Sat Nov 23 05:30:10 UTC 2024 I: starting to build libbio-tools-run-alignment-clustalw-perl/trixie/amd64 on jenkins on '2024-11-23 05:29' Sat Nov 23 05:30:10 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_24/41069/console.log Sat Nov 23 05:30:10 UTC 2024 I: Downloading source for trixie/libbio-tools-run-alignment-clustalw-perl=1.7.4-4 --2024-11-23 05:30:10-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-run-alignment-clustalw-perl/libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2514 (2.5K) [text/prs.lines.tag] Saving to: ‘libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc’ 0K .. 100% 320M=0s 2024-11-23 05:30:10 (320 MB/s) - ‘libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc’ saved [2514/2514] Sat Nov 23 05:30:10 UTC 2024 I: libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-run-alignment-clustalw-perl Binary: libbio-tools-run-alignment-clustalw-perl Architecture: all Version: 1.7.4-4 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-Clustalw Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-clustalw-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-clustalw-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: clustalw, libbio-perl-perl , libbio-perl-run-perl , libdevel-checkbin-perl, perl Package-List: libbio-tools-run-alignment-clustalw-perl deb science optional arch=all Checksums-Sha1: 926fde7762db2c2e9aa3d94295fb8cf7c9994cc7 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz afbecfb4e13107fbe55b65b6f1ca32b17bf9f32b 2628 libbio-tools-run-alignment-clustalw-perl_1.7.4-4.debian.tar.xz Checksums-Sha256: 4e322d50fd945257f61609ed6e59c3e6817948166a6230d24d5ca23b507e331e 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz 965f00a501de21962ec1c853012d0e89fd5bec0b918d69920379a8ea26a1dd67 2628 libbio-tools-run-alignment-clustalw-perl_1.7.4-4.debian.tar.xz Files: 6820fcb8ca70c5fd75baa4bf979ab274 30259 libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz f5d8d608554a3ceae1819305ee47bb80 2628 libbio-tools-run-alignment-clustalw-perl_1.7.4-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmXu9bMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGdLA/+KHzyYHubnj2tsx76crDPlYFPAwdMf4Rf Q6kOTqKh1HuGOGRhG2pFnBhsyurL05T4s2hUiu5zlOiDzqASe4nsKP7Gd8N6BvF9 A8FT7wOC1vMT9+cI39tOG8YfiakzB8/6kXYQ8wF1xRTtXJPQyzLRr+kosM+5dSzA 6w1Xe96GhgVQHOtVfLAhazxeR8GG1RW79uUFVNWR/4uh4XSBViF7cXF/8rke8WH8 hVHVw4cplZrMt9LjJUZDVt/H9obQmux6KwQzMbqT0LGQQo/B/aVJ9yxFoSDh6Qz+ poirqWbe4lJ+A9qrL8ucR/Zc1Q9jCDt6AQ4ADsGzVFuZzUQBeX6yVaW3UndpqToT c5Ei8+sjpT1V5yZPu9SZb8XA6C/28pxwdDVTtdL9AC0RFcyFsNO99HkAUhLJtWy5 9eV8K2HgF+1Bgvolf1PRK0PzDKDJjx6m2OwBHuNLYL9gSc/IJ4d3F44nd7h7ZzgZ yqvAgkeIuz3F3xmbFbHYChmt/qAiyiphazU9PxFH0d5LfuDjX0XOlXSViymdPNnG YZZnG7PujaPDdoHFz48hvzc9Wjkxz+8KOsVV3fO/g3OQnPqEuYA9dUzQ9dNMHb6x G1vasw0iMLJf5IuCoGFbPujqhcwcNTsOuT2Vf20vqDUrOn5ga66MUbxsHEP8yK78 wl3baI4oUds= =v2/Q -----END PGP SIGNATURE----- Sat Nov 23 05:30:10 UTC 2024 I: Checking whether the package is not for us Sat Nov 23 05:30:10 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sat Nov 23 05:30:10 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sat Nov 23 05:31:10 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 23:53:11 -12 2025 I: pbuilder-time-stamp: 1766749991 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc] I: copying [./libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz] I: copying [./libbio-tools-run-alignment-clustalw-perl_1.7.4-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 11 12:14:43 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc: no acceptable signature found dpkg-source: info: extracting libbio-tools-run-alignment-clustalw-perl in libbio-tools-run-alignment-clustalw-perl-1.7.4 dpkg-source: info: unpacking libbio-tools-run-alignment-clustalw-perl_1.7.4.orig.tar.gz dpkg-source: info: unpacking libbio-tools-run-alignment-clustalw-perl_1.7.4-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying doc-typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/631957/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='13e4aec005ee4d4eb61fb6c8d523592f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='631957' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/pbuilderrc_qpYE --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/b1 --logfile b1/build.log libbio-tools-run-alignment-clustalw-perl_1.7.4-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/631957/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), clustalw, libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-run-perl; however: Package libbio-perl-run-perl is not installed. pbuilder-satisfydepends-dummy depends on libdevel-checkbin-perl; however: Package libdevel-checkbin-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1t64{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 23.9 MB of archives. After unpacking 88.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libbio-perl-run-perl all 1.7.3-12 [528 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdevel-checkbin-perl all 0.04-3 [5228 B] Fetched 23.9 MB in 0s (96.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package clustalw. Preparing to unpack .../15-clustalw_2.1+lgpl-7_amd64.deb ... Unpacking clustalw (2.1+lgpl-7) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 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Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../30-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../31-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../32-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... 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Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libbio-perl-run-perl (1.7.3-12) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-tools-run-alignment-clustalw-perl_1.7.4-4_source.changes dpkg-buildpackage: info: source package libbio-tools-run-alignment-clustalw-perl dpkg-buildpackage: info: source version 1.7.4-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Locating bin:clustalw... found at /usr/bin/clustalw. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Run::Alignment::Clustalw Writing MYMETA.yml and MYMETA.json dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' cp lib/Bio/Tools/Run/Alignment/Clustalw.pm blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm Manifying 1 pod document make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' dh_auto_test make -j42 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/00-compile.t ........... 1..1 ok 1 - Bio/Tools/Run/Alignment/Clustalw.pm loaded ok ok t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-no-tabs.t ....... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/Clustalw.t ............. ok 1 - Found input file ok 2 - Found profile1 file ok 3 - Found profile2 file ok 4 - An object of class 'Bio::Tools::Run::Alignment::Clustalw' isa 'Bio::Tools::Run::Alignment::Clustalw' ok 5 - program_dir returned correct default ok 6 - error_string returned correct default ok 7 - outfile_name returned correct default ok 8 - bootstrap returned correct default ok 9 - Correct exe default name ok 10 - check clustalw version 2.1 is less than 1.8 ok 11 - No error occured ok 12 - outfile_name returned something ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 14 - Correct number of seqs returned ok 15 - Score ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 17 - Correct number of seqs returned ok 18 - Got correct sequence by position ok 19 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 20 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 21 - Correct number of seqs returned ok 22 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 23 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 24 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 25 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree' ok 26 - footprinting worked ok 27 - Got correct sequence by position ok 28 - Got correct sequence by position ok 29 - Set and got ktuple correctly ok 30 - Set and got topdiags correctly ok 31 - Set and got window correctly ok 32 - Set and got pairgap correctly ok 33 - Set and got fixedgap correctly ok 34 - Set and got floatgap correctly ok 35 - Set and got matrix correctly ok 36 - Set and got type correctly ok 37 - Set and got output correctly ok 38 - Set and got outfile correctly ok 39 - set and got quiet correctly ok 40 - set and got bootstrap correctly 1..40 ok All tests successful. Files=7, Tests=41, 8 wallclock secs ( 0.05 usr 0.01 sys + 1.62 cusr 1.44 csys = 3.12 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-run-alignment-clustalw-perl/ make -j42 install DESTDIR=/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' Manifying 1 pod document Installing /build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl/usr/share/perl5/Bio/Tools/Run/Alignment/Clustalw.pm Installing /build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4/debian/libbio-tools-run-alignment-clustalw-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::Clustalw.3pm make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-clustalw-perl-1.7.4' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-tools-run-alignment-clustalw-perl' in '../libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/631957 and its subdirectories I: Current time: Thu Dec 25 23:54:08 -12 2025 I: pbuilder-time-stamp: 1766750048 Sat Nov 23 05:31:11 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sat Nov 23 05:31:11 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sat Nov 23 05:33:12 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sat Nov 23 05:33:13 UTC 2024 I: libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.changes: Format: 1.8 Date: Mon, 11 Mar 2024 13:13:03 +0100 Source: libbio-tools-run-alignment-clustalw-perl Binary: libbio-tools-run-alignment-clustalw-perl Architecture: all Version: 1.7.4-4 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: Andreas Tille Description: libbio-tools-run-alignment-clustalw-perl - Bioperl interface to Clustal W Changes: libbio-tools-run-alignment-clustalw-perl (1.7.4-4) unstable; urgency=medium . * Team upload . [ Debian Janitor ] * Set upstream metadata fields: Bug-Database. * Update standards version to 4.6.2, no changes needed. . [ Andreas Tille ] * Add debian/salsa.ci to exclude i386 builds * Update lintian-overrides Checksums-Sha1: c07483bc41c7c04510668194453f0858d7ec628c 24488 libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb f0de49f219e33fc0fa3924405ebdffc7e4c0f5de 5154 libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo Checksums-Sha256: 6293c6c7ef73fe3559476dd5d0866877beeeedbfea644db4e332deece5a38ef7 24488 libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb 480cb0cf3a8304c15147fb4fab015ee4918f5856b59e70138b47c47a0908453e 5154 libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo Files: 447cdd4c485fc1c0434609202272617c 24488 science optional libbio-tools-run-alignment-clustalw-perl_1.7.4-4_all.deb e37b5dca916d686b4a598b27ca380c3e 5154 science optional libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo Sat Nov 23 05:33:14 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_24-41069.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/libbio-tools-run-alignment-clustalw-perl_1.7.4-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/libbio-tools-run-alignment-clustalw-perl_1.7.4-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/libbio-tools-run-alignment-clustalw-perl_1.7.4-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qd0JRaGh/b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.492s) 0.492s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 867ms CPU time consumed: 783ms Sat Nov 23 05:33:17 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sat Nov 23 05:33:17 UTC 2024 I: libbio-tools-run-alignment-clustalw-perl from trixie built successfully and reproducibly on amd64. Sat Nov 23 05:33:18 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Nov 23 05:33:19 UTC 2024 I: Submitting 8.0K b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo.asc Sat Nov 23 05:33:19 UTC 2024 I: Submitting 8.0K b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo.asc Sat Nov 23 05:33:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Nov 23 05:33:20 UTC 2024 I: Done submitting .buildinfo files. Sat Nov 23 05:33:20 UTC 2024 I: Removing signed libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo.asc files: removed './b1/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo.asc' removed './b2/libbio-tools-run-alignment-clustalw-perl_1.7.4-4_amd64.buildinfo.asc'