https://launchpad.net/ubuntu/+source/wise/2.4.1-24/+build/27939122 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-025 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le 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... 18 Mar 23:01:28 ntpdate[2011]: adjust time server 10.211.37.1 offset -0.009565 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27939122 --image-type chroot /home/buildd/filecache-default/d42c54d6e204d222772cc047f01d282d9c30a0e5 Creating target for build PACKAGEBUILD-27939122 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27939122 Starting target for build PACKAGEBUILD-27939122 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27939122 '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-27939122 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27939122 Updating target for build PACKAGEBUILD-27939122 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 ppc64el Packages [1377 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.2 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6039 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [645 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [230 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4004 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1517 kB] Fetched 30.1 MB in 14s (2126 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libnettle8* libnpth0* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu gcc-14-base gcc-powerpc64le-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: apt apt-utils optipng The following packages will be upgraded: base-files base-passwd bash bash-completion binutils binutils-common binutils-powerpc64le-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login 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 155 upgraded, 20 newly installed, 11 to remove and 3 not upgraded. Need to get 116 MB of archives. After this operation, 83.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl-dev ppc64el 1.3.0-3build2 [80.3 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.1 [225 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnss-nisplus ppc64el 1.3-5 [27.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1 [102 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-5.1build3 [185 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5-3 ppc64el 1.20.1-5.1build3 [432 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libk5crypto3 ppc64el 1.20.1-5.1build3 [108 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5support0 ppc64el 1.20.1-5.1build3 [38.5 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libacl1 ppc64el 2.3.2-1 [21.4 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapparmor1 ppc64el 4.0.0~beta2-0ubuntu3 [54.8 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit-common all 1:3.1.2-2.1 [5674 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcap-ng0 ppc64el 0.8.4-2build1 [16.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit1 ppc64el 1:3.1.2-2.1 [52.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu2 [155 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libcap2 ppc64el 1:2.66-5ubuntu1 [35.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt1 ppc64el 1:4.4.36-4 [125 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error0 ppc64el 1.47-3build1 [87.6 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcrypt20 ppc64el 1.10.3-2 [745 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma5 ppc64el 5.6.0-0.2 [156 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libzstd1 ppc64el 1.5.5+dfsg2-2 [390 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu4 [64.4 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-8-0 ppc64el 10.42-4ubuntu1 [263 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1 ppc64el 3.5-2build3 [101 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu2 [169 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-5build1 [868 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1 [41.9 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1 [6972 B] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2 [4957 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2 [1916 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu3 [16.0 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-iconv-perl ppc64el 1.7-8build2 [13.7 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build2 [9506 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu5 [2351 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu2 [376 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-dev all 255.4-1ubuntu5 [103 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu5 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd ppc64el 255.4-1ubuntu5 [3771 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu5 [526 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-5ubuntu3 [57.9 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules ppc64el 1.5.3-5ubuntu3 [320 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el bzip2 ppc64el 1.0.8-5ubuntu1 [37.6 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libbz2-1.0 ppc64el 1.0.8-5ubuntu1 [48.8 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu1 [72.8 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf-i18n all 1.5.86 [205 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf all 1.5.86 [124 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam0g ppc64el 1.5.3-5ubuntu3 [75.7 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu2 [62.5 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libargon2-1 ppc64el 0~20190702+dfsg-4 [27.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudev1 ppc64el 255.4-1ubuntu5 [200 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu2 [182 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu2 [39.3 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu2 [171 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mount ppc64el 2.39.3-9ubuntu2 [125 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libkeyutils1 ppc64el 1.6.3-3 [11.0 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl2 ppc64el 1.3.0-3build2 [48.9 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-libc-dev ppc64el 6.8.0-19.19 [1586 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-14-base ppc64el 14-20240315-1ubuntu1 [47.0 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-s1 ppc64el 14-20240315-1ubuntu1 [39.2 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el base-files ppc64el 13ubuntu7 [74.5 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debianutils ppc64el 5.17 [90.4 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el bash ppc64el 5.2.21-2ubuntu2 [977 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu2 [98.3 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el coreutils ppc64el 9.4-3ubuntu3 [1523 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el libp11-kit0 ppc64el 0.25.3-4ubuntu1 [315 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el libunistring5 ppc64el 1.1-2 [556 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main ppc64el libgnutls30 ppc64el 3.8.3-1ubuntu1 [1052 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2 [226 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++6 ppc64el 14-20240315-1ubuntu1 [897 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main ppc64el libxxhash0 ppc64el 0.8.2-2 [30.4 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapt-pkg6.0t64 ppc64el 2.7.13ubuntu1 [1063 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el tar ppc64el 1.35+dfsg-3 [307 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu4 [1342 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main ppc64el dash ppc64el 0.5.12-6ubuntu4 [109 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main ppc64el diffutils ppc64el 1:3.10-1 [200 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main ppc64el grep ppc64el 3.11-4 [189 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main ppc64el gzip ppc64el 1.12-1ubuntu2 [114 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el hostname ppc64el 3.23+nmu2ubuntu1 [11.3 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el login ppc64el 1:4.13+dfsg1-4ubuntu1 [205 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-bin ppc64el 6.4+20240113-1ubuntu1 [202 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main ppc64el sed ppc64el 4.9-2 [223 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el util-linux ppc64el 2.39.3-9ubuntu2 [1195 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu2 [11.2 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main ppc64el base-passwd ppc64el 3.6.3 [52.5 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main ppc64el init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main ppc64el sysvinit-utils ppc64el 3.08-6ubuntu2 [35.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu2 [270 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu2 [663 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg ppc64el 2.4.4-2ubuntu15 [706 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libreadline8t64 ppc64el 8.2-3.1 [182 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu15 [115 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu15 [275 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el libnpth0t64 ppc64el 1.6-3.1 [8864 B] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-3.1 [56.4 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main ppc64el libncursesw6 ppc64el 6.4+20240113-1ubuntu1 [186 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main ppc64el libtinfo6 ppc64el 6.4+20240113-1ubuntu1 [129 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main ppc64el init ppc64el 1.66ubuntu1 [6190 B] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu2 [79.0 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu2 [33.8 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main ppc64el libattr1 ppc64el 1:2.5.2-1 [12.4 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main ppc64el libmd0 ppc64el 1.1.0-2 [30.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage-common all 3.5-1build4 [10.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main ppc64el libsepol2 ppc64el 3.5-2 [386 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage2 ppc64el 3.5-1build4 [115 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main ppc64el passwd ppc64el 1:4.13+dfsg1-4ubuntu1 [878 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgv ppc64el 2.4.4-2ubuntu15 [198 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main ppc64el libffi8 ppc64el 3.4.6-1 [27.7 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main ppc64el libidn2-0 ppc64el 2.3.7-2 [69.8 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13 ppc64el 13.2.0-19ubuntu1 [14.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13 ppc64el 13.2.0-19ubuntu1 [477 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13 ppc64el 13.2.0-19ubuntu1 [1040 B] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-19ubuntu1 [10.7 MB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcc1-0 ppc64el 14-20240315-1ubuntu1 [48.1 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf0 ppc64el 2.42-3ubuntu1 [112 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf-nobfd0 ppc64el 2.42-3ubuntu1 [112 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main ppc64el libsframe1 ppc64el 2.42-3ubuntu1 [16.1 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-3ubuntu1 [2474 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main ppc64el libbinutils ppc64el 2.42-3ubuntu1 [700 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils ppc64el 2.42-3ubuntu1 [3084 B] Get:135 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-common ppc64el 2.42-3ubuntu1 [217 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++-13-dev ppc64el 13.2.0-19ubuntu1 [2448 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgomp1 ppc64el 14-20240315-1ubuntu1 [161 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libitm1 ppc64el 14-20240315-1ubuntu1 [32.2 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libatomic1 ppc64el 14-20240315-1ubuntu1 [10.7 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libasan8 ppc64el 14-20240315-1ubuntu1 [2973 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblsan0 ppc64el 14-20240315-1ubuntu1 [1325 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-13-dev ppc64el 13.2.0-19ubuntu1 [1582 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtsan2 ppc64el 14-20240315-1ubuntu1 [2702 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libubsan1 ppc64el 14-20240315-1ubuntu1 [1193 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libquadmath0 ppc64el 14-20240315-1ubuntu1 [158 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-19ubuntu1 [20.6 MB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-19ubuntu1 [12.2 MB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-base ppc64el 13.2.0-19ubuntu1 [47.8 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu1 [68.8 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu2 [18.0 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main ppc64el mawk ppc64el 1.3.4.20240123-1 [138 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main ppc64el procps ppc64el 2:4.0.4-4ubuntu1 [735 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main ppc64el sensible-utils all 0.0.22 [22.5 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates all 20240203 [159 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el krb5-locales all 1.20.1-5.1build3 [13.8 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main ppc64el libip4tc2 ppc64el 1.8.10-3ubuntu1 [26.9 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.1-1ubuntu1 [804 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main ppc64el tzdata all 2024a-1ubuntu1 [273 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main ppc64el bash-completion all 1:2.11-8 [180 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu2 [78.6 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main ppc64el libpng16-16 ppc64el 1.6.43-1 [242 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el psmisc ppc64el 23.7-1 [192 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xz-utils ppc64el 5.6.0-0.2 [281 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] Get:165 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] Get:166 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] Get:168 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] Get:169 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu4 [1074 kB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu4 [268 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main ppc64el lto-disabled-list all 47 [12.4 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main ppc64el libfakeroot ppc64el 1.33-1 [34.4 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main ppc64el fakeroot ppc64el 1.33-1 [69.2 kB] Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu4 [38.7 kB] Preconfiguring packages ... Fetched 116 MB in 9s (12.8 MB/s) (Reading database ... 13550 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build2_ppc64el.deb ... Unpacking libnsl-dev:ppc64el (1.3.0-3build2) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../2-libc6-dev_2.39-0ubuntu6_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.39-0ubuntu6) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu6_ppc64el.deb ... Unpacking libc-dev-bin (2.39-0ubuntu6) 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_ppc64el.deb ... Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1.1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libnss-nisplus_1.3-5_ppc64el.deb ... Unpacking libnss-nisplus:ppc64el (1.3-5) over (1.3-0ubuntu6) ... dpkg: libtirpc3:ppc64el: dependency problems, but removing anyway as you requested: libnsl2:ppc64el depends on libtirpc3 (>= 1.0.2). (Reading database ... 13553 files and directories currently installed.) Removing libtirpc3:ppc64el (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:ppc64el. (Reading database ... 13547 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1_ppc64el.deb ... Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:ppc64el (1.3.4+ds-1.1) ... Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-5.1build3_ppc64el.deb ... 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Setting up libpcre2-8-0:ppc64el (10.42-4ubuntu1) ... (Reading database ... 13558 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2build3_ppc64el.deb ... Unpacking libselinux1:ppc64el (3.5-2build3) over (3.5-1) ... Setting up libselinux1:ppc64el (3.5-2build3) ... (Reading database ... 13559 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-9ubuntu2_ppc64el.deb ... Unpacking libmount1:ppc64el (2.39.3-9ubuntu2) over (2.39.1-4ubuntu2) ... Setting up libmount1:ppc64el (2.39.3-9ubuntu2) ... (Reading database ... 13559 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-3.2_ppc64el.deb ... Unpacking perl (5.38.2-3.2) over (5.36.0-9ubuntu1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libdb5.3. libpam-modules:ppc64el depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14971 files and directories currently installed.) Removing libdb5.3:ppc64el (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:ppc64el. (Reading database ... 14965 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_ppc64el.deb ... Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm6 (>= 1.21). libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). (Reading database ... 14971 files and directories currently installed.) Removing libgdbm6:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm6t64:ppc64el. (Reading database ... 14966 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ... Unpacking libgdbm6t64:ppc64el (1.23-5.1) ... dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14972 files and directories currently installed.) Removing libgdbm-compat4:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:ppc64el. (Reading database ... 14967 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_ppc64el.deb ... Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ... Selecting previously unselected package libperl5.38t64:ppc64el. Preparing to unpack .../libperl5.38t64_5.38.2-3.2_ppc64el.deb ... Unpacking libperl5.38t64:ppc64el (5.38.2-3.2) ... Preparing to unpack .../perl-base_5.38.2-3.2_ppc64el.deb ... Unpacking perl-base (5.38.2-3.2) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-3.2) ... (Reading database ... 15499 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu3_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu3) over (1.07-6) ... Preparing to unpack .../libtext-iconv-perl_1.7-8build2_ppc64el.deb ... Unpacking libtext-iconv-perl:ppc64el (1.7-8build2) over (1.7-8) ... Preparing to unpack .../libtext-charwidth-perl_0.04-11build2_ppc64el.deb ... Unpacking libtext-charwidth-perl:ppc64el (0.04-11build2) over (0.04-11) ... Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.38-1ubuntu6) ... Setting up libc6:ppc64el (2.39-0ubuntu6) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... Unpacking libc-bin (2.39-0ubuntu6) over (2.38-1ubuntu6) ... Setting up libc-bin (2.39-0ubuntu6) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_ppc64el.deb ... Unpacking libsystemd-shared:ppc64el (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu2_ppc64el.deb ... Unpacking libcryptsetup12:ppc64el (2:2.7.0-1ubuntu2) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15502 files and directories currently installed.) Removing libssl3:ppc64el (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:ppc64el. (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ... Unpacking systemd-dev (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_ppc64el.deb ... Unpacking systemd-sysv (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... (Reading database ... 15546 files and directories currently installed.) Preparing to unpack .../systemd_255.4-1ubuntu5_ppc64el.deb ... Unpacking systemd (255.4-1ubuntu5) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu5_ppc64el.deb ... 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Unpacking bzip2 (1.0.8-5ubuntu1) over (1.0.8-5build1) ... dpkg: warning: old file '/bin/bzip2' is the same as several new files! (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_ppc64el.deb ... Unpacking libbz2-1.0:ppc64el (1.0.8-5ubuntu1) over (1.0.8-5build1) ... Setting up libbz2-1.0:ppc64el (1.0.8-5ubuntu1) ... 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Setting up libfakeroot:ppc64el (1.33-1) ... Setting up libkrb5support0:ppc64el (1.20.1-5.1build3) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Mar 18 23:02:15 UTC 2024. Universal Time is now: Mon Mar 18 23:02:15 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:ppc64el (13.2.0-19ubuntu1) ... 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 libquadmath0:ppc64el (14-20240315-1ubuntu1) ... Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu1) ... Setting up libpng16-16:ppc64el (1.6.43-1) ... Setting up libatomic1:ppc64el (14-20240315-1ubuntu1) ... Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu2) ... Setting up libncursesw6:ppc64el (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:ppc64el (1.20.1-5.1build3) ... Setting up logsave (1.47.0-2.4~exp1ubuntu2) ... Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-5build1) ... Setting up libubsan1:ppc64el (14-20240315-1ubuntu1) ... 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:ppc64el (1:4.4.36-4) ... Setting up libasan8:ppc64el (14-20240315-1ubuntu1) ... 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:ppc64el (1.20.1-5.1build3) ... Setting up libperl5.38t64:ppc64el (5.38.2-3.2) ... Setting up libtsan2:ppc64el (14-20240315-1ubuntu1) ... Setting up libbinutils:ppc64el (2.42-3ubuntu1) ... Setting up libc-dev-bin (2.39-0ubuntu6) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-19ubuntu1) ... Setting up openssl (3.0.13-0ubuntu2) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3.1) ... Setting up libcc1-0:ppc64el (14-20240315-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu3) ... Setting up liblsan0:ppc64el (14-20240315-1ubuntu1) ... Setting up libitm1:ppc64el (14-20240315-1ubuntu1) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libctf0:ppc64el (2.42-3ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu4) ... Setting up cpp-13 (13.2.0-19ubuntu1) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ... 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:ppc64el (1.20.1-5.1build3) ... Setting up libdpkg-perl (1.22.6ubuntu4) ... Setting up libreadline8t64:ppc64el (8.2-3.1) ... Setting up libgcc-13-dev:ppc64el (13.2.0-19ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu15) ... Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ... Setting up binutils-powerpc64le-linux-gnu (2.42-3ubuntu1) ... Setting up gpg (2.4.4-2ubuntu15) ... Setting up libstdc++-13-dev:ppc64el (13.2.0-19ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu15) ... Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1) ... Setting up binutils (2.42-3ubuntu1) ... Setting up dpkg-dev (1.22.6ubuntu4) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.1) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-19ubuntu1) ... Setting up gcc-13 (13.2.0-19ubuntu1) ... Setting up libnsl2:ppc64el (1.3.0-3build2) ... Setting up libnss-nisplus:ppc64el (1.3-5) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-19ubuntu1) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:ppc64el (1.3.0-3build2) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-19ubuntu1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... Processing triggers for debianutils (5.17) ... (Reading database ... 15644 files and directories currently installed.) Purging configuration files for libssl3:ppc64el (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-27939122 ppc64el noble-proposed -c chroot:build-PACKAGEBUILD-27939122 --arch=ppc64el --dist=noble-proposed --nolog wise_2.4.1-24.dsc Initiating build PACKAGEBUILD-27939122 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-ppc64el-025.buildd +==============================================================================+ | wise 2.4.1-24 (ppc64el) Mon, 18 Mar 2024 23:02:19 +0000 | +==============================================================================+ Package: wise Version: 2.4.1-24 Source Version: 2.4.1-24 Distribution: noble-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27939122/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/wise-z1hMcr/resolver-MNRcms' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- wise_2.4.1-24.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/wise-z1hMcr/wise-2.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/wise-z1hMcr' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [416 B] Get:5 copy:/<>/apt_archive ./ Packages [500 B] Fetched 1873 B in 0s (171 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 libgnutls30t64 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhogweed6t64 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libkpathsea6 liblcms2-2 liblerc4 liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmime-charset-perl libmount-dev libnetpbm11t64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpixman-1-0 libpkgconf3 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-0-13t64 lmodern m4 man-db media-types netbase netpbm opensp pkgconf pkgconf-bin po-debconf poppler-data python3 python3-minimal python3-packaging python3.12 python3.12-minimal sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc texlive-latex-extra imagemagick-6-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin cups-common libfftw3-bin libfftw3-dev low-memory-monitor gir1.2-glib-2.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin libxml2-utils gnutls-bin 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: libgnutls30* libhogweed6* 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 libgnutls30t64 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhogweed6t64 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libkpathsea6 liblcms2-2 liblerc4 liblqr-1-0 libltdl7 libmagic-mgc libmagic1t64 libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmime-charset-perl libmount-dev libnetpbm11t64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libpixman-1-0 libpkgconf3 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-0-13t64 lmodern m4 man-db media-types netbase netpbm opensp pkgconf pkgconf-bin po-debconf poppler-data python3 python3-minimal python3-packaging python3.12 python3.12-minimal sbuild-build-depends-main-dummy sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 178 newly installed, 3 to remove and 3 not upgraded. Need to get 244 MB of archives. After this operation, 653 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [718 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2 [208 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu2 [1154 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpng16-16t64 ppc64el 1.6.43-3 [242 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-minimal ppc64el 3.12.2-4build2 [836 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libexpat1 ppc64el 2.6.1-2 [101 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12-minimal ppc64el 3.12.2-4build2 [2447 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-minimal ppc64el 3.12.2-0ubuntu1 [27.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el media-types all 10.1.0 [27.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el netbase all 6.4 [13.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-stdlib ppc64el 3.12.2-4build2 [2082 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12 ppc64el 3.12.2-4build2 [645 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.2-0ubuntu1 [9798 B] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3 ppc64el 3.12.2-0ubuntu1 [24.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu2 [443 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbrotli1 ppc64el 1.1.0-2build1 [410 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfreetype6 ppc64el 2.13.2+dfsg-1build1 [545 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu1 [37.4 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu1 [190 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4build1 [28.8 kB] Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el libdav1d7 ppc64el 1.4.0-1 [461 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libheif-plugin-dav1d ppc64el 1.17.6-1ubuntu2 [10.3 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libde265-0 ppc64el 1.0.15-1build1 [278 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libheif-plugin-libde265 ppc64el 1.17.6-1ubuntu2 [8544 B] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libheif1 ppc64el 1.17.6-1ubuntu2 [324 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el liblqr-1-0 ppc64el 0.4.2-2.1build1 [43.5 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libltdl7 ppc64el 2.4.7-7 [48.0 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libopenjp2-7 ppc64el 2.5.0-2build2 [239 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libraw23t64 ppc64el 0.21.2-2.1 [515 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libwebp7 ppc64el 1.3.2-0.4build1 [312 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu1 [274 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4build1 [14.4 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4build1 [31.2 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libxau6 ppc64el 1:1.0.9-1build5 [8028 B] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libxdmcp6 ppc64el 1:1.1.3-0ubuntu5 [12.3 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb1 ppc64el 1.15-1 [55.5 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libx11-data all 2:1.8.7-1 [115 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libx11-6 ppc64el 2:1.8.7-1 [743 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libxext6 ppc64el 2:1.3.4-1build1 [40.0 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libicu74 ppc64el 74.2-1ubuntu1 [11.3 MB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.3ubuntu2 [840 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el imagemagick-6-common all 8:6.9.12.98+dfsg1-5.2 [69.4 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libmagickcore-6.q16-7t64 ppc64el 8:6.9.12.98+dfsg1-5.2 [2210 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libmagickwand-6.q16-7t64 ppc64el 8:6.9.12.98+dfsg1-5.2 [290 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el poppler-data all 0.4.12-1 [2060 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdbus-1-3 ppc64el 1.14.10-4ubuntu2 [244 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el ucf all 3.0043+nmu1 [56.5 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic-mgc ppc64el 1:5.45-3 [307 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic1t64 ppc64el 1:5.45-3 [106 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el file ppc64el 1:5.45-3 [22.7 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext-base ppc64el 0.21-14ubuntu1 [42.7 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el libuchardet0 ppc64el 0.0.8-1 [78.7 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el groff-base ppc64el 1.23.0-3build1 [1112 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el libpipeline1 ppc64el 1.5.7-1 [25.8 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el man-db ppc64el 2.12.0-3build4 [1274 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libelf1t64 ppc64el 0.190-1.1build2 [69.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdw1t64 ppc64el 0.190-1.1build2 [301 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debugedit ppc64el 1:5.0-5build1 [51.4 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dwz ppc64el 0.15-1build5 [142 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debhelper all 13.14.1ubuntu5 [869 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-data all 2.0.11+nmu1 [171 kB] Get:95 http://ftpmaster.internal/ubuntu noble/universe ppc64el docbook all 4.5-10 [120 kB] Get:96 http://ftpmaster.internal/ubuntu noble/universe ppc64el libosp5 ppc64el 1.5.2-15ubuntu1 [787 kB] Get:97 http://ftpmaster.internal/ubuntu noble/universe ppc64el opensp ppc64el 1.5.2-15ubuntu1 [161 kB] Get:98 http://ftpmaster.internal/ubuntu noble/universe ppc64el docbook-to-man ppc64el 1:2.0.0-45 [89.3 kB] Get:99 http://ftpmaster.internal/ubuntu noble/universe ppc64el fonts-lmodern all 2.005-1 [4799 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgs-common all 10.02.1~dfsg1-0ubuntu4 [174 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgs10-common all 10.02.1~dfsg1-0ubuntu4 [488 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libavahi-common-data ppc64el 0.8-13ubuntu4 [29.6 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libavahi-common3 ppc64el 0.8-13ubuntu4 [26.3 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libavahi-client3 ppc64el 0.8-13ubuntu4 [30.8 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcups2 ppc64el 2.4.7-1ubuntu2 [348 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el libidn12 ppc64el 1.42-1 [62.0 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main ppc64el libijs-0.35 ppc64el 0.35-15.1 [16.7 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjbig2dec0 ppc64el 0.20-1build1 [90.7 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2 [204 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgs10 ppc64el 10.02.1~dfsg1-0ubuntu4 [5257 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ghostscript ppc64el 10.02.1~dfsg1-0ubuntu4 [43.6 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libnetpbm11t64 ppc64el 2:11.05.02-1.1 [142 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el netpbm ppc64el 2:11.05.02-1.1 [2552 kB] Get:117 http://ftpmaster.internal/ubuntu noble/universe ppc64el tex-common all 6.18 [32.8 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkpathsea6 ppc64el 2023.20230311.66589-9build2 [71.3 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libptexenc1 ppc64el 2023.20230311.66589-9build2 [42.9 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsynctex2 ppc64el 2023.20230311.66589-9build2 [68.8 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtexlua53-5 ppc64el 2023.20230311.66589-9build2 [163 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main ppc64el t1utils ppc64el 1.41-4build2 [69.6 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] Get:127 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcairo2 ppc64el 1.18.0-1ubuntu1 [751 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libharfbuzz0b ppc64el 8.3.0-2build1 [580 kB] Get:131 http://ftpmaster.internal/ubuntu noble/universe ppc64el libpotrace0 ppc64el 1.16-2 [19.7 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe ppc64el libteckit0 ppc64el 2.5.12+ds1-1 [399 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxmu6 ppc64el 2:1.1.3-3build1 [56.7 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxpm4 ppc64el 1:3.5.17-1build1 [50.2 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxaw7 ppc64el 2:1.0.14-1build1 [232 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main ppc64el libxi6 ppc64el 2:1.8.1-1 [37.9 kB] Get:137 http://ftpmaster.internal/ubuntu noble/universe ppc64el libzzip-0-13t64 ppc64el 0.13.72+dfsg.1-1.2 [32.2 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el texlive-binaries ppc64el 2023.20230311.66589-9build2 [12.4 MB] Get:139 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:140 http://ftpmaster.internal/ubuntu noble/universe ppc64el texlive-base all 2023.20240207-1 [21.7 MB] Get:141 http://ftpmaster.internal/ubuntu noble/main ppc64el hicolor-icon-theme all 0.17-2 [9976 B] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el imagemagick-6.q16 ppc64el 8:6.9.12.98+dfsg1-5.2 [254 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el imagemagick ppc64el 8:6.9.12.98+dfsg1-5.2 [14.2 kB] Get:144 http://ftpmaster.internal/ubuntu noble/universe ppc64el hevea ppc64el 2.36-2 [2153 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-which-perl all 1.27-2 [12.5 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-homedir-perl all 1.006-2 [37.0 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgirepository-2.0-0 ppc64el 2.79.3-3ubuntu5 [84.2 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-bin ppc64el 2.79.3-3ubuntu5 [111 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main ppc64el libffi-dev ppc64el 3.4.6-1 [67.4 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-dev-bin ppc64el 2.79.3-3ubuntu5 [245 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-dev ppc64el 2.39.3-9ubuntu2 [37.7 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid-dev ppc64el 2.39.3-9ubuntu2 [260 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main ppc64el libsepol-dev ppc64el 3.5-2 [471 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-16-0 ppc64el 10.42-4ubuntu1 [245 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-32-0 ppc64el 10.42-4ubuntu1 [228 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-posix3 ppc64el 10.42-4ubuntu1 [7016 B] Get:159 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-dev ppc64el 10.42-4ubuntu1 [794 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1-dev ppc64el 3.5-2build3 [192 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount-dev ppc64el 2.39.3-9ubuntu2 [14.9 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main ppc64el libpkgconf3 ppc64el 1.8.1-2 [36.9 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf-bin ppc64el 1.8.1-2 [22.0 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf ppc64el 1.8.1-2 [16.7 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3.1ubuntu1 [902 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-dev ppc64el 2.79.3-3ubuntu5 [2147 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmime-charset-perl all 1.013.1-2 [31.0 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] Get:171 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsombok3 ppc64el 2.4.0-2 [27.7 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libunicode-linebreak-perl ppc64el 0.0.20190101-1build6 [95.0 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main ppc64el libyaml-tiny-perl all 1.74-1 [25.3 kB] Get:174 http://ftpmaster.internal/ubuntu noble/universe ppc64el lmodern all 2.005-1 [9542 kB] Get:175 http://ftpmaster.internal/ubuntu noble/universe ppc64el texlive-latex-base all 2023.20240207-1 [1238 kB] Get:176 http://ftpmaster.internal/ubuntu noble/universe ppc64el texlive-luatex all 2023.20240207-1 [25.8 MB] Get:177 http://ftpmaster.internal/ubuntu noble/universe ppc64el texlive-plain-generic all 2023.20240207-1 [29.0 MB] Get:178 http://ftpmaster.internal/ubuntu noble/universe ppc64el texlive-extra-utils all 2023.20240207-1 [63.0 MB] Preconfiguring packages ... Fetched 244 MB in 13s (19.1 MB/s) dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested: libgnutls30:ppc64el depends on libhogweed6 (>= 3.6). (Reading database ... 15644 files and directories currently installed.) Removing libhogweed6:ppc64el (3.9.1-2) ... Selecting previously unselected package libhogweed6t64:ppc64el. (Reading database ... 15639 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_ppc64el.deb ... Unpacking libhogweed6t64:ppc64el (3.9.1-2.2) ... dpkg: libgnutls30:ppc64el: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (Reading database ... 15645 files and directories currently installed.) Removing libgnutls30:ppc64el (3.8.3-1ubuntu1) ... Selecting previously unselected package libgnutls30t64:ppc64el. (Reading database ... 15636 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_ppc64el.deb ... Unpacking libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... Setting up libhogweed6t64:ppc64el (3.9.1-2.2) ... Setting up libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ... dpkg: libpng16-16:ppc64el: dependency problems, but removing anyway as you requested: optipng depends on libpng16-16 (>= 1.6.2-1). (Reading database ... 15667 files and directories currently installed.) Removing libpng16-16:ppc64el (1.6.43-1) ... Selecting previously unselected package libpng16-16t64:ppc64el. (Reading database ... 15657 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-3_ppc64el.deb ... Unpacking libpng16-16t64:ppc64el (1.6.43-3) ... Selecting previously unselected package libpython3.12-minimal:ppc64el. Preparing to unpack .../libpython3.12-minimal_3.12.2-4build2_ppc64el.deb ... Unpacking libpython3.12-minimal:ppc64el (3.12.2-4build2) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.6.1-2_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.6.1-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-4build2_ppc64el.deb ... Unpacking python3.12-minimal (3.12.2-4build2) ... Setting up libpython3.12-minimal:ppc64el (3.12.2-4build2) ... Setting up libexpat1:ppc64el (2.6.1-2) ... Setting up python3.12-minimal (3.12.2-4build2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15986 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.2-0ubuntu1_ppc64el.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:ppc64el. Preparing to unpack .../3-libpython3.12-stdlib_3.12.2-4build2_ppc64el.deb ... Unpacking libpython3.12-stdlib:ppc64el (3.12.2-4build2) ... Selecting previously unselected package python3.12. Preparing to unpack .../4-python3.12_3.12.2-4build2_ppc64el.deb ... Unpacking python3.12 (3.12.2-4build2) ... Selecting previously unselected package libpython3-stdlib:ppc64el. Preparing to unpack .../5-libpython3-stdlib_3.12.2-0ubuntu1_ppc64el.deb ... Unpacking libpython3-stdlib:ppc64el (3.12.2-0ubuntu1) ... Setting up python3-minimal (3.12.2-0ubuntu1) ... Selecting previously unselected package python3. (Reading database ... 16426 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.2-0ubuntu1_ppc64el.deb ... Unpacking python3 (3.12.2-0ubuntu1) ... Selecting previously unselected package libfftw3-double3:ppc64el. Preparing to unpack .../001-libfftw3-double3_3.3.10-1ubuntu2_ppc64el.deb ... Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ... Selecting previously unselected package libbrotli1:ppc64el. Preparing to unpack .../002-libbrotli1_1.1.0-2build1_ppc64el.deb ... Unpacking libbrotli1:ppc64el (1.1.0-2build1) ... Selecting previously unselected package libfreetype6:ppc64el. Preparing to unpack .../003-libfreetype6_2.13.2+dfsg-1build1_ppc64el.deb ... Unpacking libfreetype6:ppc64el (2.13.2+dfsg-1build1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:ppc64el. Preparing to unpack .../006-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../007-x11-common_1%3a7.7+23ubuntu2_all.deb ... Unpacking x11-common (1:7.7+23ubuntu2) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../008-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../009-xfonts-utils_1%3a7.7+6build2_ppc64el.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_ppc64el.deb ... Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ... Selecting previously unselected package libfontconfig1:ppc64el. Preparing to unpack .../012-libfontconfig1_2.15.0-1.1ubuntu1_ppc64el.deb ... Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu1) ... Selecting previously unselected package libsharpyuv0:ppc64el. Preparing to unpack .../013-libsharpyuv0_1.3.2-0.4build1_ppc64el.deb ... Unpacking libsharpyuv0:ppc64el (1.3.2-0.4build1) ... Selecting previously unselected package libdav1d7:ppc64el. Preparing to unpack .../014-libdav1d7_1.4.0-1_ppc64el.deb ... Unpacking libdav1d7:ppc64el (1.4.0-1) ... Selecting previously unselected package libheif-plugin-dav1d:ppc64el. Preparing to unpack .../015-libheif-plugin-dav1d_1.17.6-1ubuntu2_ppc64el.deb ... Unpacking libheif-plugin-dav1d:ppc64el (1.17.6-1ubuntu2) ... Selecting previously unselected package libde265-0:ppc64el. Preparing to unpack .../016-libde265-0_1.0.15-1build1_ppc64el.deb ... Unpacking libde265-0:ppc64el (1.0.15-1build1) ... Selecting previously unselected package libheif-plugin-libde265:ppc64el. Preparing to unpack .../017-libheif-plugin-libde265_1.17.6-1ubuntu2_ppc64el.deb ... Unpacking libheif-plugin-libde265:ppc64el (1.17.6-1ubuntu2) ... Selecting previously unselected package libheif1:ppc64el. Preparing to unpack .../018-libheif1_1.17.6-1ubuntu2_ppc64el.deb ... Unpacking libheif1:ppc64el (1.17.6-1ubuntu2) ... Selecting previously unselected package libjbig0:ppc64el. Preparing to unpack .../019-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... Selecting previously unselected package libjpeg-turbo8:ppc64el. Preparing to unpack .../020-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... Selecting previously unselected package libjpeg8:ppc64el. Preparing to unpack .../021-libjpeg8_8c-2ubuntu11_ppc64el.deb ... Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... Selecting previously unselected package liblcms2-2:ppc64el. Preparing to unpack .../022-liblcms2-2_2.14-2_ppc64el.deb ... Unpacking liblcms2-2:ppc64el (2.14-2) ... Selecting previously unselected package libglib2.0-0t64:ppc64el. Preparing to unpack .../023-libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ... Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... Selecting previously unselected package liblqr-1-0:ppc64el. Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build1_ppc64el.deb ... Unpacking liblqr-1-0:ppc64el (0.4.2-2.1build1) ... Selecting previously unselected package libltdl7:ppc64el. Preparing to unpack .../025-libltdl7_2.4.7-7_ppc64el.deb ... Unpacking libltdl7:ppc64el (2.4.7-7) ... Selecting previously unselected package libopenjp2-7:ppc64el. Preparing to unpack .../026-libopenjp2-7_2.5.0-2build2_ppc64el.deb ... Unpacking libopenjp2-7:ppc64el (2.5.0-2build2) ... Selecting previously unselected package libraw23t64:ppc64el. Preparing to unpack .../027-libraw23t64_0.21.2-2.1_ppc64el.deb ... Unpacking libraw23t64:ppc64el (0.21.2-2.1) ... Selecting previously unselected package libdeflate0:ppc64el. Preparing to unpack .../028-libdeflate0_1.19-1_ppc64el.deb ... Unpacking libdeflate0:ppc64el (1.19-1) ... Selecting previously unselected package liblerc4:ppc64el. Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... Selecting previously unselected package libwebp7:ppc64el. Preparing to unpack .../030-libwebp7_1.3.2-0.4build1_ppc64el.deb ... Unpacking libwebp7:ppc64el (1.3.2-0.4build1) ... Selecting previously unselected package libtiff6:ppc64el. Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu1_ppc64el.deb ... Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu1) ... Selecting previously unselected package libwebpdemux2:ppc64el. Preparing to unpack .../032-libwebpdemux2_1.3.2-0.4build1_ppc64el.deb ... Unpacking libwebpdemux2:ppc64el (1.3.2-0.4build1) ... Selecting previously unselected package libwebpmux3:ppc64el. Preparing to unpack .../033-libwebpmux3_1.3.2-0.4build1_ppc64el.deb ... Unpacking libwebpmux3:ppc64el (1.3.2-0.4build1) ... Selecting previously unselected package libxau6:ppc64el. Preparing to unpack .../034-libxau6_1%3a1.0.9-1build5_ppc64el.deb ... Unpacking libxau6:ppc64el (1:1.0.9-1build5) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../035-libbsd0_0.12.1-1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.12.1-1) ... Selecting previously unselected package libxdmcp6:ppc64el. Preparing to unpack .../036-libxdmcp6_1%3a1.1.3-0ubuntu5_ppc64el.deb ... Unpacking libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Selecting previously unselected package libxcb1:ppc64el. Preparing to unpack .../037-libxcb1_1.15-1_ppc64el.deb ... Unpacking libxcb1:ppc64el (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../038-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:ppc64el. Preparing to unpack .../039-libx11-6_2%3a1.8.7-1_ppc64el.deb ... Unpacking libx11-6:ppc64el (2:1.8.7-1) ... Selecting previously unselected package libxext6:ppc64el. Preparing to unpack .../040-libxext6_2%3a1.3.4-1build1_ppc64el.deb ... Unpacking libxext6:ppc64el (2:1.3.4-1build1) ... Selecting previously unselected package libicu74:ppc64el. Preparing to unpack .../041-libicu74_74.2-1ubuntu1_ppc64el.deb ... Unpacking libicu74:ppc64el (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../042-libxml2_2.9.14+dfsg-1.3ubuntu2_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu2) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../043-imagemagick-6-common_8%3a6.9.12.98+dfsg1-5.2_all.deb ... Unpacking imagemagick-6-common (8:6.9.12.98+dfsg1-5.2) ... Selecting previously unselected package libmagickcore-6.q16-7t64:ppc64el. Preparing to unpack .../044-libmagickcore-6.q16-7t64_8%3a6.9.12.98+dfsg1-5.2_ppc64el.deb ... Unpacking libmagickcore-6.q16-7t64:ppc64el (8:6.9.12.98+dfsg1-5.2) ... Selecting previously unselected package libmagickwand-6.q16-7t64:ppc64el. 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Selecting previously unselected package libunicode-linebreak-perl. Preparing to unpack .../158-libunicode-linebreak-perl_0.0.20190101-1build6_ppc64el.deb ... Unpacking libunicode-linebreak-perl (0.0.20190101-1build6) ... Selecting previously unselected package libyaml-tiny-perl. Preparing to unpack .../159-libyaml-tiny-perl_1.74-1_all.deb ... Unpacking libyaml-tiny-perl (1.74-1) ... Selecting previously unselected package lmodern. Preparing to unpack .../160-lmodern_2.005-1_all.deb ... Unpacking lmodern (2.005-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../161-texlive-latex-base_2023.20240207-1_all.deb ... Unpacking texlive-latex-base (2023.20240207-1) ... Selecting previously unselected package texlive-luatex. Preparing to unpack .../162-texlive-luatex_2023.20240207-1_all.deb ... Unpacking texlive-luatex (2023.20240207-1) ... Selecting previously unselected package texlive-plain-generic. 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Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libdatrie1:ppc64el (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:ppc64el (0.35-15.1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libgs-common (10.02.1~dfsg1-0ubuntu4) ... Setting up libbrotli1:ppc64el (1.1.0-2build1) ... Setting up libmagic1t64:ppc64el (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:ppc64el (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libffi-dev:ppc64el (3.4.6-1) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... Setting up libnetpbm11t64:ppc64el (2:11.05.02-1.1) ... Setting up libpcre2-16-0:ppc64el (10.42-4ubuntu1) ... Setting up libelf1t64:ppc64el (0.190-1.1build2) ... Setting up poppler-data (0.4.12-1) ... Setting up libdw1t64:ppc64el (0.190-1.1build2) ... Setting up libosp5 (1.5.2-15ubuntu1) ... Setting up libfontenc1:ppc64el (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:ppc64el (10.42-4ubuntu1) ... Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ... No schema files found: doing nothing. Setting up libglib2.0-data (2.79.3-3ubuntu5) ... Setting up libpkgconf3:ppc64el (1.8.1-2) ... Setting up libzzip-0-13t64:ppc64el (0.13.72+dfsg.1-1.2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:ppc64el (0.20-1build1) ... Setting up libteckit0:ppc64el (2.5.12+ds1-1) ... Setting up uuid-dev:ppc64el (2.39.3-9ubuntu2) ... Setting up libavahi-common-data:ppc64el (0.8-13ubuntu4) ... Setting up libdbus-1-3:ppc64el (1.14.10-4ubuntu2) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:ppc64el (2023.20230311.66589-9build2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:ppc64el (1.6.43-3) ... Setting up libidn12:ppc64el (1.42-1) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsepol-dev:ppc64el (3.5-2) ... Setting up ucf (3.0043+nmu1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... Setting up libltdl7:ppc64el (2.4.7-7) ... Setting up libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ... Setting up libkpathsea6:ppc64el (2023.20230311.66589-9build2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:ppc64el (1.3.2-0.4build1) ... Setting up libicu74:ppc64el (74.2-1ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3.1ubuntu1) ... Setting up libpcre2-posix3:ppc64el (10.42-4ubuntu1) ... Setting up dwz (0.15-1build5) ... Setting up libdav1d7:ppc64el (1.4.0-1) ... Setting up liblqr-1-0:ppc64el (0.4.2-2.1build1) ... Setting up libmime-charset-perl (1.013.1-2) ... Setting up libuchardet0:ppc64el (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:ppc64el (2.5.0-2build2) ... 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:ppc64el (1.0.15-1build1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libwebpmux3:ppc64el (1.3.2-0.4build1) ... Setting up libbsd0:ppc64el (0.12.1-1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu2) ... 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:ppc64el (2023.20230311.66589-9build2) ... Setting up libpotrace0:ppc64el (1.16-2) ... Setting up libjpeg8:ppc64el (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:ppc64el (2.39.3-9ubuntu2) ... Setting up libpaper1:ppc64el (1.1.29) ... Creating config file /etc/papersize with new version Setting up libice6:ppc64el (2:1.0.10-1build2) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Setting up libxcb1:ppc64el (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:ppc64el (3.12.2-4build2) ... Setting up libpcre2-dev:ppc64el (10.42-4ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libgirepository-2.0-0:ppc64el (2.79.3-3ubuntu5) ... Setting up libxcb-render0:ppc64el (1.15-1) ... Setting up libselinux1-dev:ppc64el (3.5-2build3) ... Setting up fontconfig-config (2.15.0-1.1ubuntu1) ... Setting up libwebpdemux2:ppc64el (1.3.2-0.4build1) ... Setting up python3.12 (3.12.2-4build2) ... Setting up libavahi-common3:ppc64el (0.8-13ubuntu4) ... Setting up libglib2.0-bin (2.79.3-3ubuntu5) ... Setting up libxcb-shm0:ppc64el (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up opensp (1.5.2-15ubuntu1) ... Setting up pkgconf:ppc64el (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:ppc64el (0.1.29-2) ... Setting up libptexenc1:ppc64el (2023.20230311.66589-9build2) ... Setting up libfreetype6:ppc64el (2.13.2+dfsg-1build1) ... Setting up libraw23t64:ppc64el (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:ppc64el (4.5.1+git230720-4ubuntu1) ... Setting up xml-core (0.19) ... Setting up libx11-6:ppc64el (2:1.8.7-1) ... Setting up libharfbuzz0b:ppc64el (8.3.0-2build1) ... Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu1) ... Setting up libsm6:ppc64el (2:1.2.3-1build2) ... Setting up libavahi-client3:ppc64el (0.8-13ubuntu4) ... Setting up libmount-dev:ppc64el (2.39.3-9ubuntu2) ... Setting up libpython3-stdlib:ppc64el (3.12.2-0ubuntu1) ... Setting up libxpm4:ppc64el (1:3.5.17-1build1) ... Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... Setting up libsombok3:ppc64el (2.4.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:ppc64el (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:ppc64el (1.18.0-1ubuntu1) ... Setting up python3-packaging (23.2-1) ... Setting up libunicode-linebreak-perl (0.0.20190101-1build6) ... Setting up libxt6t64:ppc64el (1:1.2.1-1.2) ... Setting up netpbm (2:11.05.02-1.1) ... Setting up libcups2:ppc64el (2.4.7-1ubuntu2) ... Setting up lmodern (2.005-1) ... Setting up libglib2.0-dev-bin (2.79.3-3ubuntu5) ... Setting up libxmu6:ppc64el (2:1.1.3-3build1) ... Setting up libxi6:ppc64el (2:1.8.1-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libxaw7:ppc64el (2:1.0.14-1build1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libglib2.0-dev:ppc64el (2.79.3-3ubuntu5) ... Setting up texlive-binaries (2023.20230311.66589-9build2) ... 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:ppc64el (10.02.1~dfsg1-0ubuntu4) ... Setting up ghostscript (10.02.1~dfsg1-0ubuntu4) ... Setting up libheif-plugin-dav1d:ppc64el (1.17.6-1ubuntu2) ... Setting up libheif-plugin-libde265:ppc64el (1.17.6-1ubuntu2) ... Setting up libheif1:ppc64el (1.17.6-1ubuntu2) ... Setting up libmagickcore-6.q16-7t64:ppc64el (8:6.9.12.98+dfsg1-5.2) ... Setting up libmagickwand-6.q16-7t64:ppc64el (8:6.9.12.98+dfsg1-5.2) ... Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5.2) ... 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+dfsg1-5.2) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... Processing triggers for systemd (255.4-1ubuntu5) ... 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) ... (Reading database ... 45443 files and directories currently installed.) Purging configuration files for libgnutls30:ppc64el (3.8.3-1ubuntu1) ... 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 (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64el (ppc64le) Toolchain package versions: binutils_2.42-3ubuntu1 dpkg-dev_1.22.6ubuntu4 g++-13_13.2.0-19ubuntu1 gcc-13_13.2.0-19ubuntu1 libc6-dev_2.39-0ubuntu6 libstdc++-13-dev_13.2.0-19ubuntu1 libstdc++6_14-20240315-1ubuntu1 linux-libc-dev_6.8.0-19.19 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 apt-utils_2.7.3 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-powerpc64le-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_13.2.0-19ubuntu1 cpp-13-powerpc64le-linux-gnu_13.2.0-19ubuntu1 cpp-powerpc64le-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_1.22.6ubuntu4 dpkg-dev_1.22.6ubuntu4 dwz_0.15-1build5 e2fsprogs_1.47.0-2.4~exp1ubuntu2 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_13.2.0-19ubuntu1 g++-13-powerpc64le-linux-gnu_13.2.0-19ubuntu1 g++-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-19ubuntu1 gcc-13-base_13.2.0-19ubuntu1 gcc-13-powerpc64le-linux-gnu_13.2.0-19ubuntu1 gcc-14-base_14-20240315-1ubuntu1 gcc-powerpc64le-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+dfsg1-5.2 imagemagick-6-common_8:6.9.12.98+dfsg1-5.2 imagemagick-6.q16_8:6.9.12.98+dfsg1-5.2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5.1build3 libacl1_2.3.2-1 libapparmor1_4.0.0~beta2-0ubuntu3 libapt-pkg6.0t64_2.7.13ubuntu1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240315-1ubuntu1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wise Binary: wise, wise-doc, wise-data Architecture: any all Version: 2.4.1-24 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/wise Vcs-Git: https://salsa.debian.org/med-team/wise.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Package-List: wise deb science optional arch=any wise-data deb doc optional arch=all wise-doc deb doc optional arch=all Checksums-Sha1: 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz decf2ee3d22049e024b6ef39bc79b1622bc31501 38496 wise_2.4.1-24.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz f1d72cd125e51a89d851ed709135fcafc153284091170be37a7ddfb34521cacc 38496 wise_2.4.1-24.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz c986434b7209337381c3f7e6cfc35de6 38496 wise_2.4.1-24.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEESjHbWh7kCWyHOZiAkDZJKUwz+bcFAmX4cZIACgkQkDZJKUwz +bckXhAAg4fyP2xZRiL+GL9LQZtGcVQiGpza3Zc7AziESu1OJa+u+xA82ye0sd++ f3oqkMDjNV5zKPA8BFlfghg6DcEs8jQqBpMj1mgY1DVt841W6gdmSEZzxiVRGj4c JXLYBB1mCN4gpUsaLGTORFmWjRaWkKEpQvaZ76TvtYaCdftygDBbna9hLwn1+OyQ V8Ymxok0k27X9Iv5zZjtakvOzGZPwPQjSQq27mdHoy47N6zuJq70DAQxf+Tq3XcG zC9XlPIRJZysGPM2mTR4mC5f17+Zqn9sh9PC/2YdeocQFab0vYM6FJkOGBzkdPpa QVxblsP7XuPlJ09RLFMRjBgoNcMtyhu6FL9Wscs7zb7ys+vu8GFyLGza5dAxnZY2 rKW27O9fYzklH8vOVtfWtgpGyNGpzbRzsaRmF8x7nqcia4UJxN/BGwTLuKKWHz9Y MrEdQpECZCFVc5QEsueOZVsss8NjKVGGqJ/6tgFnZdvJOOIQX2EdZX/Czb+4pScS KklafAD7rQUeR77MSk0KxjherQlkBFuSbOabO954NwqUYbuAORovErS8Pf5Gf0Po LWQHmAtEXbjAzPWp+XYYqg9/qoepfZzsYlI10leYjKd01VoQuLdJwFeOcWz3WIrp 9shplFQ3aZKtS+N7Nh9dx4HjCDFK6yciFxNg0k6EH6BWDajhI4g= =X2Y0 -----END PGP SIGNATURE----- gpgv: Signature made Mon Mar 18 16:53:38 2024 UTC gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-24.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_2.4.1-24.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-source: info: applying 11_consistent_manual_dates.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying implicit-function-declaration.patch dpkg-source: info: applying executable-is-script.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27939122 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27939122 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27939122 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 2.4.1-24 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/<>/src/base' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wiseconfig.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wisestring.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wiseerror.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wisememman.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wiserandom.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wisetime.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wiseoverlay.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include wisestreaminterface.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include commandline.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/<>/src/HMMer2' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c alphabet.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c core_algorithms.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c debug.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c emit.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c emulation.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c histogram.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c hmmio.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c mathsupport.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c masks.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c misc.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c modelmakers.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c plan7.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c plan9.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c prior.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c tophits.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c trace.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c aligneval.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c alignio.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c cluster.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c dayhoff.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c file.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c getopt.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c gnuregex.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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); | ^~~~~~~~~~~~~~~~~~ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c iupac.c 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c msf.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c revcomp.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c selex.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c sqerror.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c sqio.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c sre_ctype.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c sre_math.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c sre_string.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c stack.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c translate.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -c types.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/<>/src/dynlibsrc' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ packaln.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ aln.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ probability.c packaln.dy: In function ‘Wise2_read_simple_PackAln’: packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ alnrange.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ alnconvert.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ basematrix.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ matrixdebug.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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ complexsequence.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ complexevalset.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ sequence.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ sequencestream.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ seqalign.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hitlist.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hsp.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hspstream.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ codon.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ compmat.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ codonmapper.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ sequencedb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hscore.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ seqlookup.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ histogram.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ proteindb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ protein.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ pairbase.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ genomicdb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ randommodel.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ randomdb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ genomic.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ cdna.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ cdnadb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dna.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ embl.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ genomicregion.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ gene.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ transcript.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ translation.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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ btcanvas.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/<>/src/dynlibsrc' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ subseqhash.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ intallocator.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hsphandler.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=3 -c -o mott_api.o mott_api.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=3 -c -o gaplib.o gaplib.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/<>/src/socket' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ functionserver.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ functionclient.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ anonobj.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ transferinterface.c functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’: functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ | | | struct sockaddr_in * In file included from functionclient.c:7: /usr/include/powerpc64le-linux-gnu/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’ 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/dnaindex' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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); | ^ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:82: warning: passing argument 4 of ‘Wise2_lift_backward_tangled_tail’ from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected ‘int *’ but argument is of type ‘long int *’ 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/network' cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c dnal.c: In function ‘show_version’: dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c pswdb.c: In function ‘show_version’: pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘make_SeqAlign_from_align’: dbac.c:413:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~^ ~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ 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); | ^~~~~~~~~~~~ genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.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/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/wise-2.4.1-24 -Wdate-time -D_FORTIFY_SOURCE=3 -c -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-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 3 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 3 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm In function ‘Wise2_GeneWiseCodonModel_from_GeneFrequencies’, inlined from ‘Wise2_GeneParameter21_from_GeneFrequency21’ at geneparameter.dy:205:15, inlined from ‘Wise2_GeneParameter21_wrap’ at gwrap.dy:76:9, inlined from ‘build_db_objects’ at genewisedb.c:554:11: geneparameter.dy:115:34: warning: iteration 3 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 3 invokes undefined behavior [-Waggressive-loop-optimizations] 97 | out->in_donor[perm] += donor->gsc[l]->number / 64.0; | ^ geneparameter.dy:90:14: note: within this loop 90 | for(i=0;i<4;i++) | ^ cc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` make[3]: Leaving directory '/<>/src/models' make bin make[3]: Entering directory '/<>/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /<>/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' /usr/bin/make -C debian/manpages.d make[2]: Entering directory '/<>/debian/manpages.d' docbook-to-man dba.sgml > dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make[2]: Leaving directory '/<>/debian/manpages.d' find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 198. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 9. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 205 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 6. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 207 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 208 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 209 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 210. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 215 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 5. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 16. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 17. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 218 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 219. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 8. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 229 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 23 0. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 231 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 233. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 234. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 235. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 239. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 389. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 39 1. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 3. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 395. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 397. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 399. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 400. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 401. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 402. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 03. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 10. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 411. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 2. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 413. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 4. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 415. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 416. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 417 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 423. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 424. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 5. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 26. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 427. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 433 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 434. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 435 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 441. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 2. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 443. LaTeX Warning: Reference `object_AlnBlock' on page 12 undefined on input line 4 51. LaTeX Warning: Reference `object_AlnColumn' on page 12 undefined on input line 453. LaTeX Warning: Reference `object_AlnUnit' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `object_AlnSequence' on page 12 undefined on input lin e 457. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 464. Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [12] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) LaTeX Warning: Reference `accessing_fields' on page 13 undefined on input line 513. [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 555. [14] LaTeX Warning: Reference `accessing_fields' on page 15 undefined on input line 623. [15] LaTeX Warning: Reference `object_AlnRange' on page 16 undefined on input line 6 52. LaTeX Warning: Reference `object_AlnRangeSet' on page 16 undefined on input lin e 654. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 661. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 688. [16] LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 741. LaTeX Warning: Reference `accessing_fields' on page 17 undefined on input line 748. [17] [18] [19] LaTeX Warning: Reference `object_cDNADB' on page 20 undefined on input line 884 . LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 924. [20] LaTeX Warning: Reference `object_CodonTable' on page 21 undefined on input line 1005. [21] [22] [23] [24] LaTeX Warning: Reference `accessing_fields' on page 25 undefined on input line 1213. [25] [26] [27] LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin e 1363. LaTeX Warning: Reference `accessing_fields' on page 28 undefined on input line 1391. [28] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input line 1442. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 29 undefined o n input line 1444. LaTeX Warning: Reference `accessing_fields' on page 29 undefined on input line 1451. [29] LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1482. LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15 17. LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1524. [30] [31] LaTeX Warning: Reference `object_DBSearchImpl' on page 32 undefined on input li ne 1624. [32] LaTeX Warning: Reference `accessing_fields' on page 33 undefined on input line 1671. [33] LaTeX Warning: Reference `object_DnaMatrix' on page 34 undefined on input line 1736. LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l ine 1738. [34] LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1799. LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1812. [35] LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1844. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1851. [36] [37] LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19 48. LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l ine 1950. [38] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 2038. [39] [40] LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line 2150. [41] LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 2168. Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2213. [43] LaTeX Warning: Reference `object_GenomicRegion' on page 44 undefined on input l ine 2298. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2305. [44] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [45] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [46] [47] LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 2505. [48] LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line 2553. Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [49] [50] [51] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [52] [53] [54] LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 293 0. LaTeX Warning: Reference `object_DataScore' on page 55 undefined on input line 2932. LaTeX Warning: Reference `object_DataEntry' on page 55 undefined on input line 2934. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2961. Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [55] [56] [57] LaTeX Warning: Reference `accessing_fields' on page 58 undefined on input line 3162. [58] LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line 3188. LaTeX Warning: Reference `object_PackAln' on page 59 undefined on input line 32 29. [59] LaTeX Warning: Reference `object_PackAlnUnit' on page 60 undefined on input lin e 3231. LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3238. [60] LaTeX Warning: Reference `accessing_fields' on page 61 undefined on input line 3308. [61] [62] LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34 31. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3438. [63] LaTeX Warning: Reference `object_ProteinDB' on page 64 undefined on input line 3488. LaTeX Warning: Reference `accessing_fields' on page 64 undefined on input line 3545. [64] LaTeX Warning: Reference `object_RandomProteinDB' on page 65 undefined on input line 3590. LaTeX Warning: Reference `object_RandomDNADB' on page 65 undefined on input lin e 3592. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3599. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3620. [65] LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input line 3642. LaTeX Warning: Reference `object_RandomModel' on page 66 undefined on input lin e 3644. LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3682. [66] LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line 3697. LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3 713. LaTeX Warning: Reference `object_SequenceSet' on page 67 undefined on input lin e 3715. [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3779. [68] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [69] [70] [71] [72] [73] [74] LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 4176. [75] [76] LaTeX Warning: Reference `object_SequenceDB' on page 77 undefined on input line 4265. LaTeX Warning: Reference `object_FileSource' on page 77 undefined on input line 4267. LaTeX Warning: Reference `accessing_fields' on page 77 undefined on input line 4294. [77] LaTeX Warning: Reference `accessing_fields' on page 78 undefined on input line 4355. LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4381. LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line 4383. [78] LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4390. LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4413. [79] LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin e 4482. LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 4489. Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [80] LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line 4549. [81] LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4579. LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin e 4602. Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [82] LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 4655. Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [83] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [84] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [85] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [86] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input line 4830. LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l ine 4832. LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input line 4834. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4879. Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4906. [88] LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4921. LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input line 4937. LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4944. [89] LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input line 4990. LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li ne 4992. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4999. Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [90] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 5065. [91] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 92 undefined on input li ne 5107. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 92 undefined on input line 5109. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5116. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5152. [92] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [93] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in put line 5243. LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input line 5245. LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line 5247. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5254. Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [95] LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5307. LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5320. Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [96] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [97] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [98] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [99] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [100] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l ine 5552. LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line 5559. [101] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [103] [104] LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu t line 5732. LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input line 5734. LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5775. [105] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [106] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5890. [107] [108] (./api.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tctt1000.tfm. Output written on tctt1000.600gf (128 characters, 19540 bytes). Transcript written on tctt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. Output written on api.pdf (108 pages, 304186 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib /texmf/fonts/map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 233. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 239. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 389. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 26. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 435 . Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [20] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [47] [48] [49] Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [50] [51] [52] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [53] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [54] [55] [56] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [57] [58] [59] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [60] [61] [62] Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [88] [89] Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [90] Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [91] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [92] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [93] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [94] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [95] Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [96] [97] Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [98] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) [99] [100] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [101] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [103] Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [104] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [105] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [106] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [107] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [108] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) [109] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [110] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [111] [112] [113] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [114] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [115] [116] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (116 pages, 318788 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 77. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [7] [8] [9] [10] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [11] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [12] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [13] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [14] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [15] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [16] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [17] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [19] [20] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [22] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [23] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [24] [25] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [26] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [27] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [28] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [29] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [30] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [34] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [36] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [37] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [40] [41] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [42] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [43] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [44] [45] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [46] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [47] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [48] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [49] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] [51] [52] [53] [54] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [55] [56] [57] [58] [59] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [60] [61] [62] (./dynamite.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (62 pages, 221231 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [9] [10] [11] [12] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [13] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [14] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [16] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [17] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [18] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [19] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [21] [22] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [24] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [25] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [26] [27] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [28] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [29] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [30] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [31] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [32] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [36] [37] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] [40] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [41] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [42] [43] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [44] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [45] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [46] [47] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [48] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [49] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [51] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [52] [53] [54] [55] [56] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [57] [58] [59] [60] [61] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [62] [63] [64] (./dynamite.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (64 pages, 224793 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 110 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 113. Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [5] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 297. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 6. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 455 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 66. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 3. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 3. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 13. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 708. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 900. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [22] [23] [24] [25] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [26] LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11 81. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 121 0. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1276. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [30] [31] LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137 7. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 9. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 561. [37] [38] [39] [40] [41] [42] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (42 pages, 213100 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [6] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 708. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [23] [24] [25] [26] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [27] [28] [29] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (43 pages, 215391 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory '/<>' rm -f debian/wise.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/wise.substvars rm -fr -- debian/.debhelper/generated/wise/ debian/wise/ debian/tmp/ dh_installdirs -a install -m0755 -d debian/wise/usr/bin dh_install -a install -m0755 -d debian/wise/usr/bin cp --reflink=auto -a ./src/bin/dba ./src/bin/dnal ./src/bin/estwise ./src/bin/estwisedb ./src/bin/genewise ./src/bin/genewisedb ./src/bin/promoterwise ./src/bin/psw ./src/bin/pswdb ./src/bin/scanwise ./src/bin/scanwise_server ./src/models/genomewise debian/wise/usr/bin/ dh_installdocs -a install -m0755 -d debian/wise/usr/share/doc/wise install -m0755 -d debian/wise/usr/share/doc/wise cp --reflink=auto -a ./README debian/wise/usr/share/doc/wise cp --reflink=auto -a ./debian/tests/run-unit-test debian/wise/usr/share/doc/wise chmod -R u\+rw,go=rX debian/wise/usr/share/doc install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright dh_installchangelogs -a install -m0755 -d debian/wise/usr/share/doc/wise install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian dh_installexamples -a dh_installman -a install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 debian/wise/usr/share/man/man1/estwise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/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/pswdb.1 debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/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/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/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 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 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/powerpc64le-linux-gnu dwz -mdebian/wise/usr/lib/debug/.dwz/powerpc64le-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/powerpc64le-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/powerpc64le-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/powerpc64le-linux-gnu/wise.debug dh_strip -a debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/estwise debugedit: debian/wise/usr/bin/estwise: Unknown DWARF DW_FORM_0x1f20 a8d0a69482a63e9928671a63b0312737fcfd89fa install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/d0a69482a63e9928671a63b0312737fcfd89fa.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/d0a69482a63e9928671a63b0312737fcfd89fa.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripvsT01H debian/wise/usr/bin/estwise chmod --reference debian/wise/usr/bin/estwise /tmp/eR8z3fDlIl/stripvsT01H cat '/tmp/eR8z3fDlIl/stripvsT01H' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/eR8z3fDlIl/stripvsT01H debian/wise/usr/bin/estwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/d0a69482a63e9928671a63b0312737fcfd89fa.debug debian/wise/usr/bin/estwise /tmp/eR8z3fDlIl/objcopyHxyrpW chmod --reference debian/wise/usr/bin/estwise /tmp/eR8z3fDlIl/objcopyHxyrpW cat '/tmp/eR8z3fDlIl/objcopyHxyrpW' > 'debian/wise/usr/bin/estwise' chmod --reference /tmp/eR8z3fDlIl/objcopyHxyrpW debian/wise/usr/bin/estwise debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/scanwise debugedit: debian/wise/usr/bin/scanwise: Unknown DWARF DW_FORM_0x1f20 a6706793680bbea46ae3bff95d5fb3c84c7aef2d install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6/706793680bbea46ae3bff95d5fb3c84c7aef2d.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6/706793680bbea46ae3bff95d5fb3c84c7aef2d.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripGhKDFB debian/wise/usr/bin/scanwise chmod --reference debian/wise/usr/bin/scanwise /tmp/eR8z3fDlIl/stripGhKDFB cat '/tmp/eR8z3fDlIl/stripGhKDFB' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/eR8z3fDlIl/stripGhKDFB debian/wise/usr/bin/scanwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6/706793680bbea46ae3bff95d5fb3c84c7aef2d.debug debian/wise/usr/bin/scanwise /tmp/eR8z3fDlIl/objcopyqLfNxF chmod --reference debian/wise/usr/bin/scanwise /tmp/eR8z3fDlIl/objcopyqLfNxF cat '/tmp/eR8z3fDlIl/objcopyqLfNxF' > 'debian/wise/usr/bin/scanwise' chmod --reference /tmp/eR8z3fDlIl/objcopyqLfNxF debian/wise/usr/bin/scanwise debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/dba debugedit: debian/wise/usr/bin/dba: Unknown DWARF DW_FORM_0x1f20 bdd9b3bc4b8d2e575b60e215b13ebb935517c76e install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bd/d9b3bc4b8d2e575b60e215b13ebb935517c76e.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bd/d9b3bc4b8d2e575b60e215b13ebb935517c76e.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/strip_Ov4kY debian/wise/usr/bin/dba chmod --reference debian/wise/usr/bin/dba /tmp/eR8z3fDlIl/strip_Ov4kY cat '/tmp/eR8z3fDlIl/strip_Ov4kY' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/eR8z3fDlIl/strip_Ov4kY debian/wise/usr/bin/dba objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bd/d9b3bc4b8d2e575b60e215b13ebb935517c76e.debug debian/wise/usr/bin/dba /tmp/eR8z3fDlIl/objcopyYqsYhG chmod --reference debian/wise/usr/bin/dba /tmp/eR8z3fDlIl/objcopyYqsYhG cat '/tmp/eR8z3fDlIl/objcopyYqsYhG' > 'debian/wise/usr/bin/dba' chmod --reference /tmp/eR8z3fDlIl/objcopyYqsYhG debian/wise/usr/bin/dba debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/estwisedb debugedit: debian/wise/usr/bin/estwisedb: Unknown DWARF DW_FORM_0x1f20 3b968d6f05209c2317122de2c8c51a9bc3be5737 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/3b/968d6f05209c2317122de2c8c51a9bc3be5737.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/3b/968d6f05209c2317122de2c8c51a9bc3be5737.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripr9Fot7 debian/wise/usr/bin/estwisedb chmod --reference debian/wise/usr/bin/estwisedb /tmp/eR8z3fDlIl/stripr9Fot7 cat '/tmp/eR8z3fDlIl/stripr9Fot7' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/eR8z3fDlIl/stripr9Fot7 debian/wise/usr/bin/estwisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/3b/968d6f05209c2317122de2c8c51a9bc3be5737.debug debian/wise/usr/bin/estwisedb /tmp/eR8z3fDlIl/objcopyNDkuRq chmod --reference debian/wise/usr/bin/estwisedb /tmp/eR8z3fDlIl/objcopyNDkuRq cat '/tmp/eR8z3fDlIl/objcopyNDkuRq' > 'debian/wise/usr/bin/estwisedb' chmod --reference /tmp/eR8z3fDlIl/objcopyNDkuRq debian/wise/usr/bin/estwisedb debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/dnal debugedit: debian/wise/usr/bin/dnal: Unknown DWARF DW_FORM_0x1f20 d4cbe367e7d15371cfa2c59e94ebdb9b413676a9 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/cbe367e7d15371cfa2c59e94ebdb9b413676a9.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/cbe367e7d15371cfa2c59e94ebdb9b413676a9.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripdNyk9t debian/wise/usr/bin/dnal chmod --reference debian/wise/usr/bin/dnal /tmp/eR8z3fDlIl/stripdNyk9t cat '/tmp/eR8z3fDlIl/stripdNyk9t' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/eR8z3fDlIl/stripdNyk9t debian/wise/usr/bin/dnal objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/cbe367e7d15371cfa2c59e94ebdb9b413676a9.debug debian/wise/usr/bin/dnal /tmp/eR8z3fDlIl/objcopyzIPFit chmod --reference debian/wise/usr/bin/dnal /tmp/eR8z3fDlIl/objcopyzIPFit cat '/tmp/eR8z3fDlIl/objcopyzIPFit' > 'debian/wise/usr/bin/dnal' chmod --reference /tmp/eR8z3fDlIl/objcopyzIPFit debian/wise/usr/bin/dnal debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/genewisedb debugedit: debian/wise/usr/bin/genewisedb: Unknown DWARF DW_FORM_0x1f20 b0f35e1da5e68d95105e639244aefefd4a669046 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/f35e1da5e68d95105e639244aefefd4a669046.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/f35e1da5e68d95105e639244aefefd4a669046.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/striprzrFZ9 debian/wise/usr/bin/genewisedb chmod --reference debian/wise/usr/bin/genewisedb /tmp/eR8z3fDlIl/striprzrFZ9 cat '/tmp/eR8z3fDlIl/striprzrFZ9' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/eR8z3fDlIl/striprzrFZ9 debian/wise/usr/bin/genewisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/f35e1da5e68d95105e639244aefefd4a669046.debug debian/wise/usr/bin/genewisedb /tmp/eR8z3fDlIl/objcopy2mVSXI chmod --reference debian/wise/usr/bin/genewisedb /tmp/eR8z3fDlIl/objcopy2mVSXI cat '/tmp/eR8z3fDlIl/objcopy2mVSXI' > 'debian/wise/usr/bin/genewisedb' chmod --reference /tmp/eR8z3fDlIl/objcopy2mVSXI debian/wise/usr/bin/genewisedb debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/genomewise debugedit: debian/wise/usr/bin/genomewise: Unknown DWARF DW_FORM_0x1f20 9008e038956f535b41a977b5d98fb30b18ace969 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/90/08e038956f535b41a977b5d98fb30b18ace969.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/90/08e038956f535b41a977b5d98fb30b18ace969.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripXmOJUE debian/wise/usr/bin/genomewise chmod --reference debian/wise/usr/bin/genomewise /tmp/eR8z3fDlIl/stripXmOJUE cat '/tmp/eR8z3fDlIl/stripXmOJUE' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/eR8z3fDlIl/stripXmOJUE debian/wise/usr/bin/genomewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/90/08e038956f535b41a977b5d98fb30b18ace969.debug debian/wise/usr/bin/genomewise /tmp/eR8z3fDlIl/objcopyUF1gyB chmod --reference debian/wise/usr/bin/genomewise /tmp/eR8z3fDlIl/objcopyUF1gyB cat '/tmp/eR8z3fDlIl/objcopyUF1gyB' > 'debian/wise/usr/bin/genomewise' chmod --reference /tmp/eR8z3fDlIl/objcopyUF1gyB debian/wise/usr/bin/genomewise debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/promoterwise debugedit: debian/wise/usr/bin/promoterwise: Unknown DWARF DW_FORM_0x1f20 43a22a4bee7dda444d8d8036ad422cbaf449fa07 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/43 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/43/a22a4bee7dda444d8d8036ad422cbaf449fa07.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/43/a22a4bee7dda444d8d8036ad422cbaf449fa07.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/strip2LQf1R debian/wise/usr/bin/promoterwise chmod --reference debian/wise/usr/bin/promoterwise /tmp/eR8z3fDlIl/strip2LQf1R cat '/tmp/eR8z3fDlIl/strip2LQf1R' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/eR8z3fDlIl/strip2LQf1R debian/wise/usr/bin/promoterwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/43/a22a4bee7dda444d8d8036ad422cbaf449fa07.debug debian/wise/usr/bin/promoterwise /tmp/eR8z3fDlIl/objcopyvsbKG7 chmod --reference debian/wise/usr/bin/promoterwise /tmp/eR8z3fDlIl/objcopyvsbKG7 cat '/tmp/eR8z3fDlIl/objcopyvsbKG7' > 'debian/wise/usr/bin/promoterwise' chmod --reference /tmp/eR8z3fDlIl/objcopyvsbKG7 debian/wise/usr/bin/promoterwise debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/scanwise_server debugedit: debian/wise/usr/bin/scanwise_server: Unknown DWARF DW_FORM_0x1f21 fafab33fe481021de5965b64e4ec940b797d6806 install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fa objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fa/fab33fe481021de5965b64e4ec940b797d6806.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fa/fab33fe481021de5965b64e4ec940b797d6806.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripHltoUM debian/wise/usr/bin/scanwise_server chmod --reference debian/wise/usr/bin/scanwise_server /tmp/eR8z3fDlIl/stripHltoUM cat '/tmp/eR8z3fDlIl/stripHltoUM' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/eR8z3fDlIl/stripHltoUM debian/wise/usr/bin/scanwise_server objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fa/fab33fe481021de5965b64e4ec940b797d6806.debug debian/wise/usr/bin/scanwise_server /tmp/eR8z3fDlIl/objcopyl9AJPU chmod --reference debian/wise/usr/bin/scanwise_server /tmp/eR8z3fDlIl/objcopyl9AJPU cat '/tmp/eR8z3fDlIl/objcopyl9AJPU' > 'debian/wise/usr/bin/scanwise_server' chmod --reference /tmp/eR8z3fDlIl/objcopyl9AJPU debian/wise/usr/bin/scanwise_server debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/genewise debugedit: debian/wise/usr/bin/genewise: Unknown DWARF DW_FORM_0x1f21 7e30085716c1e90dc247fdac09fdab9d4a657e6f install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7e objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7e/30085716c1e90dc247fdac09fdab9d4a657e6f.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7e/30085716c1e90dc247fdac09fdab9d4a657e6f.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripgIMfKE debian/wise/usr/bin/genewise chmod --reference debian/wise/usr/bin/genewise /tmp/eR8z3fDlIl/stripgIMfKE cat '/tmp/eR8z3fDlIl/stripgIMfKE' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/eR8z3fDlIl/stripgIMfKE debian/wise/usr/bin/genewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7e/30085716c1e90dc247fdac09fdab9d4a657e6f.debug debian/wise/usr/bin/genewise /tmp/eR8z3fDlIl/objcopyn_AyHL chmod --reference debian/wise/usr/bin/genewise /tmp/eR8z3fDlIl/objcopyn_AyHL cat '/tmp/eR8z3fDlIl/objcopyn_AyHL' > 'debian/wise/usr/bin/genewise' chmod --reference /tmp/eR8z3fDlIl/objcopyn_AyHL debian/wise/usr/bin/genewise debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/pswdb debugedit: debian/wise/usr/bin/pswdb: Unknown DWARF DW_FORM_0x1f20 8f74d87c592efe069176ce49c2b9c2698d459afc install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8f objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8f/74d87c592efe069176ce49c2b9c2698d459afc.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8f/74d87c592efe069176ce49c2b9c2698d459afc.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripiFC708 debian/wise/usr/bin/pswdb chmod --reference debian/wise/usr/bin/pswdb /tmp/eR8z3fDlIl/stripiFC708 cat '/tmp/eR8z3fDlIl/stripiFC708' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/eR8z3fDlIl/stripiFC708 debian/wise/usr/bin/pswdb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8f/74d87c592efe069176ce49c2b9c2698d459afc.debug debian/wise/usr/bin/pswdb /tmp/eR8z3fDlIl/objcopy5EMttF chmod --reference debian/wise/usr/bin/pswdb /tmp/eR8z3fDlIl/objcopy5EMttF cat '/tmp/eR8z3fDlIl/objcopy5EMttF' > 'debian/wise/usr/bin/pswdb' chmod --reference /tmp/eR8z3fDlIl/objcopy5EMttF debian/wise/usr/bin/pswdb debugedit --build-id --build-id-seed=wise/2.4.1-24 debian/wise/usr/bin/psw debugedit: debian/wise/usr/bin/psw: Unknown DWARF DW_FORM_0x1f20 b9dd2749e44e1af8c451e7b67a99edba46267bce install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9/dd2749e44e1af8c451e7b67a99edba46267bce.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9/dd2749e44e1af8c451e7b67a99edba46267bce.debug strip --remove-section=.comment --remove-section=.note -o /tmp/eR8z3fDlIl/stripnDpsSO debian/wise/usr/bin/psw chmod --reference debian/wise/usr/bin/psw /tmp/eR8z3fDlIl/stripnDpsSO cat '/tmp/eR8z3fDlIl/stripnDpsSO' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/eR8z3fDlIl/stripnDpsSO debian/wise/usr/bin/psw objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9/dd2749e44e1af8c451e7b67a99edba46267bce.debug debian/wise/usr/bin/psw /tmp/eR8z3fDlIl/objcopyj6I_aS chmod --reference debian/wise/usr/bin/psw /tmp/eR8z3fDlIl/objcopyj6I_aS cat '/tmp/eR8z3fDlIl/objcopyj6I_aS' > 'debian/wise/usr/bin/psw' chmod --reference /tmp/eR8z3fDlIl/objcopyj6I_aS debian/wise/usr/bin/psw install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/powerpc64le-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/estwise debian/wise/usr/bin/scanwise debian/wise/usr/bin/dba debian/wise/usr/bin/estwisedb debian/wise/usr/bin/dnal debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/genewise debian/wise/usr/bin/pswdb debian/wise/usr/bin/psw 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=3b968d6f05209c2317122de2c8c51a9bc3be5737 43a22a4bee7dda444d8d8036ad422cbaf449fa07 7e30085716c1e90dc247fdac09fdab9d4a657e6f 8f74d87c592efe069176ce49c2b9c2698d459afc 9008e038956f535b41a977b5d98fb30b18ace969 a6706793680bbea46ae3bff95d5fb3c84c7aef2d a8d0a69482a63e9928671a63b0312737fcfd89fa b0f35e1da5e68d95105e639244aefefd4a669046 b9dd2749e44e1af8c451e7b67a99edba46267bce bdd9b3bc4b8d2e575b60e215b13ebb935517c76e d4cbe367e7d15371cfa2c59e94ebdb9b413676a9 fafab33fe481021de5965b64e4ec940b797d6806" -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: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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. 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_2.4.1-24_ppc64el.deb'. dpkg-deb: building package 'wise' in '../wise_2.4.1-24_ppc64el.deb'. Renaming wise-dbgsym_2.4.1-24_ppc64el.deb to wise-dbgsym_2.4.1-24_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-wise/wise-dbgsym_2.4.1-24_ppc64el.deb ../wise-dbgsym_2.4.1-24_ppc64el.ddeb dpkg-genbuildinfo --build=any -O../wise_2.4.1-24_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../wise_2.4.1-24_ppc64el.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 2024-03-18T23:05:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ wise_2.4.1-24_ppc64el.changes: ------------------------------ Format: 1.8 Date: Mon, 18 Mar 2024 22:32:37 +0700 Source: wise Binary: wise Built-For-Profiles: noudeb Architecture: ppc64el Version: 2.4.1-24 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Lance Lin Description: wise - comparison of biopolymers, like DNA and protein sequences Closes: 1066705 Changes: wise (2.4.1-24) unstable; urgency=medium . * Team upload. * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * watch file standard 4 (routine-update) * d/patches: Fix implicit-function-declaration errors (Closes: #1066705) * d/patches: Mark patch Forwarded fields as not-needed, since no upstream bug tracking, and update spelling.patch * d/patches: Fix executable-not-elf-or-script lintian warning * d/watch: Remove debian uupdate and access secure uri Checksums-Sha1: 119a9c6abdac7fc81ef8279b7f802ba6d90a20d4 3899646 wise-dbgsym_2.4.1-24_ppc64el.ddeb 11e8df490888b48d9c182e5d05db2557abadb478 11100 wise_2.4.1-24_ppc64el.buildinfo f9e9383e661f32426f8accf233e9ac2d8840fba4 1073740 wise_2.4.1-24_ppc64el.deb Checksums-Sha256: f5949ad74c2bbb0b01534d4153290675dbe5aa388b6d42b678cfb97c48c7a035 3899646 wise-dbgsym_2.4.1-24_ppc64el.ddeb fa4a4ad9777ee553ef5b4bb18c69e0dfa6fea56c5dbea71bc487467636c6a07b 11100 wise_2.4.1-24_ppc64el.buildinfo c4e3fba1b728b51e60b6381f04868ebd83bba3060e6ca6d81c34ba078a5edf04 1073740 wise_2.4.1-24_ppc64el.deb Files: 83e3a75f2d497e4000912bfa2699ec96 3899646 debug optional wise-dbgsym_2.4.1-24_ppc64el.ddeb 1b707fb387735b96a2e20b8045f77114 11100 science optional wise_2.4.1-24_ppc64el.buildinfo e56d916b0074014119396c1085e1e272 1073740 science optional wise_2.4.1-24_ppc64el.deb /<>/wise_2.4.1-24_ppc64el.changes.new could not be renamed to /<>/wise_2.4.1-24_ppc64el.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: wise Binary: wise wise-dbgsym Architecture: ppc64el Version: 2.4.1-24 Checksums-Md5: 83e3a75f2d497e4000912bfa2699ec96 3899646 wise-dbgsym_2.4.1-24_ppc64el.ddeb e56d916b0074014119396c1085e1e272 1073740 wise_2.4.1-24_ppc64el.deb Checksums-Sha1: 119a9c6abdac7fc81ef8279b7f802ba6d90a20d4 3899646 wise-dbgsym_2.4.1-24_ppc64el.ddeb f9e9383e661f32426f8accf233e9ac2d8840fba4 1073740 wise_2.4.1-24_ppc64el.deb Checksums-Sha256: f5949ad74c2bbb0b01534d4153290675dbe5aa388b6d42b678cfb97c48c7a035 3899646 wise-dbgsym_2.4.1-24_ppc64el.ddeb c4e3fba1b728b51e60b6381f04868ebd83bba3060e6ca6d81c34ba078a5edf04 1073740 wise_2.4.1-24_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Mon, 18 Mar 2024 23:05:50 +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-powerpc64le-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 (= 13.2.0-19ubuntu1), cpp-13-powerpc64le-linux-gnu (= 13.2.0-19ubuntu1), cpp-powerpc64le-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 (= 1.22.6ubuntu4), dpkg-dev (= 1.22.6ubuntu4), 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 (= 13.2.0-19ubuntu1), g++-13-powerpc64le-linux-gnu (= 13.2.0-19ubuntu1), g++-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-19ubuntu1), gcc-13-base (= 13.2.0-19ubuntu1), gcc-13-powerpc64le-linux-gnu (= 13.2.0-19ubuntu1), gcc-14-base (= 14-20240315-1ubuntu1), gcc-powerpc64le-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+dfsg1-5.2), imagemagick-6-common (= 8:6.9.12.98+dfsg1-5.2), imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-5.2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240315-1ubuntu1), libatomic1 (= 14-20240315-1ubuntu1), 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 (= 1.1.0-2build1), libbsd0 (= 0.12.1-1), libbz2-1.0 (= 1.0.8-5ubuntu1), libc-bin (= 2.39-0ubuntu6), libc-dev-bin (= 2.39-0ubuntu6), libc6 (= 2.39-0ubuntu6), libc6-dev (= 2.39-0ubuntu6), libcairo2 (= 1.18.0-1ubuntu1), libcap-ng0 (= 0.8.4-2build1), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240315-1ubuntu1), libcom-err2 (= 1.47.0-2.4~exp1ubuntu2), 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+dfsg2-5build1), libdbus-1-3 (= 1.14.10-4ubuntu2), libde265-0 (= 1.0.15-1build1), libdebconfclient0 (= 0.271ubuntu2), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.6ubuntu4), libdw1t64 (= 0.190-1.1build2), libelf1t64 (= 0.190-1.1build2), libexpat1 (= 2.6.1-2), libffi-dev (= 3.4.6-1), libffi8 (= 3.4.6-1), libfftw3-double3 (= 3.3.10-1ubuntu2), 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 (= 1:1.1.8-1), libfreetype6 (= 2.13.2+dfsg-1build1), libgcc-13-dev (= 13.2.0-19ubuntu1), libgcc-s1 (= 14-20240315-1ubuntu1), 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 (= 14-20240315-1ubuntu1), 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 (= 1.20.1-5.1build3), 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 (= 14-20240315-1ubuntu1), 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 (= 1.20.1-5.1build3), libkeyutils1 (= 1.6.3-3), libkpathsea6 (= 2023.20230311.66589-9build2), libkrb5-3 (= 1.20.1-5.1build3), libkrb5support0 (= 1.20.1-5.1build3), liblcms2-2 (= 2.14-2), liblerc4 (= 4.0.0+ds-4ubuntu1), liblqr-1-0 (= 0.4.2-2.1build1), liblsan0 (= 14-20240315-1ubuntu1), 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.q16-7t64 (= 8:6.9.12.98+dfsg1-5.2), libmagickwand-6.q16-7t64 (= 8:6.9.12.98+dfsg1-5.2), 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 (= 2.5.0-2build2), 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 (= 2023.20230311.66589-9build2), libpython3-stdlib (= 3.12.2-0ubuntu1), libpython3.12-minimal (= 3.12.2-4build2), libpython3.12-stdlib (= 3.12.2-4build2), libquadmath0 (= 14-20240315-1ubuntu1), libraw23t64 (= 0.21.2-2.1), libreadline8t64 (= 8.2-3.1), libseccomp2 (= 2.5.5-1ubuntu2), libselinux1 (= 3.5-2build3), libselinux1-dev (= 3.5-2build3), 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 (= 3.0.13-0ubuntu2), libstdc++-13-dev (= 13.2.0-19ubuntu1), libstdc++6 (= 14-20240315-1ubuntu1), libsub-override-perl (= 0.10-1), libsynctex2 (= 2023.20230311.66589-9build2), libsystemd0 (= 255.4-1ubuntu5), libtasn1-6 (= 4.19.0-3), libteckit0 (= 2.5.12+ds1-1), libtexlua53-5 (= 2023.20230311.66589-9build2), 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), libtsan2 (= 14-20240315-1ubuntu1), libubsan1 (= 14-20240315-1ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu5), 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-1.3ubuntu2), 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-0-13t64 (= 0.13.72+dfsg.1-1.2), linux-libc-dev (= 6.8.0-19.19), 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 (= 2023.20230311.66589-9build2), 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="1710775957" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ wise_2.4.1-24_ppc64el.deb ------------------------- new Debian package, version 2.0. size 1073740 bytes: control archive=1950 bytes. 1804 bytes, 34 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-24 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4676 Depends: libc6 (>= 2.34), libglib2.0-0t64 (>= 2.12.0), wise-data (= 2.4.1-24) Suggests: wise-doc (= 2.4.1-24) 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. drwxr-xr-x root/root 0 2024-03-18 15:32 ./ drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/ drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/bin/ -rwxr-xr-x root/root 199008 2024-03-18 15:32 ./usr/bin/dba -rwxr-xr-x root/root 133400 2024-03-18 15:32 ./usr/bin/dnal -rwxr-xr-x root/root 395680 2024-03-18 15:32 ./usr/bin/estwise -rwxr-xr-x root/root 526800 2024-03-18 15:32 ./usr/bin/estwisedb -rwxr-xr-x root/root 1182144 2024-03-18 15:32 ./usr/bin/genewise -rwxr-xr-x root/root 1116672 2024-03-18 15:32 ./usr/bin/genewisedb -rwxr-xr-x root/root 198936 2024-03-18 15:32 ./usr/bin/genomewise -rwxr-xr-x root/root 198936 2024-03-18 15:32 ./usr/bin/promoterwise -rwxr-xr-x root/root 133400 2024-03-18 15:32 ./usr/bin/psw -rwxr-xr-x root/root 198992 2024-03-18 15:32 ./usr/bin/pswdb -rwxr-xr-x root/root 264472 2024-03-18 15:32 ./usr/bin/scanwise -rwxr-xr-x root/root 198936 2024-03-18 15:32 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/share/ drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/share/doc/wise/ -rw-r--r-- root/root 1973 2007-07-01 20:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 320 2024-03-14 14:39 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 1052 2024-03-18 15:32 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4297 2024-03-14 14:42 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 312 2024-03-14 14:39 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-18 15:32 ./usr/share/man/man1/ -rw-r--r-- root/root 846 2024-03-18 15:32 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2024-03-18 15:32 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2024-03-18 15:32 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2024-03-18 15:32 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2024-03-18 15:32 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2024-03-18 15:32 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2024-03-18 15:32 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2024-03-18 15:32 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2024-03-18 15:32 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2024-03-18 15:32 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2024-03-18 15:32 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2024-03-18 15:32 ./usr/share/man/man1/scanwise_server.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 174004 Build-Time: 126 Distribution: noble-proposed Host Architecture: ppc64el Install-Time: 85 Job: wise_2.4.1-24.dsc Machine Architecture: ppc64el Package: wise Package-Time: 212 Source-Version: 2.4.1-24 Space: 174004 Status: successful Version: 2.4.1-24 -------------------------------------------------------------------------------- Finished at 2024-03-18T23:05:51Z Build needed 00:03:32, 174004k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27939122 Scanning for processes to kill in build PACKAGEBUILD-27939122