-utils all 2023.20240207-1 [63.0 MB] Preconfiguring packages ... Fetched 234 MB in 11s (20.6 MB/s) dpkg: libpng16-16:s390x: dependency problems, but removing anyway as you requested: optipng depends on libpng16-16 (>= 1.6.2-1). (Reading database ... 15497 files and directories currently installed.) Removing libpng16-16:s390x (1.6.43-1) ... Selecting previously unselected package libpng16-16t64:s390x. (Reading database ... 15487 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-3_s390x.deb ... Unpacking libpng16-16t64:s390x (1.6.43-3) ... Selecting previously unselected package libpython3.12-minimal:s390x. Preparing to unpack .../libpython3.12-minimal_3.12.2-4build2_s390x.deb ... Unpacking libpython3.12-minimal:s390x (3.12.2-4build2) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.6.1-2_s390x.deb ... Unpacking libexpat1:s390x (2.6.1-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-4build2_s390x.deb ... Unpacking python3.12-minimal (3.12.2-4build2) ... Setting up libpython3.12-minimal:s390x (3.12.2-4build2) ... Setting up libexpat1:s390x (2.6.1-2) ... Setting up python3.12-minimal (3.12.2-4build2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15816 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.2-0ubuntu1_s390x.deb ... Unpacking python3-minimal (3.12.2-0ubuntu1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libpython3.12-stdlib:s390x. Preparing to unpack .../3-libpython3.12-stdlib_3.12.2-4build2_s390x.deb ... Unpacking libpython3.12-stdlib:s390x (3.12.2-4build2) ... Selecting previously unselected package python3.12. Preparing to unpack .../4-python3.12_3.12.2-4build2_s390x.deb ... Unpacking python3.12 (3.12.2-4build2) ... Selecting previously unselected package libpython3-stdlib:s390x. Preparing to unpack .../5-libpython3-stdlib_3.12.2-0ubuntu1_s390x.deb ... Unpacking libpython3-stdlib:s390x (3.12.2-0ubuntu1) ... Setting up python3-minimal (3.12.2-0ubuntu1) ... Selecting previously unselected package python3. (Reading database ... 16256 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.2-0ubuntu1_s390x.deb ... Unpacking python3 (3.12.2-0ubuntu1) ... Selecting previously unselected package libfftw3-double3:s390x. Preparing to unpack .../001-libfftw3-double3_3.3.10-1ubuntu1_s390x.deb ... Unpacking libfftw3-double3:s390x (3.3.10-1ubuntu1) ... Selecting previously unselected package libbrotli1:s390x. Preparing to unpack .../002-libbrotli1_1.1.0-2_s390x.deb ... Unpacking libbrotli1:s390x (1.1.0-2) ... 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Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../009-xfonts-utils_1%3a7.7+6build2_s390x.deb ... Unpacking xfonts-utils (1:7.7+6build2) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../010-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.15.0-1.1ubuntu1_s390x.deb ... Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ... Selecting previously unselected package libfontconfig1:s390x. Preparing to unpack .../012-libfontconfig1_2.15.0-1.1ubuntu1_s390x.deb ... Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu1) ... Selecting previously unselected package libsharpyuv0:s390x. Preparing to unpack .../013-libsharpyuv0_1.3.2-0.4build1_s390x.deb ... Unpacking libsharpyuv0:s390x (1.3.2-0.4build1) ... Selecting previously unselected package libdav1d7:s390x. Preparing to unpack .../014-libdav1d7_1.4.0-1_s390x.deb ... Unpacking libdav1d7:s390x (1.4.0-1) ... Selecting previously unselected package libheif-plugin-dav1d:s390x. Preparing to unpack .../015-libheif-plugin-dav1d_1.17.6-1ubuntu2_s390x.deb ... Unpacking libheif-plugin-dav1d:s390x (1.17.6-1ubuntu2) ... Selecting previously unselected package libde265-0:s390x. Preparing to unpack .../016-libde265-0_1.0.15-1_s390x.deb ... Unpacking libde265-0:s390x (1.0.15-1) ... Selecting previously unselected package libheif-plugin-libde265:s390x. Preparing to unpack .../017-libheif-plugin-libde265_1.17.6-1ubuntu2_s390x.deb ... Unpacking libheif-plugin-libde265:s390x (1.17.6-1ubuntu2) ... Selecting previously unselected package libheif1:s390x. Preparing to unpack .../018-libheif1_1.17.6-1ubuntu2_s390x.deb ... Unpacking libheif1:s390x (1.17.6-1ubuntu2) ... Selecting previously unselected package libjbig0:s390x. 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Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu1) ... Selecting previously unselected package libwebpdemux2:s390x. Preparing to unpack .../031-libwebpdemux2_1.3.2-0.4build1_s390x.deb ... Unpacking libwebpdemux2:s390x (1.3.2-0.4build1) ... Selecting previously unselected package libwebpmux3:s390x. Preparing to unpack .../032-libwebpmux3_1.3.2-0.4build1_s390x.deb ... Unpacking libwebpmux3:s390x (1.3.2-0.4build1) ... Selecting previously unselected package libxau6:s390x. Preparing to unpack .../033-libxau6_1%3a1.0.9-1build5_s390x.deb ... Unpacking libxau6:s390x (1:1.0.9-1build5) ... Selecting previously unselected package libbsd0:s390x. Preparing to unpack .../034-libbsd0_0.12.1-1_s390x.deb ... Unpacking libbsd0:s390x (0.12.1-1) ... Selecting previously unselected package libxdmcp6:s390x. Preparing to unpack .../035-libxdmcp6_1%3a1.1.3-0ubuntu5_s390x.deb ... Unpacking libxdmcp6:s390x (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:s390x. 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Preparing to unpack .../047-libdbus-1-3_1.14.10-4ubuntu2_s390x.deb ... Unpacking libdbus-1-3:s390x (1.14.10-4ubuntu2) ... Selecting previously unselected package libglib2.0-data. Preparing to unpack .../048-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... Unpacking libglib2.0-data (2.79.3-3ubuntu5) ... Selecting previously unselected package ucf. Preparing to unpack .../049-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../050-libmagic-mgc_1%3a5.45-3_s390x.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:s390x. Preparing to unpack .../051-libmagic1t64_1%3a5.45-3_s390x.deb ... Unpacking libmagic1t64:s390x (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../052-file_1%3a5.45-3_s390x.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. 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Setting up libxau6:s390x (1:1.0.9-1build5) ... Setting up imagemagick-6-common (8:6.9.12.98+dfsg1-5.1build2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libdatrie1:s390x (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... 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~dfsg1-0ubuntu4) ... Setting up libbrotli1:s390x (1.1.0-2) ... Setting up libmagic1t64:s390x (1:5.45-3) ... 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 libzzip-0-13:s390x (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.45-3) ... 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 (2:11.05.02-1.1) ... Setting up libpcre2-16-0:s390x (10.42-4ubuntu1) ... Setting up libelf1t64:s390x (0.190-1.1build1) ... Setting up poppler-data (0.4.12-1) ... Setting up libdw1t64:s390x (0.190-1.1build1) ... Setting up libosp5 (1.5.2-15ubuntu1) ... Setting up libfontenc1:s390x (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:s390x (10.42-4ubuntu1) ... Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ... No schema files found: doing nothing. Setting up libglib2.0-data (2.79.3-3ubuntu5) ... Setting up libpkgconf3:s390x (1.8.1-2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:s390x (0.20-1build1) ... Setting up libteckit0:s390x (2.5.12+ds1-1) ... Setting up uuid-dev:s390x (2.39.3-9ubuntu2) ... Setting up libavahi-common-data:s390x (0.8-13ubuntu4) ... Setting up libdbus-1-3:s390x (1.14.10-4ubuntu2) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:s390x (2023.20230311.66589-9build1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:s390x (1.6.43-3) ... 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 (3.3.10-1ubuntu1) ... Setting up libkpathsea6:s390x (2023.20230311.66589-9build1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:s390x (1.3.2-0.4build1) ... Setting up libicu74:s390x (74.2-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu1) ... Setting up libpcre2-posix3:s390x (10.42-4ubuntu1) ... Setting up dwz (0.15-1build5) ... Setting up libdav1d7:s390x (1.4.0-1) ... Setting up liblqr-1-0:s390x (0.4.2-2.1build1) ... 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 (2.5.0-2build1) ... Setting up libsub-override-perl (0.10-1) ... 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 (1.0.15-1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libwebpmux3:s390x (1.3.2-0.4build1) ... Setting up libbsd0:s390x (0.12.1-1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu1) ... 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 (2023.20230311.66589-9build1) ... 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 (2.39.3-9ubuntu2) ... 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 (3.12.2-4build2) ... Setting up libpcre2-dev:s390x (10.42-4ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libgirepository-2.0-0:s390x (2.79.3-3ubuntu5) ... Setting up libxcb-render0:s390x (1.15-1) ... Setting up libselinux1-dev:s390x (3.5-2build2) ... Setting up fontconfig-config (2.15.0-1.1ubuntu1) ... Setting up libwebpdemux2:s390x (1.3.2-0.4build1) ... Setting up python3.12 (3.12.2-4build2) ... Setting up libavahi-common3:s390x (0.8-13ubuntu4) ... Setting up libglib2.0-bin (2.79.3-3ubuntu5) ... Setting up libxcb-shm0:s390x (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up opensp (1.5.2-15ubuntu1) ... 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 (2023.20230311.66589-9build1) ... Setting up libfreetype6:s390x (2.13.2+dfsg-1build1) ... Setting up libraw23t64:s390x (0.21.2-2.1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build1) ... Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu1) ... Setting up xml-core (0.19) ... Setting up libx11-6:s390x (2:1.8.7-1) ... Setting up libharfbuzz0b:s390x (8.3.0-2build1) ... Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu1) ... Setting up libsm6:s390x (2:1.2.3-1build2) ... Setting up libavahi-client3:s390x (0.8-13ubuntu4) ... Setting up libmount-dev:s390x (2.39.3-9ubuntu2) ... Setting up libpython3-stdlib:s390x (3.12.2-0ubuntu1) ... Setting up libxpm4:s390x (1:3.5.17-1build1) ... 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 (3.12.2-0ubuntu1) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up man-db (2.12.0-3build4) ... 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 (1.18.0-1ubuntu1) ... Setting up python3-packaging (23.2-1) ... Setting up libunicode-linebreak-perl (0.0.20190101-1build6) ... Setting up libxt6t64:s390x (1:1.2.1-1.2) ... Setting up netpbm (2:11.05.02-1.1) ... Setting up libcups2:s390x (2.4.7-1ubuntu2) ... Setting up lmodern (2.005-1) ... Setting up libglib2.0-dev-bin (2.79.3-3ubuntu5) ... Setting up libxmu6:s390x (2:1.1.3-3build1) ... Setting up libxi6:s390x (2:1.8.1-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libxaw7:s390x (2:1.0.14-1build1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libglib2.0-dev:s390x (2.79.3-3ubuntu5) ... Setting up texlive-binaries (2023.20230311.66589-9build1) ... 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-common (10.02.1~dfsg1-0ubuntu4) ... Setting up texlive-luatex (2023.20240207-1) ... Setting up texlive-plain-generic (2023.20240207-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-extra-utils (2023.20240207-1) ... Setting up libgs10:s390x (10.02.1~dfsg1-0ubuntu4) ... Setting up ghostscript (10.02.1~dfsg1-0ubuntu4) ... Setting up libheif-plugin-dav1d:s390x (1.17.6-1ubuntu2) ... Setting up libheif-plugin-libde265:s390x (1.17.6-1ubuntu2) ... Setting up libheif1:s390x (1.17.6-1ubuntu2) ... Setting up libmagickcore-6.q16-7:s390x (8:6.9.12.98+dfsg1-5build1) ... Setting up libmagickwand-6.q16-7t64:s390x (8:6.9.12.98+dfsg1-5.1build2) ... Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5.1build2) ... 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+dfsg1-5.1build2) ... Processing triggers for libc-bin (2.39-0ubuntu5) ... Processing triggers for systemd (255.4-1ubuntu4) ... 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_2.42-3ubuntu1 dpkg-dev_1.22.5ubuntu4 g++-13_13.2.0-17ubuntu2 gcc-13_13.2.0-17ubuntu2 libc6-dev_2.39-0ubuntu5 libstdc++-13-dev_13.2.0-17ubuntu2 libstdc++6_14-20240303-1ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.13ubuntu1 apt-utils_2.7.13ubuntu1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu7 base-passwd_3.6.3 bash_5.2.21-2ubuntu2 bash-completion_1:2.11-8 binutils_2.42-3ubuntu1 binutils-common_2.42-3ubuntu1 binutils-s390x-linux-gnu_2.42-3ubuntu1 bsdextrautils_2.39.3-9ubuntu2 bsdutils_1:2.39.3-9ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5ubuntu1 ca-certificates_20240203 coreutils_9.4-3ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-17ubuntu2 cpp-13-s390x-linux-gnu_13.2.0-17ubuntu2 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu4 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17 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_1.22.5ubuntu4 dpkg-dev_1.22.5ubuntu4 dwz_0.15-1build5 e2fsprogs_1.47.0-2.3ubuntu1 fakeroot_1.33-1 file_1:5.45-3 findutils_4.9.0-5 fontconfig-config_2.15.0-1.1ubuntu1 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_13.2.0-17ubuntu2 g++-13-s390x-linux-gnu_13.2.0-17ubuntu2 g++-s390x-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-17ubuntu2 gcc-13-base_13.2.0-17ubuntu2 gcc-13-s390x-linux-gnu_13.2.0-17ubuntu2 gcc-14-base_14-20240303-1ubuntu1 gcc-s390x-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 ghostscript_10.02.1~dfsg1-0ubuntu4 gpg_2.4.4-2ubuntu15 gpg-agent_2.4.4-2ubuntu15 gpgconf_2.4.4-2ubuntu15 gpgv_2.4.4-2ubuntu15 grep_3.11-4 groff-base_1.23.0-3build1 gzip_1.12-1ubuntu2 hevea_2.36-2 hicolor-icon-theme_0.17-2 hostname_3.23+nmu2ubuntu1 imagemagick_8:6.9.12.98+dfsg1-5.1build2 imagemagick-6-common_8:6.9.12.98+dfsg1-5.1build2 imagemagick-6.q16_8:6.9.12.98+dfsg1-5.1build2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5.1build2 libacl1_2.3.2-1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0t64_2.7.13ubuntu1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240303-1ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240303-1ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libavahi-client3_0.8-13ubuntu4 libavahi-common-data_0.8-13ubuntu4 libavahi-common3_0.8-13ubuntu4 libbinutils_2.42-3ubuntu1 libblkid-dev_2.39.3-9ubuntu2 libblkid1_2.39.3-9ubuntu2 libbrotli1_1.1.0-2 libbsd0_0.12.1-1 libbz2-1.0_1.0.8-5ubuntu1 libc-bin_2.39-0ubuntu5 libc-dev-bin_2.39-0ubuntu5 libc6_2.39-0ubuntu5 libc6-dev_2.39-0ubuntu5 libcairo2_1.18.0-1ubuntu1 libcap-ng0_0.8.4-2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240303-1ubuntu1 libcom-err2t64_1.47.0-2.3ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu2 libctf-nobfd0_2.42-3ubuntu1 libctf0_2.42-3ubuntu1 libcups2_2.4.7-1ubuntu2 libdatrie1_0.2.13-3 libdav1d7_1.4.0-1 libdb5.3t64_5.3.28+dfsg2-5 libdbus-1-3_1.14.10-4ubuntu2 libde265-0_1.0.15-1 libdebconfclient0_0.271ubuntu2 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-3ubuntu2 libdpkg-perl_1.22.5ubuntu4 libdw1t64_0.190-1.1build1 libelf1t64_0.190-1.1build1 libexpat1_2.6.1-2 libext2fs2t64_1.47.0-2.3ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu2 libffi-dev_3.4.6-1 libffi8_3.4.6-1 libfftw3-double3_3.3.10-1ubuntu1 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libfontconfig1_2.15.0-1.1ubuntu1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.13.2+dfsg-1build1 libgcc-13-dev_13.2.0-17ubuntu2 libgcc-s1_14-20240303-1ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4t64_1.23-5.1 libgdbm6t64_1.23-5.1 libgirepository-2.0-0_2.79.3-3ubuntu5 libglib2.0-0t64_2.79.3-3ubuntu5 libglib2.0-bin_2.79.3-3ubuntu5 libglib2.0-data_2.79.3-3ubuntu5 libglib2.0-dev_2.79.3-3ubuntu5 libglib2.0-dev-bin_2.79.3-3ubuntu5 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30t64_3.8.3-1.1ubuntu2 libgomp1_14-20240303-1ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgraphite2-3_1.3.14-2 libgs-common_10.02.1~dfsg1-0ubuntu4 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libmagic1t64_1:5.45-3 libmagickcore-6.q16-7_8:6.9.12.98+dfsg1-5build1 libmagickwand-6.q16-7t64_8:6.9.12.98+dfsg1-5.1build2 libmd0_1.1.0-2 libmime-charset-perl_1.013.1-2 libmount-dev_2.39.3-9ubuntu2 libmount1_2.39.3-9ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1ubuntu1 libnetpbm11t64_2:11.05.02-1.1 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libnsl-dev_1.3.0-3build2 libnsl2_1.3.0-3build2 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-5 libopenjp2-7_2.5.0-2build1 libosp5_1.5.2-15ubuntu1 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.3-5ubuntu3 libpam-modules-bin_1.5.3-5ubuntu3 libpam-runtime_1.5.3-5ubuntu3 libpam0g_1.5.3-5ubuntu3 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 libperl5.36_5.36.0-9ubuntu1 libperl5.38t64_5.38.2-3.2 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpkgconf3_1.8.1-2 libpng16-16t64_1.6.43-3 libpotrace0_1.16-2 libproc2-0_2:4.0.4-4ubuntu1 libptexenc1_2023.20230311.66589-9build1 libpython3-stdlib_3.12.2-0ubuntu1 libpython3.12-minimal_3.12.2-4build2 libpython3.12-stdlib_3.12.2-4build2 libraw23t64_0.21.2-2.1 libreadline8t64_8.2-3.1 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build2 libselinux1-dev_3.5-2build2 libsemanage-common_3.5-1build3 libsemanage2_3.5-1build3 libsepol-dev_3.5-2 libsepol2_3.5-2 libsframe1_2.42-3ubuntu1 libsharpyuv0_1.3.2-0.4build1 libsm6_2:1.2.3-1build2 libsmartcols1_2.39.3-9ubuntu2 libsombok3_2.4.0-2 libsqlite3-0_3.45.1-1ubuntu1 libss2t64_1.47.0-2.3ubuntu1 libssl3t64_3.0.13-0ubuntu1 libstdc++-13-dev_13.2.0-17ubuntu2 libstdc++6_14-20240303-1ubuntu1 libsub-override-perl_0.10-1 libsynctex2_2023.20230311.66589-9build1 libsystemd-shared_255.4-1ubuntu4 libsystemd0_255.4-1ubuntu4 libtasn1-6_4.19.0-3 libteckit0_2.5.12+ds1-1 libtexlua53-5_2023.20230311.66589-9build1 libtext-charwidth-perl_0.04-11build2 libtext-iconv-perl_1.7-8build2 libtext-wrapi18n-perl_0.06-10 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login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2.3ubuntu1 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3build4 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.39.3-9ubuntu2 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 netbase_6.4 netpbm_2:11.05.02-1.1 opensp_1.5.2-15ubuntu1 openssl_3.0.13-0ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3.2 perl-base_5.38.2-3.2 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2 pinentry-curses_1.2.1-3ubuntu3 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_2:4.0.4-4ubuntu1 psmisc_23.7-1 python3_3.12.2-0ubuntu1 python3-minimal_3.12.2-0ubuntu1 python3-packaging_23.2-1 python3.12_3.12.2-4build2 python3.12-minimal_3.12.2-4build2 readline-common_8.2-3.1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sgml-base_1.31 sgml-data_2.0.11+nmu1 systemd_255.4-1ubuntu4 systemd-dev_255.4-1ubuntu4 systemd-sysv_255.4-1ubuntu4 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_2023.20230311.66589-9build1 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_2.39.3-9ubuntu2 uuid-dev_2.39.3-9ubuntu2 uuid-runtime_2.39.3-9ubuntu2 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_5.6.0-0.2 zlib1g_1:1.3.dfsg-3.1ubuntu1 zlib1g-dev_1:1.3.dfsg-3.1ubuntu1 +------------------------------------------------------------------------------+ | 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: 2.4.1-23build2 Maintainer: Ubuntu Developers Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.5.0 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 (= 12), 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 f129b09ef3543fe3eb64045cf3509c3b55b80c57 27276 wise_2.4.1-23build2.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz c97fbfca48e582baa72811c77d53fe1f49c0e619fd93b810165720efad16c3f9 27276 wise_2.4.1-23build2.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz 59e808173ddb12de225477db2c6c4042 27276 wise_2.4.1-23build2.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmXvmkkaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz3bRg//WTFHsZxVrAq40/2/375C qf0gchCWl8t9FHUlMfaLU8V0v54yU7rynpuOrOUUpJ6dTXoXGaJfE0NUGozijHwq u6tH8uBqGqNTj+EZxU0RpFYv6zSSvPITCaZ1q2wt+ymwtTUuyYZUf+7iakNplI7j 4qN2VdjiR82v2Oo1XUDXIGjG62xn19Q8YPk7dPPwTeSV4eiWmWGBIp3l2QXRGAN5 35Av6Cf7DWICeQsEd2Jh4cro3Zcrw+0p9FNdQgPcmGrBGrnSCWbH7xJvf+cjIzxt vZ9teTO1Mm7b9MEe9s8JLQliHKs0HLKIG44ZjklAQuYFS7dCDpIfOJP9O2LNN4kU KI7ZBj0wGYbt47YodJ17B43aVulzyWp8qbzhtWSrLvg+AUATA3LbN7Dc8m4P/Csw /hM+R7kidPABhJnEvmSqJwXsJxLTkB4cAk7erA+Z/kO/27i6leO/NSC0DSw2PBq3 soxSlPapBcDxHItFrf+4ZylNdtUtmLxWNsCcVngrUb0T4v9IvRWrNykniULooTUS uOHz92Fx1ChEsnC6RGMg2RgB6Pe6/FrsuRMCnt5sZaV+NLJjKp5oKnVbSb2Tz4Ck OmUhuj3ygAqKiTX8AfTHCgkWLzvmWbCEspfQfXccMAZRLZdVQNMORr4AdtA3qwcd /Rw+U1RoVWWb4Ro/93TghbQ= =ZydM -----END PGP SIGNATURE----- gpgv: Signature made Mon Mar 11 23:56:57 2024 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-23build2.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_2.4.1-23build2.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 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-27904284 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27904284 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27904284 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 2.4.1-23build2 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 prior.c: In function ‘P7ReadPrior’: prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ prior.c:10:1: note: include ‘’ or provide a declaration of ‘strcmp’ 9 | #include "funcs.h" +++ |+#include 10 | #include "squid.h" 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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); | ^~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 mott_api.c: In function ‘InitPvaluesMott’: mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration] 64 | free(freq0); | ^~~~ mott_api.c:5:1: note: include ‘’ or provide a declaration of ‘free’ 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c:64:3: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 64 | free(freq0); | ^~~~ mott_api.c:64:3: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘SW_PValueMott’: mott_api.c:104:7: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 104 | free(freqA); | ^~~~ mott_api.c:104:7: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘KarlinAltschulStatistics2’: mott_api.c:144:5: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 144 | free(h+hmin); | ^~~~ mott_api.c:144:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c:155:5: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 155 | free(h+hmin); | ^~~~ mott_api.c:155:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘GetHistogram’: mott_api.c:179:16: warning: implicit declaration of function ‘calloc’ [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^~~~~~ mott_api.c:179:16: note: include ‘’ or provide a declaration of ‘calloc’ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch] mott_api.c:179:16: note: include ‘’ or provide a declaration of ‘calloc’ mott_api.c: In function ‘PseudoResidueFrequencies2’: mott_api.c:207:12: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^~~~~~~ mott_api.c:5:1: note: include ‘’ or provide a declaration of ‘toupper’ 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c: In function ‘RobinsonResidueFrequencies2’: mott_api.c:230:27: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch] 230 | double *freq = (double*)calloc(256, sizeof(double)); | ^~~~~~ mott_api.c:230:27: note: include ‘’ or provide a declaration of ‘calloc’ 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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); | ^ 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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); | ~~~~~~^~~~~~~~~~~ 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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); | ^~~~~~~~~~~~ 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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); | ^~~~~~~~~~~~ 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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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); | ^~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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/ 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-2.4.1-23build2 -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/ 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); | ^~~~~~~~~~~~ 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-2.4.1-23build2 -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); | ^~~~~~~~~~~~ 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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-2.4.1-23build2 -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 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-2.4.1-23build2 -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-2.4.1-23build2 -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-2.4.1-23build2 -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 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); | ^~~~~~~~~~~~ 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-2.4.1-23build2 -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 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 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 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 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, 304185 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, 318781 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, 221219 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, 224783 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, 213078 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, 215377 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/estwisedb.1 debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.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 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/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/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/2.4.1-23build2 debian/wise/usr/bin/genewise debugedit: debian/wise/usr/bin/genewise: Unknown DWARF DW_FORM_0x1f20 e71120368325f714173e2d619c2f419536eeadcf 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/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/1120368325f714173e2d619c2f419536eeadcf.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/1120368325f714173e2d619c2f419536eeadcf.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripR1S5gS debian/wise/usr/bin/genewise chmod --reference debian/wise/usr/bin/genewise /tmp/B3zc3h6xP2/stripR1S5gS cat '/tmp/B3zc3h6xP2/stripR1S5gS' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/B3zc3h6xP2/stripR1S5gS debian/wise/usr/bin/genewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/1120368325f714173e2d619c2f419536eeadcf.debug debian/wise/usr/bin/genewise /tmp/B3zc3h6xP2/objcopyTgPbmT chmod --reference debian/wise/usr/bin/genewise /tmp/B3zc3h6xP2/objcopyTgPbmT cat '/tmp/B3zc3h6xP2/objcopyTgPbmT' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/B3zc3h6xP2/objcopyTgPbmT debian/wise/usr/bin/genewise debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/estwisedb debugedit: debian/wise/usr/bin/estwisedb: Unknown DWARF DW_FORM_0x1f20 d3706e3aab6822b1e7e526734fe457d66a2d4002 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/706e3aab6822b1e7e526734fe457d66a2d4002.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/706e3aab6822b1e7e526734fe457d66a2d4002.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/striptnOkNG debian/wise/usr/bin/estwisedb chmod --reference debian/wise/usr/bin/estwisedb /tmp/B3zc3h6xP2/striptnOkNG cat '/tmp/B3zc3h6xP2/striptnOkNG' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/B3zc3h6xP2/striptnOkNG debian/wise/usr/bin/estwisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/706e3aab6822b1e7e526734fe457d66a2d4002.debug debian/wise/usr/bin/estwisedb /tmp/B3zc3h6xP2/objcopyenIwHH chmod --reference debian/wise/usr/bin/estwisedb /tmp/B3zc3h6xP2/objcopyenIwHH cat '/tmp/B3zc3h6xP2/objcopyenIwHH' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/B3zc3h6xP2/objcopyenIwHH debian/wise/usr/bin/estwisedb debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/scanwise debugedit: debian/wise/usr/bin/scanwise: Unknown DWARF DW_FORM_0x1f21 f810f35a84ad3e2b95ab2da819f791173f70fbe4 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/10f35a84ad3e2b95ab2da819f791173f70fbe4.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/10f35a84ad3e2b95ab2da819f791173f70fbe4.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripcSAPuG debian/wise/usr/bin/scanwise chmod --reference debian/wise/usr/bin/scanwise /tmp/B3zc3h6xP2/stripcSAPuG cat '/tmp/B3zc3h6xP2/stripcSAPuG' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/B3zc3h6xP2/stripcSAPuG debian/wise/usr/bin/scanwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/10f35a84ad3e2b95ab2da819f791173f70fbe4.debug debian/wise/usr/bin/scanwise /tmp/B3zc3h6xP2/objcopypp2GMq chmod --reference debian/wise/usr/bin/scanwise /tmp/B3zc3h6xP2/objcopypp2GMq cat '/tmp/B3zc3h6xP2/objcopypp2GMq' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/B3zc3h6xP2/objcopypp2GMq debian/wise/usr/bin/scanwise debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/scanwise_server debugedit: debian/wise/usr/bin/scanwise_server: Unknown DWARF DW_FORM_0x1f20 f606cd8dd3211d1a7c7966da8822d076ee56b397 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f6 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f6/06cd8dd3211d1a7c7966da8822d076ee56b397.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f6/06cd8dd3211d1a7c7966da8822d076ee56b397.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripzpL6ED debian/wise/usr/bin/scanwise_server chmod --reference debian/wise/usr/bin/scanwise_server /tmp/B3zc3h6xP2/stripzpL6ED cat '/tmp/B3zc3h6xP2/stripzpL6ED' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/B3zc3h6xP2/stripzpL6ED debian/wise/usr/bin/scanwise_server objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f6/06cd8dd3211d1a7c7966da8822d076ee56b397.debug debian/wise/usr/bin/scanwise_server /tmp/B3zc3h6xP2/objcopyFcktcM chmod --reference debian/wise/usr/bin/scanwise_server /tmp/B3zc3h6xP2/objcopyFcktcM cat '/tmp/B3zc3h6xP2/objcopyFcktcM' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/B3zc3h6xP2/objcopyFcktcM debian/wise/usr/bin/scanwise_server debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/estwise debugedit: debian/wise/usr/bin/estwise: Unknown DWARF DW_FORM_0x1f21 f56f5a64fc8a295cf05046546020fe4af897a3cd install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f5/6f5a64fc8a295cf05046546020fe4af897a3cd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f5/6f5a64fc8a295cf05046546020fe4af897a3cd.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripjcuBxj debian/wise/usr/bin/estwise chmod --reference debian/wise/usr/bin/estwise /tmp/B3zc3h6xP2/stripjcuBxj cat '/tmp/B3zc3h6xP2/stripjcuBxj' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/B3zc3h6xP2/stripjcuBxj debian/wise/usr/bin/estwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f5/6f5a64fc8a295cf05046546020fe4af897a3cd.debug debian/wise/usr/bin/estwise /tmp/B3zc3h6xP2/objcopyM3KDZs chmod --reference debian/wise/usr/bin/estwise /tmp/B3zc3h6xP2/objcopyM3KDZs cat '/tmp/B3zc3h6xP2/objcopyM3KDZs' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/B3zc3h6xP2/objcopyM3KDZs debian/wise/usr/bin/estwise debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/promoterwise debugedit: debian/wise/usr/bin/promoterwise: Unknown DWARF DW_FORM_0x1f20 76dcb2db9896dc117d2e30983b22d655534ff3e2 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/dcb2db9896dc117d2e30983b22d655534ff3e2.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/dcb2db9896dc117d2e30983b22d655534ff3e2.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/strip3fGFv5 debian/wise/usr/bin/promoterwise chmod --reference debian/wise/usr/bin/promoterwise /tmp/B3zc3h6xP2/strip3fGFv5 cat '/tmp/B3zc3h6xP2/strip3fGFv5' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/B3zc3h6xP2/strip3fGFv5 debian/wise/usr/bin/promoterwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/dcb2db9896dc117d2e30983b22d655534ff3e2.debug debian/wise/usr/bin/promoterwise /tmp/B3zc3h6xP2/objcopyXsx1SP chmod --reference debian/wise/usr/bin/promoterwise /tmp/B3zc3h6xP2/objcopyXsx1SP cat '/tmp/B3zc3h6xP2/objcopyXsx1SP' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/B3zc3h6xP2/objcopyXsx1SP debian/wise/usr/bin/promoterwise debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/dnal debugedit: debian/wise/usr/bin/dnal: Unknown DWARF DW_FORM_0x1f21 6ca8d21eb5749957b45c7a8bee73f53ed3d55f65 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6c objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6c/a8d21eb5749957b45c7a8bee73f53ed3d55f65.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6c/a8d21eb5749957b45c7a8bee73f53ed3d55f65.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripx8d4zf debian/wise/usr/bin/dnal chmod --reference debian/wise/usr/bin/dnal /tmp/B3zc3h6xP2/stripx8d4zf cat '/tmp/B3zc3h6xP2/stripx8d4zf' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/B3zc3h6xP2/stripx8d4zf debian/wise/usr/bin/dnal objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6c/a8d21eb5749957b45c7a8bee73f53ed3d55f65.debug debian/wise/usr/bin/dnal /tmp/B3zc3h6xP2/objcopyRUEmk7 chmod --reference debian/wise/usr/bin/dnal /tmp/B3zc3h6xP2/objcopyRUEmk7 cat '/tmp/B3zc3h6xP2/objcopyRUEmk7' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/B3zc3h6xP2/objcopyRUEmk7 debian/wise/usr/bin/dnal debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/genomewise debugedit: debian/wise/usr/bin/genomewise: Unknown DWARF DW_FORM_0x1f21 81dbc4e804a14a2164394bfb6a59962d71044af3 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/81 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/81/dbc4e804a14a2164394bfb6a59962d71044af3.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/81/dbc4e804a14a2164394bfb6a59962d71044af3.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/strip03YDSu debian/wise/usr/bin/genomewise chmod --reference debian/wise/usr/bin/genomewise /tmp/B3zc3h6xP2/strip03YDSu cat '/tmp/B3zc3h6xP2/strip03YDSu' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/B3zc3h6xP2/strip03YDSu debian/wise/usr/bin/genomewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/81/dbc4e804a14a2164394bfb6a59962d71044af3.debug debian/wise/usr/bin/genomewise /tmp/B3zc3h6xP2/objcopywoqwE4 chmod --reference debian/wise/usr/bin/genomewise /tmp/B3zc3h6xP2/objcopywoqwE4 cat '/tmp/B3zc3h6xP2/objcopywoqwE4' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/B3zc3h6xP2/objcopywoqwE4 debian/wise/usr/bin/genomewise debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/psw debugedit: debian/wise/usr/bin/psw: Unknown DWARF DW_FORM_0x1f20 497a34bff54d4b64e5585124d7faa85bd3acbb37 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/49/7a34bff54d4b64e5585124d7faa85bd3acbb37.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/49/7a34bff54d4b64e5585124d7faa85bd3acbb37.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripAuaDws debian/wise/usr/bin/psw chmod --reference debian/wise/usr/bin/psw /tmp/B3zc3h6xP2/stripAuaDws cat '/tmp/B3zc3h6xP2/stripAuaDws' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/B3zc3h6xP2/stripAuaDws debian/wise/usr/bin/psw objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/49/7a34bff54d4b64e5585124d7faa85bd3acbb37.debug debian/wise/usr/bin/psw /tmp/B3zc3h6xP2/objcopyynASh4 chmod --reference debian/wise/usr/bin/psw /tmp/B3zc3h6xP2/objcopyynASh4 cat '/tmp/B3zc3h6xP2/objcopyynASh4' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/B3zc3h6xP2/objcopyynASh4 debian/wise/usr/bin/psw debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/dba debugedit: debian/wise/usr/bin/dba: Unknown DWARF DW_FORM_0x1f21 a94febfd5daf80b8c5eed29371b4977480ffc692 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/4febfd5daf80b8c5eed29371b4977480ffc692.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/4febfd5daf80b8c5eed29371b4977480ffc692.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/strip9mKXlq debian/wise/usr/bin/dba chmod --reference debian/wise/usr/bin/dba /tmp/B3zc3h6xP2/strip9mKXlq cat '/tmp/B3zc3h6xP2/strip9mKXlq' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/B3zc3h6xP2/strip9mKXlq debian/wise/usr/bin/dba objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/4febfd5daf80b8c5eed29371b4977480ffc692.debug debian/wise/usr/bin/dba /tmp/B3zc3h6xP2/objcopyVRDVRq chmod --reference debian/wise/usr/bin/dba /tmp/B3zc3h6xP2/objcopyVRDVRq cat '/tmp/B3zc3h6xP2/objcopyVRDVRq' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/B3zc3h6xP2/objcopyVRDVRq debian/wise/usr/bin/dba debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/genewisedb debugedit: debian/wise/usr/bin/genewisedb: Unknown DWARF DW_FORM_0x1f20 7761b2a22b75fd0d7b8c4efd80adde5c8ace7f49 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/77 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/77/61b2a22b75fd0d7b8c4efd80adde5c8ace7f49.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/77/61b2a22b75fd0d7b8c4efd80adde5c8ace7f49.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripC3LSnG debian/wise/usr/bin/genewisedb chmod --reference debian/wise/usr/bin/genewisedb /tmp/B3zc3h6xP2/stripC3LSnG cat '/tmp/B3zc3h6xP2/stripC3LSnG' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/B3zc3h6xP2/stripC3LSnG debian/wise/usr/bin/genewisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/77/61b2a22b75fd0d7b8c4efd80adde5c8ace7f49.debug debian/wise/usr/bin/genewisedb /tmp/B3zc3h6xP2/objcopyktAtfl chmod --reference debian/wise/usr/bin/genewisedb /tmp/B3zc3h6xP2/objcopyktAtfl cat '/tmp/B3zc3h6xP2/objcopyktAtfl' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/B3zc3h6xP2/objcopyktAtfl debian/wise/usr/bin/genewisedb debugedit --build-id --build-id-seed=wise/2.4.1-23build2 debian/wise/usr/bin/pswdb debugedit: debian/wise/usr/bin/pswdb: Unknown DWARF DW_FORM_0x1f20 a46619a876084f3bd59544926a9afbfaf5c963a8 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/6619a876084f3bd59544926a9afbfaf5c963a8.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/6619a876084f3bd59544926a9afbfaf5c963a8.debug strip --remove-section=.comment --remove-section=.note -o /tmp/B3zc3h6xP2/stripwrXQAo debian/wise/usr/bin/pswdb chmod --reference debian/wise/usr/bin/pswdb /tmp/B3zc3h6xP2/stripwrXQAo cat '/tmp/B3zc3h6xP2/stripwrXQAo' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/B3zc3h6xP2/stripwrXQAo debian/wise/usr/bin/pswdb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/6619a876084f3bd59544926a9afbfaf5c963a8.debug debian/wise/usr/bin/pswdb /tmp/B3zc3h6xP2/objcopyNnpffO chmod --reference debian/wise/usr/bin/pswdb /tmp/B3zc3h6xP2/objcopyNnpffO cat '/tmp/B3zc3h6xP2/objcopyNnpffO' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/B3zc3h6xP2/objcopyNnpffO 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=497a34bff54d4b64e5585124d7faa85bd3acbb37 6ca8d21eb5749957b45c7a8bee73f53ed3d55f65 76dcb2db9896dc117d2e30983b22d655534ff3e2 7761b2a22b75fd0d7b8c4efd80adde5c8ace7f49 81dbc4e804a14a2164394bfb6a59962d71044af3 a46619a876084f3bd59544926a9afbfaf5c963a8 a94febfd5daf80b8c5eed29371b4977480ffc692 d3706e3aab6822b1e7e526734fe457d66a2d4002 e71120368325f714173e2d619c2f419536eeadcf f56f5a64fc8a295cf05046546020fe4af897a3cd f606cd8dd3211d1a7c7966da8822d076ee56b397 f810f35a84ad3e2b95ab2da819f791173f70fbe4" -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_2.4.1-23build2_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_2.4.1-23build2_s390x.deb'. Renaming wise-dbgsym_2.4.1-23build2_s390x.deb to wise-dbgsym_2.4.1-23build2_s390x.ddeb mv debian/.debhelper/scratch-space/build-wise/wise-dbgsym_2.4.1-23build2_s390x.deb ../wise-dbgsym_2.4.1-23build2_s390x.ddeb dpkg-genbuildinfo --build=any -O../wise_2.4.1-23build2_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../wise_2.4.1-23build2_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 2024-03-12T05:33:13Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ wise_2.4.1-23build2_s390x.changes: ---------------------------------- Format: 1.8 Date: Mon, 11 Mar 2024 23:56:56 +0000 Source: wise Binary: wise Built-For-Profiles: noudeb Architecture: s390x Version: 2.4.1-23build2 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: wise - comparison of biopolymers, like DNA and protein sequences Changes: wise (2.4.1-23build2) noble; urgency=medium . * No-change rebuild against libglib2.0-0t64 Checksums-Sha1: c235302b309e608fa732960c0328099b373e7771 3289298 wise-dbgsym_2.4.1-23build2_s390x.ddeb 6e7f373eface7ef2c3f85939ce0596e38e2a160e 10938 wise_2.4.1-23build2_s390x.buildinfo b1657136dfb1ef982b445eee589f7d7e7d9cfdda 938300 wise_2.4.1-23build2_s390x.deb Checksums-Sha256: 3ae5d4255c4e719b034550c06f7f4757fd89ab07dd09991ea6f0a881800c0968 3289298 wise-dbgsym_2.4.1-23build2_s390x.ddeb 7eb2316a01094bf51958ff5bc19e2ee33e0b93447f1ed1764a3f015e1cd0886f 10938 wise_2.4.1-23build2_s390x.buildinfo 7653d441fefeba1673aad57b6ecebb30afc48328a9fef8095533a9ba6d797027 938300 wise_2.4.1-23build2_s390x.deb Files: 89e847f76aa3ac4ee5709f547bea7366 3289298 debug optional wise-dbgsym_2.4.1-23build2_s390x.ddeb a49967bb44fa3af5af72b3d10f33ac2f 10938 science optional wise_2.4.1-23build2_s390x.buildinfo e3ffb50d96d34ac33ce33c45d4abcebf 938300 science optional wise_2.4.1-23build2_s390x.deb Original-Maintainer: Debian Med Packaging Team /<>/wise_2.4.1-23build2_s390x.changes.new could not be renamed to /<>/wise_2.4.1-23build2_s390x.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: wise Binary: wise wise-dbgsym Architecture: s390x Version: 2.4.1-23build2 Checksums-Md5: 89e847f76aa3ac4ee5709f547bea7366 3289298 wise-dbgsym_2.4.1-23build2_s390x.ddeb e3ffb50d96d34ac33ce33c45d4abcebf 938300 wise_2.4.1-23build2_s390x.deb Checksums-Sha1: c235302b309e608fa732960c0328099b373e7771 3289298 wise-dbgsym_2.4.1-23build2_s390x.ddeb b1657136dfb1ef982b445eee589f7d7e7d9cfdda 938300 wise_2.4.1-23build2_s390x.deb Checksums-Sha256: 3ae5d4255c4e719b034550c06f7f4757fd89ab07dd09991ea6f0a881800c0968 3289298 wise-dbgsym_2.4.1-23build2_s390x.ddeb 7653d441fefeba1673aad57b6ecebb30afc48328a9fef8095533a9ba6d797027 938300 wise_2.4.1-23build2_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Tue, 12 Mar 2024 05:33:13 +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 (= 13ubuntu7), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu2), binutils (= 2.42-3ubuntu1), binutils-common (= 2.42-3ubuntu1), binutils-s390x-linux-gnu (= 2.42-3ubuntu1), bsdextrautils (= 2.39.3-9ubuntu2), bsdutils (= 1:2.39.3-9ubuntu2), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5ubuntu1), coreutils (= 9.4-3ubuntu3), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-17ubuntu2), cpp-13-s390x-linux-gnu (= 13.2.0-17ubuntu2), cpp-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu4), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17), 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 (= 1.22.5ubuntu4), dpkg-dev (= 1.22.5ubuntu4), dwz (= 0.15-1build5), file (= 1:5.45-3), findutils (= 4.9.0-5), fontconfig-config (= 2.15.0-1.1ubuntu1), 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 (= 13.2.0-17ubuntu2), g++-13-s390x-linux-gnu (= 13.2.0-17ubuntu2), g++-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-17ubuntu2), gcc-13-base (= 13.2.0-17ubuntu2), gcc-13-s390x-linux-gnu (= 13.2.0-17ubuntu2), gcc-14-base (= 14-20240303-1ubuntu1), gcc-s390x-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), ghostscript (= 10.02.1~dfsg1-0ubuntu4), grep (= 3.11-4), groff-base (= 1.23.0-3build1), gzip (= 1.12-1ubuntu2), hevea (= 2.36-2), hicolor-icon-theme (= 0.17-2), hostname (= 3.23+nmu2ubuntu1), imagemagick (= 8:6.9.12.98+dfsg1-5.1build2), imagemagick-6-common (= 8:6.9.12.98+dfsg1-5.1build2), imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-5.1build2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240303-1ubuntu1), libatomic1 (= 14-20240303-1ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libavahi-client3 (= 0.8-13ubuntu4), libavahi-common-data (= 0.8-13ubuntu4), libavahi-common3 (= 0.8-13ubuntu4), libbinutils (= 2.42-3ubuntu1), libblkid-dev (= 2.39.3-9ubuntu2), libblkid1 (= 2.39.3-9ubuntu2), libbrotli1 (= 1.1.0-2), libbsd0 (= 0.12.1-1), libbz2-1.0 (= 1.0.8-5ubuntu1), libc-bin (= 2.39-0ubuntu5), libc-dev-bin (= 2.39-0ubuntu5), libc6 (= 2.39-0ubuntu5), libc6-dev (= 2.39-0ubuntu5), libcairo2 (= 1.18.0-1ubuntu1), libcap-ng0 (= 0.8.4-2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240303-1ubuntu1), libcom-err2t64 (= 1.47.0-2.3ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-3ubuntu1), libctf0 (= 2.42-3ubuntu1), libcups2 (= 2.4.7-1ubuntu2), libdatrie1 (= 0.2.13-3), libdav1d7 (= 1.4.0-1), libdb5.3t64 (= 5.3.28+dfsg2-5), libdbus-1-3 (= 1.14.10-4ubuntu2), libde265-0 (= 1.0.15-1), libdebconfclient0 (= 0.271ubuntu2), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.5ubuntu4), libdw1t64 (= 0.190-1.1build1), libelf1t64 (= 0.190-1.1build1), libexpat1 (= 2.6.1-2), libffi-dev (= 3.4.6-1), libffi8 (= 3.4.6-1), libfftw3-double3 (= 3.3.10-1ubuntu1), libfile-homedir-perl (= 1.006-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfile-which-perl (= 1.27-2), libfontconfig1 (= 2.15.0-1.1ubuntu1), libfontenc1 (= 1:1.1.4-1build3), libfreetype6 (= 2.13.2+dfsg-1build1), libgcc-13-dev (= 13.2.0-17ubuntu2), libgcc-s1 (= 14-20240303-1ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1), libgdbm6t64 (= 1.23-5.1), libgirepository-2.0-0 (= 2.79.3-3ubuntu5), libglib2.0-0t64 (= 2.79.3-3ubuntu5), libglib2.0-bin (= 2.79.3-3ubuntu5), libglib2.0-data (= 2.79.3-3ubuntu5), libglib2.0-dev (= 2.79.3-3ubuntu5), libglib2.0-dev-bin (= 2.79.3-3ubuntu5), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu2), libgomp1 (= 14-20240303-1ubuntu1), libgpg-error0 (= 1.47-3build1), libgraphite2-3 (= 1.3.14-2), libgs-common (= 10.02.1~dfsg1-0ubuntu4), libgs10 (= 10.02.1~dfsg1-0ubuntu4), libgs10-common (= 10.02.1~dfsg1-0ubuntu4), libgssapi-krb5-2 (= 1.20.1-5.1build2), libharfbuzz0b (= 8.3.0-2build1), libheif-plugin-dav1d (= 1.17.6-1ubuntu2), libheif-plugin-libde265 (= 1.17.6-1ubuntu2), libheif1 (= 1.17.6-1ubuntu2), libhogweed6t64 (= 3.9.1-2.2), 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 (= 14-20240303-1ubuntu1), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6.1ubuntu1), libjbig2dec0 (= 0.20-1build1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libk5crypto3 (= 1.20.1-5.1build2), libkeyutils1 (= 1.6.3-3), libkpathsea6 (= 2023.20230311.66589-9build1), libkrb5-3 (= 1.20.1-5.1build2), libkrb5support0 (= 1.20.1-5.1build2), liblcms2-2 (= 2.14-2), liblqr-1-0 (= 0.4.2-2.1build1), libltdl7 (= 2.4.7-7), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.0-0.2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmagickcore-6.q16-7 (= 8:6.9.12.98+dfsg1-5build1), libmagickwand-6.q16-7t64 (= 8:6.9.12.98+dfsg1-5.1build2), libmd0 (= 1.1.0-2), libmime-charset-perl (= 1.013.1-2), libmount-dev (= 2.39.3-9ubuntu2), libmount1 (= 2.39.3-9ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnetpbm11t64 (= 2:11.05.02-1.1), libnettle8t64 (= 3.9.1-2.2), libopenjp2-7 (= 2.5.0-2build1), libosp5 (= 1.5.2-15ubuntu1), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.3-5ubuntu3), libpam-modules-bin (= 1.5.3-5ubuntu3), libpam-runtime (= 1.5.3-5ubuntu3), libpam0g (= 1.5.3-5ubuntu3), 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 (= 5.38.2-3.2), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpkgconf3 (= 1.8.1-2), libpng16-16t64 (= 1.6.43-3), libpotrace0 (= 1.16-2), libptexenc1 (= 2023.20230311.66589-9build1), libpython3-stdlib (= 3.12.2-0ubuntu1), libpython3.12-minimal (= 3.12.2-4build2), libpython3.12-stdlib (= 3.12.2-4build2), libraw23t64 (= 0.21.2-2.1), libreadline8t64 (= 8.2-3.1), libseccomp2 (= 2.5.5-1ubuntu1), libselinux1 (= 3.5-2build2), libselinux1-dev (= 3.5-2build2), libsepol-dev (= 3.5-2), libsepol2 (= 3.5-2), libsframe1 (= 2.42-3ubuntu1), libsharpyuv0 (= 1.3.2-0.4build1), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.39.3-9ubuntu2), libsombok3 (= 2.4.0-2), libsqlite3-0 (= 3.45.1-1ubuntu1), libssl3t64 (= 3.0.13-0ubuntu1), libstdc++-13-dev (= 13.2.0-17ubuntu2), libstdc++6 (= 14-20240303-1ubuntu1), libsub-override-perl (= 0.10-1), libsynctex2 (= 2023.20230311.66589-9build1), libsystemd0 (= 255.4-1ubuntu4), libtasn1-6 (= 4.19.0-3), libteckit0 (= 2.5.12+ds1-1), libtexlua53-5 (= 2023.20230311.66589-9build1), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtiff6 (= 4.5.1+git230720-4ubuntu1), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libubsan1 (= 14-20240303-1ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu4), libunicode-linebreak-perl (= 0.0.20190101-1build6), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu2), libwebp7 (= 1.3.2-0.4build1), libwebpdemux2 (= 1.3.2-0.4build1), libwebpmux3 (= 1.3.2-0.4build1), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxaw7 (= 2:1.0.14-1build1), 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-1.3ubuntu1), libxmu6 (= 2:1.1.3-3build1), libxpm4 (= 1:3.5.17-1build1), libxrender1 (= 1:0.9.10-1.1), libxt6t64 (= 1:1.2.1-1.2), libyaml-tiny-perl (= 1.74-1), libzstd1 (= 1.5.5+dfsg2-2), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 6.8.0-11.11), 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 (= 2.12.0-3build4), 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 (= 2:11.05.02-1.1), opensp (= 1.5.2-15ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2), perl-base (= 5.38.2-3.2), perl-modules-5.38 (= 5.38.2-3.2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), python3 (= 3.12.2-0ubuntu1), python3-minimal (= 3.12.2-0ubuntu1), python3-packaging (= 23.2-1), python3.12 (= 3.12.2-4build2), python3.12-minimal (= 3.12.2-4build2), readline-common (= 8.2-3.1), 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 (= 2023.20230311.66589-9build1), 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 (= 2.39.3-9ubuntu2), uuid-dev (= 2.39.3-9ubuntu2), 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 (= 5.6.0-0.2), zlib1g (= 1:1.3.dfsg-3.1ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1710201416" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ wise_2.4.1-23build2_s390x.deb ----------------------------- new Debian package, version 2.0. size 938300 bytes: control archive=1954 bytes. 1820 bytes, 34 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-23build2 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 3747 Depends: libc6 (>= 2.34), libglib2.0-0t64 (>= 2.12.0), wise-data (= 2.4.1-23build2) Suggests: wise-doc (= 2.4.1-23build2) 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 2024-03-11 23:56 ./ drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/ drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/bin/ -rwxr-xr-x root/root 141488 2024-03-11 23:56 ./usr/bin/dba -rwxr-xr-x root/root 67680 2024-03-11 23:56 ./usr/bin/dnal -rwxr-xr-x root/root 358720 2024-03-11 23:56 ./usr/bin/estwise -rwxr-xr-x root/root 440696 2024-03-11 23:56 ./usr/bin/estwisedb -rwxr-xr-x root/root 1055072 2024-03-11 23:56 ./usr/bin/genewise -rwxr-xr-x root/root 907680 2024-03-11 23:56 ./usr/bin/genewisedb -rwxr-xr-x root/root 153696 2024-03-11 23:56 ./usr/bin/genomewise -rwxr-xr-x root/root 157792 2024-03-11 23:56 ./usr/bin/promoterwise -rwxr-xr-x root/root 96352 2024-03-11 23:56 ./usr/bin/psw -rwxr-xr-x root/root 129176 2024-03-11 23:56 ./usr/bin/pswdb -rwxr-xr-x root/root 178272 2024-03-11 23:56 ./usr/bin/scanwise -rwxr-xr-x root/root 108640 2024-03-11 23:56 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/share/ drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-11 23:56 ./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 2020-04-18 15:57 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 830 2024-03-11 23:56 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4297 2020-04-18 15:57 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 312 2020-04-18 15:57 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-11 23:56 ./usr/share/man/man1/ -rw-r--r-- root/root 846 2024-03-11 23:56 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2024-03-11 23:56 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2024-03-11 23:56 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2024-03-11 23:56 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2024-03-11 23:56 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2024-03-11 23:56 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2024-03-11 23:56 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2024-03-11 23:56 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2024-03-11 23:56 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2024-03-11 23:56 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2024-03-11 23:56 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2024-03-11 23:56 ./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: 145576 Build-Time: 193 Distribution: noble-proposed Host Architecture: s390x Install-Time: 128 Job: wise_2.4.1-23build2.dsc Machine Architecture: s390x Package: wise Package-Time: 323 Source-Version: 2.4.1-23build2 Space: 145576 Status: successful Version: 2.4.1-23build2 -------------------------------------------------------------------------------- Finished at 2024-03-12T05:33:13Z Build needed 00:05:23, 145576k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27904284 Scanning for processes to kill in build PACKAGEBUILD-27904284