Running as unit: rb-build-arm64_3-108974.service ==================================================================================== Fri Aug 8 00:07:44 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_3) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Fri Aug 8 00:07:44 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-1J4SCyaY" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Aug 8 00:07:44 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Aug 8 00:07:44 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-S4EpJO' Fri Aug 8 00:07:45 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Aug 8 00:07:45 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-sB33kA' ok, let's check if libbio-tools-run-alignment-tcoffee-perl is building anywhere yet… ok, libbio-tools-run-alignment-tcoffee-perl is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libbio-tools-run-alignment-tcoffee-perl in trixie on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Fri Aug 8 00:08:06 UTC 2025 I: starting to build libbio-tools-run-alignment-tcoffee-perl/trixie/arm64 on jenkins on '2025-08-08 00:07' Fri Aug 8 00:08:06 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/108974/console.log 1754611686 arm64 trixie libbio-tools-run-alignment-tcoffee-perl Fri Aug 8 00:08:06 UTC 2025 I: Downloading source for trixie/libbio-tools-run-alignment-tcoffee-perl=1.7.4-3 --2025-08-08 00:08:07-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-run-alignment-tcoffee-perl/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2533 (2.5K) [text/prs.lines.tag] Saving to: ‘libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc’ 0K .. 100% 287M=0s 2025-08-08 00:08:07 (287 MB/s) - ‘libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc’ saved [2533/2533] --2025-08-08 00:08:07-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-run-alignment-tcoffee-perl/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2533 (2.5K) [text/prs.lines.tag] Saving to: ‘libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc’ 0K .. 100% 287M=0s 2025-08-08 00:08:07 (287 MB/s) - ‘libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc’ saved [2533/2533] Fri Aug 8 00:08:07 UTC 2025 I: libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-run-alignment-tcoffee-perl Binary: libbio-tools-run-alignment-tcoffee-perl Architecture: all Version: 1.7.4-3 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Run-Alignment-TCoffee Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-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, libtest-exception-perl , perl, t-coffee Package-List: libbio-tools-run-alignment-tcoffee-perl deb science optional arch=all Checksums-Sha1: dda94eb00899c2865e61c7feb6205971c317a26a 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 9cfe1c2bfcc88a86fff487599a91d70fd296550f 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz Checksums-Sha256: 3d8b41b9701933249cde26dd0e8a919958b218f1f585183a7a225e6a254d6523 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 4935d6d288109914fd62dab352c8607fdb6f98c6d1d86051bcb3aee6a4fd391a 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz Files: 49c2a232f3c64b8a4add2560f1c0322b 29373 libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz 9166dd5e7ea488e1517195b5b459cd14 2536 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEsjhixBXWVlpOhsvXV5wWDUyeI+gFAmNJeyYACgkQV5wWDUye I+jWxxAAn5gP4C1VG50fdXjUx+a0nAUTUQEM6Vv5yKxmb1+bBM8j8d8gsxHt7I+x zLWEutCiBLRpK71vibCkt2uLqvmmhNj2pvpvmsjneuLfqZS3UDYIjWd0XzGCcu5V 7oqI25YWatKjqQrn3lW0rdutyo3MF4jYizYB4XbJB07Fx2rZ9FR6X1SnAYPfMeXu Zt6ID0SvI7vY5egSSyiuT4at3WZvcTlutGUZIVCJomnItqgXqImeNu5eY9WlYzuQ QBxCdWFaHfgbsZiFnGnD9gq6eYU67Fs6i2teloXrilbL1NjL2tX5sMrdwV0T7eOR kw9+LHUpGM3c+4BeQ+LmFQABcPFkHGf/mrFgXlsoVgerRmbcSxHQWewD4N7Xp+z8 CDbfCKjKXsUY1YbbeXx1WurBwUQdPF5ynytmJmbgYTc3VmmrtW3Yx3lTfgRpeHdU hvHzVtTyFHUM2tcSoVKLJM7SHgnU7mxakVXVButZIS3oFfsKJ6oF6XT1qEuCU61w bjH5nk37DSdNRKhVudfWkH+hmQARQQ6OgsbSzEltH4TN815A2GNVKRkXmhYYUqCb VlbhP8dglJPv9sywKH6sogsSFKA1wycA+cew77Kfk4DlTZjr85IDfC4O93LdKHJz oR0pfJjQmmSFaVW9DYLByf6MIy5vISXxrRx3cbmArtPGPFshvZ8= =0S/o -----END PGP SIGNATURE----- Fri Aug 8 00:08:07 UTC 2025 I: Checking whether the package is not for us Fri Aug 8 00:08:07 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Fri Aug 8 00:08:07 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Fri Aug 8 00:08:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Aug 8 00:08:07 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-xarzv8' ==================================================================================== Thu Sep 10 06:31:08 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 libbio-tools-run-alignment-tcoffee-perl trixie /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT 1.7.4-3" as arguments. Thu Sep 10 06:31:08 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-Fjj53Q48" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 10 06:31:08 UTC 2026 I: Downloading source for trixie/libbio-tools-run-alignment-tcoffee-perl=1.7.4-3 Reading package lists... NOTICE: 'libbio-tools-run-alignment-tcoffee-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 34.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (dsc) [2533 B] Get:2 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (tar) [29.4 kB] Get:3 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (diff) [2536 B] Fetched 34.4 kB in 0s (596 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-tools-run-alignment-tcoffee-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 34.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (dsc) [2533 B] Get:2 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (tar) [29.4 kB] Get:3 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (diff) [2536 B] Fetched 34.4 kB in 0s (596 kB/s) Download complete and in download only mode ============================================================================= Building libbio-tools-run-alignment-tcoffee-perl in trixie on arm64 on codethink03-arm64 now. Date: Thu Sep 10 07:31:08 BST 2026 Date UTC: Thu Sep 10 06:31:08 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 18:31:08 -12 2026 I: pbuilder-time-stamp: 1789021868 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-tcoffee-perl_1.7.4-3.dsc] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc: no acceptable signature found dpkg-source: info: extracting libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl-1.7.4 dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.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/2214685/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bc7197f0f73f4e5dbf77c63b7242157d' 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='2214685' 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.TgDpOUBT/pbuilderrc_3x7h --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.TgDpOUBT/b1 --logfile b1/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2214685/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: arm64 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, libtest-exception-perl, perl, t-coffee dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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. pbuilder-satisfydepends-dummy depends on libtest-exception-perl; however: Package libtest-exception-perl is not installed. pbuilder-satisfydepends-dummy depends on t-coffee; however: Package t-coffee 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} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-exception-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t-coffee{a} The following packages are RECOMMENDED but will NOT be installed: amap-align clustalo curl dialign-tx fsa kalign 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 mafft muscle mustang ncbi-blast+ perl-tk poa prank probcons proda tm-align wget 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 15.9 MB of archives. After unpacking 60.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 clustalw arm64 2.1+lgpl-7+b2 [256 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b3 [34.0 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1 [937 kB] Fetched 15.9 MB in 0s (70.0 MB/s) Preconfiguring packages ... 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 ... 19965 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbio-tools-run-alignment-tcoffee-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-tcoffee-perl_1.7.4-3_source.changes dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl dpkg-buildpackage: info: source version 1.7.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Jelmer Vernooij dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Locating bin:t_coffee... found at /usr/bin/t_coffee. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Run::Alignment::TCoffee Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' cp lib/Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm Manifying 1 pod document make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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/TCoffee.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 ! 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[Final Evaluation][TOT= 397][100 %] t/TCoffee.t .............. ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' ok 2 - set factory parameter ok 3 - get factory parameter ok 4 - Code tested only on t_coffee versions > 1.22 #Single Thread ok 5 ok 6 #Single Thread ok 7 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 8 ok 9 - no T-COFFEE errors ok 10 ok 11 ok 12 #Single Thread #Single Thread ok 13 ok 14 ok 15 #Single Thread #Single Thread ok 16 ok 17 - expect 21 >= val >= 23 ok 18 - expect 47 or 48 #Single Thread ok 19 - simple generic run ok 20 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 21 ok 22 - no T-COFFEE errors ok 23 ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 1..25 rmdir /tmp/bF_xMNAZ5S ok All tests successful. Files=7, Tests=26, 24 wallclock secs ( 0.04 usr 0.01 sys + 4.39 cusr 4.88 csys = 9.32 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-run-alignment-tcoffee-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' Manifying 1 pod document Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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-tcoffee-perl' in '../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.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/2214685 and its subdirectories I: Current time: Wed Sep 9 18:32:05 -12 2026 I: pbuilder-time-stamp: 1789021925 Thu Sep 10 06:32:05 UTC 2026 I: Signing ./b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo as libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc Thu Sep 10 06:32:05 UTC 2026 I: Signed ./b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo as ./b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc Thu Sep 10 06:32:05 UTC 2026 - build #1 for libbio-tools-run-alignment-tcoffee-perl/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Thu Sep 10 06:32:05 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Fjj53Q48, removing. /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 8 00:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 8 00:08 b2 -rw-r--r-- 1 jenkins jenkins 2533 Oct 14 2022 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -rw------- 1 jenkins jenkins 3866 Aug 8 00:08 rbuildlog.G9OxQJq /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b1: total 100 -rw-r--r-- 1 jenkins jenkins 43085 Aug 8 00:09 build.log -rw-r--r-- 1 jenkins jenkins 2536 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2533 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -rw-r--r-- 1 jenkins jenkins 23072 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb -rw-r--r-- 1 jenkins jenkins 5177 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6059 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1401 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1615 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2: total 0 Fri Aug 8 00:09:06 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 18:31:08 -12 2026 I: pbuilder-time-stamp: 1789021868 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-tcoffee-perl_1.7.4-3.dsc] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc: no acceptable signature found dpkg-source: info: extracting libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl-1.7.4 dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.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/2214685/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bc7197f0f73f4e5dbf77c63b7242157d' 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='2214685' 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.TgDpOUBT/pbuilderrc_3x7h --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.TgDpOUBT/b1 --logfile b1/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2214685/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: arm64 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, libtest-exception-perl, perl, t-coffee dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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. pbuilder-satisfydepends-dummy depends on libtest-exception-perl; however: Package libtest-exception-perl is not installed. pbuilder-satisfydepends-dummy depends on t-coffee; however: Package t-coffee 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} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-exception-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t-coffee{a} The following packages are RECOMMENDED but will NOT be installed: amap-align clustalo curl dialign-tx fsa kalign 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 mafft muscle mustang ncbi-blast+ perl-tk poa prank probcons proda tm-align wget 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 15.9 MB of archives. After unpacking 60.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 clustalw arm64 2.1+lgpl-7+b2 [256 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b3 [34.0 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1 [937 kB] Fetched 15.9 MB in 0s (70.0 MB/s) Preconfiguring packages ... 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 ... 19965 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-12) ... 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-tcoffee-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-tcoffee-perl_1.7.4-3_source.changes dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl dpkg-buildpackage: info: source version 1.7.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Jelmer Vernooij dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Locating bin:t_coffee... found at /usr/bin/t_coffee. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Run::Alignment::TCoffee Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' cp lib/Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm Manifying 1 pod document make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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/TCoffee.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 ! 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[Final Evaluation][TOT= 397][100 %] t/TCoffee.t .............. ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' ok 2 - set factory parameter ok 3 - get factory parameter ok 4 - Code tested only on t_coffee versions > 1.22 #Single Thread ok 5 ok 6 #Single Thread ok 7 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 8 ok 9 - no T-COFFEE errors ok 10 ok 11 ok 12 #Single Thread #Single Thread ok 13 ok 14 ok 15 #Single Thread #Single Thread ok 16 ok 17 - expect 21 >= val >= 23 ok 18 - expect 47 or 48 #Single Thread ok 19 - simple generic run ok 20 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 21 ok 22 - no T-COFFEE errors ok 23 ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 1..25 rmdir /tmp/bF_xMNAZ5S ok All tests successful. Files=7, Tests=26, 24 wallclock secs ( 0.04 usr 0.01 sys + 4.39 cusr 4.88 csys = 9.32 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-run-alignment-tcoffee-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' Manifying 1 pod document Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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-tcoffee-perl' in '../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.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/2214685 and its subdirectories I: Current time: Wed Sep 9 18:32:05 -12 2026 I: pbuilder-time-stamp: 1789021925 Fri Aug 8 00:09:07 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Aug 8 00:09:07 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Aug 8 00:09:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Aug 8 00:09:07 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-rBRmiX' ==================================================================================== Fri Aug 8 00:09:08 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 libbio-tools-run-alignment-tcoffee-perl trixie /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT 1.7.4-3" as arguments. Fri Aug 8 00:09:08 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-vCrRsz88" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Aug 8 00:09:08 UTC 2025 I: Downloading source for trixie/libbio-tools-run-alignment-tcoffee-perl=1.7.4-3 Reading package lists... NOTICE: 'libbio-tools-run-alignment-tcoffee-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 34.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (dsc) [2533 B] Get:2 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (tar) [29.4 kB] Get:3 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (diff) [2536 B] Fetched 34.4 kB in 0s (2765 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-tools-run-alignment-tcoffee-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-run-alignment-tcoffee-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 34.4 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (dsc) [2533 B] Get:2 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (tar) [29.4 kB] Get:3 http://deb.debian.org/debian trixie/main libbio-tools-run-alignment-tcoffee-perl 1.7.4-3 (diff) [2536 B] Fetched 34.4 kB in 0s (2765 kB/s) Download complete and in download only mode ============================================================================= Re-Building libbio-tools-run-alignment-tcoffee-perl in trixie on arm64 on codethink04-arm64 now. Date: Fri Aug 8 01:09:08 BST 2025 Date UTC: Fri Aug 8 00:09:08 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/pbuilderrc_ygJK + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libbio-tools-run-alignment-tcoffee-perl = debian-installer -o libbio-tools-run-alignment-tcoffee-perl = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libbio-tools-run-alignment-tcoffee-perl = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/pbuilderrc_ygJK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2 --logfile b2/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 8 14:09:09 +14 2025 I: pbuilder-time-stamp: 1754611749 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-tcoffee-perl_1.7.4-3.dsc] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz] I: copying [./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc: no acceptable signature found dpkg-source: info: extracting libbio-tools-run-alignment-tcoffee-perl in libbio-tools-run-alignment-tcoffee-perl-1.7.4 dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4.orig.tar.gz dpkg-source: info: unpacking libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.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/1137382/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Aug 8 00:09 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=acf688435dc745518f4a16d9a76ad507 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1137382 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/pbuilderrc_ygJK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2 --logfile b2/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1137382/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: arm64 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, libtest-exception-perl, perl, t-coffee dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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. pbuilder-satisfydepends-dummy depends on libtest-exception-perl; however: Package libtest-exception-perl is not installed. pbuilder-satisfydepends-dummy depends on t-coffee; however: Package t-coffee 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} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-uplevel-perl{a} libtest-exception-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} t-coffee{a} The following packages are RECOMMENDED but will NOT be installed: amap-align clustalo curl dialign-tx fsa kalign 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 mafft muscle mustang ncbi-blast+ perl-tk poa prank probcons proda tm-align wget 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 15.9 MB of archives. After unpacking 60.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 clustalw arm64 2.1+lgpl-7+b2 [256 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b3 [34.0 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1 [937 kB] Fetched 15.9 MB in 0s (127 MB/s) Preconfiguring packages ... 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 ... 19965 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package clustalw. Preparing to unpack .../15-clustalw_2.1+lgpl-7+b2_arm64.deb ... Unpacking clustalw (2.1+lgpl-7+b2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... 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) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../33-libio-pty-perl_1%3a1.20-1+b3_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1+b3) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../34-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libfile-sort-perl. Preparing to unpack .../35-libfile-sort-perl_1.01-3_all.deb ... Unpacking libfile-sort-perl (1.01-3) ... Selecting previously unselected package libbio-perl-run-perl. Preparing to unpack .../36-libbio-perl-run-perl_1.7.3-13_all.deb ... Unpacking libbio-perl-run-perl (1.7.3-13) ... Selecting previously unselected package libdevel-checkbin-perl. Preparing to unpack .../37-libdevel-checkbin-perl_0.04-3_all.deb ... Unpacking libdevel-checkbin-perl (0.04-3) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../38-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../39-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package t-coffee. Preparing to unpack .../40-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1_arm64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.20-1+b3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up clustalw (2.1+lgpl-7+b2) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libbio-perl-run-perl (1.7.3-13) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/1137382/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl dpkg-buildpackage: info: source version 1.7.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Jelmer Vernooij dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Locating bin:t_coffee... found at /usr/bin/t_coffee. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Run::Alignment::TCoffee Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' cp lib/Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm Manifying 1 pod document make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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/TCoffee.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 ! 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[Final Evaluation][TOT= 396][100 %] t/TCoffee.t .............. ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' ok 2 - set factory parameter ok 3 - get factory parameter ok 4 - Code tested only on t_coffee versions > 1.22 #Single Thread ok 5 ok 6 #Single Thread ok 7 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 8 ok 9 - no T-COFFEE errors ok 10 ok 11 ok 12 #Single Thread #Single Thread ok 13 ok 14 ok 15 #Single Thread #Single Thread ok 16 ok 17 - expect 21 >= val >= 23 ok 18 - expect 47 or 48 #Single Thread ok 19 - simple generic run ok 20 #Single Thread #Single Thread #Single Thread #Single Thread #Single Thread ok 21 ok 22 - no T-COFFEE errors ok 23 ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 1..25 rmdir /tmp/dLIi5Ml47i ok All tests successful. Files=7, Tests=26, 21 wallclock secs ( 0.05 usr 0.01 sys + 4.41 cusr 5.27 csys = 9.74 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-run-alignment-tcoffee-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' Manifying 1 pod document Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm Installing /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/debian/libbio-tools-run-alignment-tcoffee-perl/usr/share/man/man3/Bio::Tools::Run::Alignment::TCoffee.3pm make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-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-tcoffee-perl' in '../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.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: user script /srv/workspace/pbuilder/1137382/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/B01_cleanup finished 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/1137382 and its subdirectories I: Current time: Fri Aug 8 14:10:01 +14 2025 + false + set +x I: pbuilder-time-stamp: 1754611801 Fri Aug 8 00:10:01 UTC 2025 I: Signing ./b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo as libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc Fri Aug 8 00:10:01 UTC 2025 I: Signed ./b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo as ./b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc Fri Aug 8 00:10:01 UTC 2025 - build #2 for libbio-tools-run-alignment-tcoffee-perl/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Aug 8 00:10:01 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-vCrRsz88, removing. /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT: total 60 drwxr-xr-x 2 jenkins jenkins 4096 Aug 8 00:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 8 00:10 b2 -rw-r--r-- 1 jenkins jenkins 2533 Oct 14 2022 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -rw------- 1 jenkins jenkins 47252 Aug 8 00:09 rbuildlog.G9OxQJq /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b1: total 100 -rw-r--r-- 1 jenkins jenkins 43085 Aug 8 00:09 build.log -rw-r--r-- 1 jenkins jenkins 2536 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2533 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -rw-r--r-- 1 jenkins jenkins 23072 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb -rw-r--r-- 1 jenkins jenkins 5177 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6059 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1401 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1615 Aug 8 00:09 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2: total 100 -rw-r--r-- 1 jenkins jenkins 45027 Aug 8 00:10 build.log -rw-r--r-- 1 jenkins jenkins 2536 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2533 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc -rw-r--r-- 1 jenkins jenkins 23072 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb -rw-r--r-- 1 jenkins jenkins 5177 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6059 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1401 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 1615 Aug 8 00:10 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes Fri Aug 8 00:10:02 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Aug 8 00:10:02 UTC 2025 I: libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes: Format: 1.8 Date: Fri, 14 Oct 2022 16:06:32 +0100 Source: libbio-tools-run-alignment-tcoffee-perl Binary: libbio-tools-run-alignment-tcoffee-perl Architecture: all Version: 1.7.4-3 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: Jelmer Vernooij Description: libbio-tools-run-alignment-tcoffee-perl - Bioperl interface to T-Coffee Changes: libbio-tools-run-alignment-tcoffee-perl (1.7.4-3) unstable; urgency=medium . [ Debian Janitor ] * Remove constraints unnecessary since buster * Update standards version to 4.6.0, no changes needed. Checksums-Sha1: a0954a3f8e15b3729f9744dc8b4bf478eadae987 23072 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb 0b61a579fe3eb2907c0eafc477d1c1794fc5b1a3 5177 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo Checksums-Sha256: 2e29cae32a146ec9bbbb7d263543a9c6855574b30a6cf1309db55d8d3e3898eb 23072 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb 4026f1631ce68a77b520be5bff4c2f8c8683ca2f138bd1e5b375adf5e93f2fba 5177 libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo Files: 0c4166f737df61d96b3cf6e007f38fbc 23072 science optional libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_all.deb 7bbf01bf555aecf6a177cd277bcef4d4 5177 science optional libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-08 00:09:06.318288825 +0000 +++ b2/build.log 2025-08-08 00:10:02.166359878 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 9 18:31:08 -12 2026 -I: pbuilder-time-stamp: 1789021868 +I: Current time: Fri Aug 8 14:09:09 +14 2025 +I: pbuilder-time-stamp: 1754611749 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ 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/2214685/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 8 00:09 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1137382/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='bc7197f0f73f4e5dbf77c63b7242157d' - 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='2214685' - PS1='# ' - PS2='> ' + INVOCATION_ID=acf688435dc745518f4a16d9a76ad507 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1137382 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.TgDpOUBT/pbuilderrc_3x7h --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.TgDpOUBT/b1 --logfile b1/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/pbuilderrc_ygJK --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2 --logfile b2/build.log libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2214685/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -158,7 +190,7 @@ Get: 39 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1 [937 kB] -Fetched 15.9 MB in 0s (70.0 MB/s) +Fetched 15.9 MB in 0s (127 MB/s) Preconfiguring packages ... 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 ... 19965 files and directories currently installed.) @@ -337,7 +369,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libbio-tools-run-alignment-tcoffee-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-tcoffee-perl_1.7.4-3_source.changes +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_source.changes dpkg-buildpackage: info: source package libbio-tools-run-alignment-tcoffee-perl dpkg-buildpackage: info: source version 1.7.4-3 dpkg-buildpackage: info: source distribution unstable @@ -388,7 +424,7 @@ ! [Final Evaluation][TOT= 383][ 0 %] ! [Final Evaluation][TOT= 383][ 1 %] ! [Final Evaluation][TOT= 383][ 2 %] ! [Final Evaluation][TOT= 383][ 3 %] ! [Final Evaluation][TOT= 383][ 4 %] ! [Final Evaluation][TOT= 383][ 5 %] ! [Final Evaluation][TOT= 383][ 6 %] ! [Final Evaluation][TOT= 383][ 7 %] ! [Final Evaluation][TOT= 383][ 8 %] ! [Final Evaluation][TOT= 383][ 9 %] ! [Final Evaluation][TOT= 383][ 10 %] ! [Final Evaluation][TOT= 383][ 11 %] ! [Final Evaluation][TOT= 383][ 12 %] ! [Final Evaluation][TOT= 383][ 13 %] ! [Final Evaluation][TOT= 383][ 14 %] ! [Final Evaluation][TOT= 383][ 15 %] ! [Final Evaluation][TOT= 383][ 16 %] ! [Final Evaluation][TOT= 383][ 17 %] ! [Final Evaluation][TOT= 383][ 18 %] ! [Final Evaluation][TOT= 383][ 19 %] ! [Final Evaluation][TOT= 383][ 20 %] ! [Final Evaluation][TOT= 383][ 21 %] ! [Final Evaluation][TOT= 383][ 22 %] ! [Final Evaluation][TOT= 383][ 23 %] ! [Final Evaluation][TOT= 383][ 24 %] ! [Final Evaluation][TOT= 383][ 25 %] ! 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[Final Evaluation][TOT= 396][100 %] t/TCoffee.t .............. ok 1 - An object of class 'Bio::Tools::Run::Alignment::TCoffee' isa 'Bio::Tools::Run::Alignment::TCoffee' @@ -434,10 +470,10 @@ ok 24 - expect 13 or 14 ok 25 - expect 41 or 42 1..25 -rmdir /tmp/bF_xMNAZ5S +rmdir /tmp/dLIi5Ml47i ok All tests successful. -Files=7, Tests=26, 24 wallclock secs ( 0.04 usr 0.01 sys + 4.39 cusr 4.88 csys = 9.32 CPU) +Files=7, Tests=26, 21 wallclock secs ( 0.05 usr 0.01 sys + 4.41 cusr 5.27 csys = 9.74 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-run-alignment-tcoffee-perl-1.7.4' create-stamp debian/debhelper-build-stamp @@ -471,12 +507,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1137382/tmp/hooks/B01_cleanup finished 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/2214685 and its subdirectories -I: Current time: Wed Sep 9 18:32:05 -12 2026 -I: pbuilder-time-stamp: 1789021925 +I: removing directory /srv/workspace/pbuilder/1137382 and its subdirectories +I: Current time: Fri Aug 8 14:10:01 +14 2025 +I: pbuilder-time-stamp: 1754611801 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diff: 80.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diff.gz b2/build.log: 81.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.7% -- replaced with stdout Fri Aug 8 00:10:03 UTC 2025 I: diffoscope 303 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libbio-tools-run-alignment-tcoffee-perl_trixie_arm64_1754611803 + touch /var/log/reproducible-builds/diffoscope_stamp_libbio-tools-run-alignment-tcoffee-perl_trixie_arm64_1754611803 + RESULT=0 + systemd-run '--description=diffoscope on libbio-tools-run-alignment-tcoffee-perl/1.7.4-3 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_3-108974 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT --run-session -c jenkins-reproducible-trixie-diffoscope-7033967a-45d7-4099-b71c-d4c1a109e658 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/dbd-tmp-51rwUfR ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_3-108974.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TgDpOUBT/b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 173ms CPU time consumed: 175ms _ _ _ _ _ _ _ | (_) |__ | |__ (_) ___ | |_ ___ ___ | |___ _ __ _ _ _ __ | | | '_ \| '_ \| |/ _ \ _____| __/ _ \ / _ \| / __|_____| '__| | | | '_ \ | | | |_) | |_) | | (_) |_____| || (_) | (_) | \__ \_____| | | |_| | | | | |_|_|_.__/|_.__/|_|\___/ \__\___/ \___/|_|___/ |_| \__,_|_| |_| _ _ _ _ __ __ _| (_) __ _ _ __ _ __ ___ ___ _ __ | |_ | |_ ___ ___ / _| _____ / _` | | |/ _` | '_ \| '_ ` _ \ / _ \ '_ \| __|____| __/ __/ _ \| |_ |_____| (_| | | | (_| | | | | | | | | | __/ | | | ||_____| || (_| (_) | _| \__,_|_|_|\__, |_| |_|_| |_| |_|\___|_| |_|\__| \__\___\___/|_| |___/ __ _ / _| ___ ___ _ __ ___ _ __| | | |_ / _ \/ _ \_____| '_ \ / _ \ '__| | | _| __/ __/_____| |_) | __/ | | | |_| \___|\___| | .__/ \___|_| |_| |_| Fri Aug 8 00:10:04 UTC 2025 I: diffoscope 303 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 8 00:10:04 UTC 2025 I: libbio-tools-run-alignment-tcoffee-perl from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-08 00:10:04] INFO: Starting at 2025-08-08 00:10:04.686527 [2025-08-08 00:10:04] INFO: Generating the pages of 1 package(s) [2025-08-08 00:10:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diff.gz is missing [2025-08-08 00:10:04] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl didn't produce a buildlog, even though it has been built. [2025-08-08 00:10:04] INFO: Finished at 2025-08-08 00:10:04.892451, took: 0:00:00.205928 Fri Aug 8 00:10:04 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl.html Fri Aug 8 00:10:04 UTC 2025 I: Removing signed libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc files: removed './b1/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc' removed './b2/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3_arm64.buildinfo.asc' 1754611804 arm64 trixie libbio-tools-run-alignment-tcoffee-perl Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.rbuild.log: 78.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.rbuild.log.gz [2025-08-08 00:10:05] INFO: Starting at 2025-08-08 00:10:05.150885 [2025-08-08 00:10:05] INFO: Generating the pages of 1 package(s) [2025-08-08 00:10:05] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/libbio-tools-run-alignment-tcoffee-perl_1.7.4-3.diff.gz is missing [2025-08-08 00:10:05] INFO: Finished at 2025-08-08 00:10:05.353186, took: 0:00:00.202305 All cleanup done. Fri Aug 8 00:10:05 UTC 2025 - total duration: 0h 2m 20s. Fri Aug 8 00:10:05 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-1J4SCyaY, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 21.013s CPU time consumed: 4.423s