Running as unit: rb-build-arm64_12-79215.service ==================================================================================== Wed Jan 22 20:04:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_12) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Wed Jan 22 20:04:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Cm9olvd7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jan 22 20:04:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Jan 22 20:04:38 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-HjWZyg' Wed Jan 22 20:04:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Jan 22 20:04:38 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-3WdT7z' ok, let's check if libbio-tools-phylo-paml-perl is building anywhere yet… ok, libbio-tools-phylo-paml-perl is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libbio-tools-phylo-paml-perl in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Wed Jan 22 20:04:53 UTC 2025 I: starting to build libbio-tools-phylo-paml-perl/unstable/arm64 on jenkins on '2025-01-22 20:04' Wed Jan 22 20:04:53 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/79215/console.log 1737576293 arm64 unstable libbio-tools-phylo-paml-perl Wed Jan 22 20:04:53 UTC 2025 I: Downloading source for unstable/libbio-tools-phylo-paml-perl=1.7.3-4 --2025-01-22 20:04:53-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-phylo-paml-perl/libbio-tools-phylo-paml-perl_1.7.3-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2341 (2.3K) [text/prs.lines.tag] Saving to: ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ 0K .. 100% 391M=0s 2025-01-22 20:04:53 (391 MB/s) - ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ saved [2341/2341] --2025-01-22 20:04:53-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-phylo-paml-perl/libbio-tools-phylo-paml-perl_1.7.3-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2341 (2.3K) [text/prs.lines.tag] Saving to: ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ 0K .. 100% 391M=0s 2025-01-22 20:04:53 (391 MB/s) - ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ saved [2341/2341] Wed Jan 22 20:04:53 UTC 2025 I: libbio-tools-phylo-paml-perl_1.7.3-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-phylo-paml-perl Binary: libbio-tools-phylo-paml-perl Architecture: all Version: 1.7.3-4 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Phylo-PAML Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl Package-List: libbio-tools-phylo-paml-perl deb science optional arch=all Checksums-Sha1: 4ced4b0905ad258cb119656f84b442bca950487a 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz 234b33e8fc175f177e68c60041fa8a1bdabc5f86 2784 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz Checksums-Sha256: 424dccca82b61e3daf62f52e33de35efdbe1b69644d07015e987671fa7130cb4 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz f88ff3149e7272680b64d89a0d95890eecebb6497a60a74aa2aa842c325ccee1 2784 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz Files: 0030a118c958b93967a470b8bc3e21a0 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz b4cf89175f37313b9dc0fc1f21c1cc33 2784 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEsjhixBXWVlpOhsvXV5wWDUyeI+gFAmNJdpAACgkQV5wWDUye I+gqLg/+Ku4XXZstK3dvLrd+rN1e3wlK9Fsw1yKcQXRtYcSmKzedT/zsh6b1P2dG fJlzOzE3QJ6taQhe7Z5nsU7tOi7TiqVXHgg/tYWRSfupUcjX8SoHKii4tT9KhcLQ OFV1cxJPQSDJHhhrGxZCL04AkcFacqUrb2tSnIEt9W6TJ0VV1B2gNv7FT+MFqbt4 +rPckZusLu6zYcG4WANwbSd2Da/31kZuzHXYvkScIKfi13VTSfQEF9wWhEDkworM dSmqqm0PQzbwW3dBjUCPKevG6/C47VWyTQFwhvH4toHN2iJZnRo/kMNbL79w27s1 dTR1GBRdfhxj7BJtenlSvnTdYt/NivjD9fyifvA+B7taEzZMjtEF/kDPrE3vziOz Myo05Gh3E2GWTaQeZxcTzy4xrdJTHY99kJFbGyVwM5DsBFOaOsEbjPoWr4VU20r6 hnDrRO5AAU9mqlfwJITwFmWf+6WrmiET3wKkg32lNUQhlAul7TddkyU8Fy7wJUeU FyzOO7J8/gK1FNr6hzlTbrCWChqQbzGfk636zfh1XN0UMMnR+z/FKlGI2ugS7SML 7uXj2ZVnWSWphvBdhuqcnMS8irzSR5kI+G+hDevz1WdjXK5tPh1DVkxbAAMZgx2Q OTlwTn16NHsb/76LbBIMGhZQHDVgTl7c/bB7gAacSUJry2x8/VE= =wlFv -----END PGP SIGNATURE----- Wed Jan 22 20:04:53 UTC 2025 I: Checking whether the package is not for us Wed Jan 22 20:04:53 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Jan 22 20:04:53 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Wed Jan 22 20:04:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Jan 22 20:04:53 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-44jwPp' ==================================================================================== Wed Jan 22 20:04:54 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 libbio-tools-phylo-paml-perl unstable /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy 1.7.3-4" as arguments. Wed Jan 22 20:04:54 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-L7equzam" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jan 22 20:04:54 UTC 2025 I: Downloading source for unstable/libbio-tools-phylo-paml-perl=1.7.3-4 Reading package lists... NOTICE: 'libbio-tools-phylo-paml-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 143 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (dsc) [2341 B] Get:2 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (tar) [138 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (diff) [2784 B] Fetched 143 kB in 0s (1269 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-tools-phylo-paml-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 143 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (dsc) [2341 B] Get:2 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (tar) [138 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (diff) [2784 B] Fetched 143 kB in 0s (1269 kB/s) Download complete and in download only mode ============================================================================= Building libbio-tools-phylo-paml-perl in unstable on arm64 on codethink04-arm64 now. Date: Wed Jan 22 20:04:55 GMT 2025 Date UTC: Wed Jan 22 20:04:55 UTC 2025 ============================================================================= 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 Jan 22 08:04:55 -12 2025 I: pbuilder-time-stamp: 1737576295 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-phylo-paml-perl_1.7.3-4.dsc] I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz] I: copying [./libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: unsupported subcommand dpkg-source: info: extracting libbio-tools-phylo-paml-perl in libbio-tools-phylo-paml-perl-1.7.3 dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying evolver-program-name.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3923641/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='921dcedd2d1a4ea8a08f9971abc5e8d0' 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='3923641' 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.ToWrpYBy/pbuilderrc_5VxN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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 codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3923641/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), libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 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 libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on paml; however: Package paml 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1t64{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} paml{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 24.5 MB of archives. After unpacking 95.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 paml arm64 4.9j+dfsg-5+b1 [663 kB] Fetched 24.5 MB in 0s (94.0 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... 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_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_arm64.deb ... Unpacking bsdextrautils (2.40.4-1) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... 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Unpacking paml (4.9j+dfsg-5+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up paml (4.9j+dfsg-5+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libbio-perl-run-perl (1.7.3-13) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-5) ... 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-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl dpkg-buildpackage: info: source version 1.7.3-4 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-phylo-paml-perl-1.7.3=. -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-phylo-paml-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Warning: prerequisite Bio::Tools::Run::Alignment::Clustalw 0 not found. Warning: prerequisite Bio::Tools::Run::Alignment::TCoffee 0 not found. Locating bin:basemlg... found at /usr/bin/basemlg. Locating bin:codeml... found at /usr/bin/codeml. Locating bin:paml-evolver... found at /usr/bin/paml-evolver. Locating bin:yn00... found at /usr/bin/yn00. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Phylo::PAML Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks Manifying 1 pod document Manifying 8 pod documents make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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..9 ok 1 - Bio/Tools/Phylo/PAML.pm loaded ok ok 2 - Bio/Tools/Phylo/PAML/Codeml.pm loaded ok ok 3 - Bio/Tools/Phylo/PAML/ModelResult.pm loaded ok ok 4 - Bio/Tools/Phylo/PAML/Result.pm loaded ok ok 5 - Bio/Tools/Run/Phylo/PAML/Baseml.pm loaded ok ok 6 - Bio/Tools/Run/Phylo/PAML/Codeml.pm loaded ok ok 7 - Bio/Tools/Run/Phylo/PAML/Evolver.pm loaded ok ok 8 - Bio/Tools/Run/Phylo/PAML/Yn00.pm loaded ok ok 9 # skip bin/bp_pairwise_kaks isn't perl ok t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-no-tabs.t ....... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/PAML-parser.t .......... ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 - node\#8 reconstructed seq ok 163 - ancestral AA ok 164 - ancestral AA ok 165 - derived AA ok 166 - ancestral AA ok 167 - ancestral AA ok 168 - derived AA ok 169 - derived AA ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 - codeml 4.3 runmode=-2 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 - codeml 4.3 two NSSites models ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 - NEB positively selected sites ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 - bug 3040 ok 251 - bug 3365 ok 252 - bug 3366 ok 253 - bug 3367 ok 254 - bug 3332 ok 255 - bug 3331 1..255 ok t/PAML-run.t ............. ok 1 ok 2 ok 3 - got results ok 4 - got a result ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - got results ok 15 - got a result ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 - got results ok 29 1..29 ok All tests successful. Files=8, Tests=293, 2 wallclock secs ( 0.03 usr 0.02 sys + 1.44 cusr 0.15 csys = 1.64 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-phylo-paml-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_install sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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-phylo-paml-perl' in '../libbio-tools-phylo-paml-perl_1.7.3-4_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_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/3923641 and its subdirectories I: Current time: Wed Jan 22 08:05:24 -12 2025 I: pbuilder-time-stamp: 1737576324 Wed Jan 22 20:05:24 UTC 2025 I: Signing ./b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo as libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Wed Jan 22 20:05:24 UTC 2025 I: Signed ./b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo as ./b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Wed Jan 22 20:05:24 UTC 2025 - build #1 for libbio-tools-phylo-paml-perl/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Wed Jan 22 20:05:24 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-L7equzam, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 22 20:05 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 22 20:04 b2 -rw-r--r-- 1 jenkins jenkins 2341 Oct 14 2022 libbio-tools-phylo-paml-perl_1.7.3-4.dsc -rw------- 1 jenkins jenkins 3601 Jan 22 20:04 rbuildlog.cCOpjC3 /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1: total 144 -rw-r--r-- 1 jenkins jenkins 31433 Jan 22 20:05 build.log -rw-r--r-- 1 jenkins jenkins 2784 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2341 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.dsc -rw-r--r-- 1 jenkins jenkins 78500 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb -rw-r--r-- 1 jenkins jenkins 5058 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5940 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1356 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 1553 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2: total 0 Wed Jan 22 20:05:25 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 22 08:04:55 -12 2025 I: pbuilder-time-stamp: 1737576295 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-phylo-paml-perl_1.7.3-4.dsc] I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz] I: copying [./libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: unsupported subcommand dpkg-source: info: extracting libbio-tools-phylo-paml-perl in libbio-tools-phylo-paml-perl-1.7.3 dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying evolver-program-name.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3923641/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='921dcedd2d1a4ea8a08f9971abc5e8d0' 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='3923641' 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.ToWrpYBy/pbuilderrc_5VxN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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 codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3923641/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), libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 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 libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on paml; however: Package paml 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1t64{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} paml{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 24.5 MB of archives. After unpacking 95.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 paml arm64 4.9j+dfsg-5+b1 [663 kB] Fetched 24.5 MB in 0s (94.0 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... 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_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_arm64.deb ... Unpacking bsdextrautils (2.40.4-1) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... 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+b2_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... 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 paml. Preparing to unpack .../38-paml_4.9j+dfsg-5+b1_arm64.deb ... Unpacking paml (4.9j+dfsg-5+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up paml (4.9j+dfsg-5+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libbio-perl-run-perl (1.7.3-13) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-5) ... 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-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl dpkg-buildpackage: info: source version 1.7.3-4 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-phylo-paml-perl-1.7.3=. -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-phylo-paml-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Warning: prerequisite Bio::Tools::Run::Alignment::Clustalw 0 not found. Warning: prerequisite Bio::Tools::Run::Alignment::TCoffee 0 not found. Locating bin:basemlg... found at /usr/bin/basemlg. Locating bin:codeml... found at /usr/bin/codeml. Locating bin:paml-evolver... found at /usr/bin/paml-evolver. Locating bin:yn00... found at /usr/bin/yn00. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Phylo::PAML Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks Manifying 1 pod document Manifying 8 pod documents make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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..9 ok 1 - Bio/Tools/Phylo/PAML.pm loaded ok ok 2 - Bio/Tools/Phylo/PAML/Codeml.pm loaded ok ok 3 - Bio/Tools/Phylo/PAML/ModelResult.pm loaded ok ok 4 - Bio/Tools/Phylo/PAML/Result.pm loaded ok ok 5 - Bio/Tools/Run/Phylo/PAML/Baseml.pm loaded ok ok 6 - Bio/Tools/Run/Phylo/PAML/Codeml.pm loaded ok ok 7 - Bio/Tools/Run/Phylo/PAML/Evolver.pm loaded ok ok 8 - Bio/Tools/Run/Phylo/PAML/Yn00.pm loaded ok ok 9 # skip bin/bp_pairwise_kaks isn't perl ok t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-no-tabs.t ....... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/PAML-parser.t .......... ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 - node\#8 reconstructed seq ok 163 - ancestral AA ok 164 - ancestral AA ok 165 - derived AA ok 166 - ancestral AA ok 167 - ancestral AA ok 168 - derived AA ok 169 - derived AA ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 - codeml 4.3 runmode=-2 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 - codeml 4.3 two NSSites models ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 - NEB positively selected sites ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 - bug 3040 ok 251 - bug 3365 ok 252 - bug 3366 ok 253 - bug 3367 ok 254 - bug 3332 ok 255 - bug 3331 1..255 ok t/PAML-run.t ............. ok 1 ok 2 ok 3 - got results ok 4 - got a result ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - got results ok 15 - got a result ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 - got results ok 29 1..29 ok All tests successful. Files=8, Tests=293, 2 wallclock secs ( 0.03 usr 0.02 sys + 1.44 cusr 0.15 csys = 1.64 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-phylo-paml-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_install sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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-phylo-paml-perl' in '../libbio-tools-phylo-paml-perl_1.7.3-4_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_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/3923641 and its subdirectories I: Current time: Wed Jan 22 08:05:24 -12 2025 I: pbuilder-time-stamp: 1737576324 Wed Jan 22 20:05:26 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Wed Jan 22 20:05:26 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Wed Jan 22 20:05:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Jan 22 20:05:26 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ejSbYk' ==================================================================================== Wed Feb 25 02:28:28 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 libbio-tools-phylo-paml-perl unstable /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy 1.7.3-4" as arguments. Wed Feb 25 02:28:28 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-gWbx65nn" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Feb 25 02:28:28 UTC 2026 I: Downloading source for unstable/libbio-tools-phylo-paml-perl=1.7.3-4 Reading package lists... NOTICE: 'libbio-tools-phylo-paml-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 143 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (dsc) [2341 B] Get:2 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (tar) [138 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (diff) [2784 B] Fetched 143 kB in 0s (7783 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbio-tools-phylo-paml-perl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Please use: git clone https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 143 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (dsc) [2341 B] Get:2 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (tar) [138 kB] Get:3 http://deb.debian.org/debian unstable/main libbio-tools-phylo-paml-perl 1.7.3-4 (diff) [2784 B] Fetched 143 kB in 0s (7783 kB/s) Download complete and in download only mode ============================================================================= Re-Building libbio-tools-phylo-paml-perl in unstable on arm64 on codethink03-arm64 now. Date: Wed Feb 25 02:28:28 GMT 2026 Date UTC: Wed Feb 25 02:28:28 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/pbuilderrc_1OEc + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libbio-tools-phylo-paml-perl = debian-installer -o libbio-tools-phylo-paml-perl = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libbio-tools-phylo-paml-perl = u-boot ']' + case "${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.ToWrpYBy/pbuilderrc_1OEc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2 --logfile b2/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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: Wed Feb 25 16:28:29 +14 2026 I: pbuilder-time-stamp: 1771986509 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-phylo-paml-perl_1.7.3-4.dsc] I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz] I: copying [./libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: unsupported subcommand dpkg-source: info: extracting libbio-tools-phylo-paml-perl in libbio-tools-phylo-paml-perl-1.7.3 dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying evolver-program-name.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/815311/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-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 Feb 25 02:28 /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/815311/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/815311/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=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=41f6a61ef4ee4a5887ec6c91abb633a1 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=815311 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.ToWrpYBy/pbuilderrc_1OEc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2 --logfile b2/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/815311/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), libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 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 libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on paml; however: Package paml 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1t64{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} paml{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk wget 0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 24.5 MB of archives. After unpacking 95.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 paml arm64 4.9j+dfsg-5+b1 [663 kB] Fetched 24.5 MB in 0s (160 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. 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Unpacking paml (4.9j+dfsg-5+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up paml (4.9j+dfsg-5+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libbio-perl-run-perl (1.7.3-13) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-5) ... 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/815311/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/815311/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl dpkg-buildpackage: info: source version 1.7.3-4 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-phylo-paml-perl-1.7.3=. -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-phylo-paml-perl-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" Warning: prerequisite Bio::Tools::Run::Alignment::Clustalw 0 not found. Warning: prerequisite Bio::Tools::Run::Alignment::TCoffee 0 not found. Locating bin:basemlg... found at /usr/bin/basemlg. Locating bin:codeml... found at /usr/bin/codeml. Locating bin:paml-evolver... found at /usr/bin/paml-evolver. Locating bin:yn00... found at /usr/bin/yn00. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Phylo::PAML Writing MYMETA.yml and MYMETA.json dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks Manifying 1 pod document Manifying 8 pod documents make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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..9 ok 1 - Bio/Tools/Phylo/PAML.pm loaded ok ok 2 - Bio/Tools/Phylo/PAML/Codeml.pm loaded ok ok 3 - Bio/Tools/Phylo/PAML/ModelResult.pm loaded ok ok 4 - Bio/Tools/Phylo/PAML/Result.pm loaded ok ok 5 - Bio/Tools/Run/Phylo/PAML/Baseml.pm loaded ok ok 6 - Bio/Tools/Run/Phylo/PAML/Codeml.pm loaded ok ok 7 - Bio/Tools/Run/Phylo/PAML/Evolver.pm loaded ok ok 8 - Bio/Tools/Run/Phylo/PAML/Yn00.pm loaded ok ok 9 # skip bin/bp_pairwise_kaks isn't perl ok t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-no-tabs.t ....... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/PAML-parser.t .......... ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 - node\#8 reconstructed seq ok 163 - ancestral AA ok 164 - ancestral AA ok 165 - derived AA ok 166 - ancestral AA ok 167 - ancestral AA ok 168 - derived AA ok 169 - derived AA ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 - codeml 4.3 runmode=-2 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 - codeml 4.3 two NSSites models ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 - NEB positively selected sites ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 - bug 3040 ok 251 - bug 3365 ok 252 - bug 3366 ok 253 - bug 3367 ok 254 - bug 3332 ok 255 - bug 3331 1..255 ok t/PAML-run.t ............. ok 1 ok 2 ok 3 - got results ok 4 - got a result ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - got results ok 15 - got a result ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 - got results ok 29 1..29 ok All tests successful. Files=8, Tests=293, 3 wallclock secs ( 0.09 usr 0.02 sys + 2.20 cusr 0.24 csys = 2.55 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbio-tools-phylo-paml-perl/ make -j12 install DESTDIR=/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' dh_install sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' 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-phylo-paml-perl' in '../libbio-tools-phylo-paml-perl_1.7.3-4_all.deb'. dpkg-genbuildinfo --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo dpkg-genchanges --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_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/815311/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/815311/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/815311 and its subdirectories I: Current time: Wed Feb 25 16:28:57 +14 2026 I: pbuilder-time-stamp: 1771986537 + false + set +x Wed Feb 25 02:28:57 UTC 2026 I: Signing ./b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo as libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Wed Feb 25 02:28:57 UTC 2026 I: Signed ./b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo as ./b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Wed Feb 25 02:28:57 UTC 2026 - build #2 for libbio-tools-phylo-paml-perl/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Wed Feb 25 02:28:57 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-gWbx65nn, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy: total 48 drwxr-xr-x 2 jenkins jenkins 4096 Jan 22 20:05 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 22 20:05 b2 -rw-r--r-- 1 jenkins jenkins 2341 Oct 14 2022 libbio-tools-phylo-paml-perl_1.7.3-4.dsc -rw------- 1 jenkins jenkins 35335 Jan 22 20:05 rbuildlog.cCOpjC3 /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1: total 148 -rw-r--r-- 1 jenkins jenkins 31433 Jan 22 20:05 build.log -rw-r--r-- 1 jenkins jenkins 2784 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2341 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.dsc -rw-r--r-- 1 jenkins jenkins 78500 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb -rw-r--r-- 1 jenkins jenkins 5058 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5940 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1356 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 1553 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2: total 148 -rw-r--r-- 1 jenkins jenkins 33367 Jan 22 20:05 build.log -rw-r--r-- 1 jenkins jenkins 2784 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2341 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4.dsc -rw-r--r-- 1 jenkins jenkins 78500 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb -rw-r--r-- 1 jenkins jenkins 5058 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5940 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1356 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 1553 Jan 22 20:05 libbio-tools-phylo-paml-perl_1.7.3-4_source.changes Wed Jan 22 20:05:57 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Wed Jan 22 20:05:58 UTC 2025 I: libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes: Format: 1.8 Date: Fri, 14 Oct 2022 15:47:06 +0100 Source: libbio-tools-phylo-paml-perl Binary: libbio-tools-phylo-paml-perl Architecture: all Version: 1.7.3-4 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: Jelmer Vernooij Description: libbio-tools-phylo-paml-perl - Bioperl interface to the PAML suite Changes: libbio-tools-phylo-paml-perl (1.7.3-4) unstable; urgency=medium . [ Debian Janitor ] * Update standards version to 4.5.1, no changes needed. * Remove constraints unnecessary since buster * Update standards version to 4.6.0, no changes needed. Checksums-Sha1: bdb0a2e9a66d46c5888e4e1820074c3b72eaad98 78500 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb 370f8e22a685dba4b1eeeba4840a8c9e98a27c6c 5058 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo Checksums-Sha256: 66a6093f1cb7ffd2ded6fe818f7c3833801075e2e9bee988407aef827164933c 78500 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb 7355c6467a97dc65bb4d16447b46b521bdbddfed593e33cefd0c48858f54e842 5058 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo Files: 1891fafabb7f2c9bf8bfdc5972900129 78500 science optional libbio-tools-phylo-paml-perl_1.7.3-4_all.deb cbb3de1535ffdce2791591bd90a36905 5058 science optional libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-01-22 20:05:25.578896031 +0000 +++ b2/build.log 2025-01-22 20:05:57.673455335 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 22 08:04:55 -12 2025 -I: pbuilder-time-stamp: 1737576295 +I: Current time: Wed Feb 25 16:28:29 +14 2026 +I: pbuilder-time-stamp: 1771986509 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying evolver-program-name.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3923641/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/815311/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Feb 25 02:28 /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/815311/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/815311/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='921dcedd2d1a4ea8a08f9971abc5e8d0' - 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='3923641' - PS1='# ' - PS2='> ' + INVOCATION_ID=41f6a61ef4ee4a5887ec6c91abb633a1 + 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=815311 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.ToWrpYBy/pbuilderrc_5VxN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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.ToWrpYBy/pbuilderrc_1OEc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2 --logfile b2/build.log libbio-tools-phylo-paml-perl_1.7.3-4.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 codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3923641/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/815311/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -154,7 +186,7 @@ Get: 37 http://deb.debian.org/debian unstable/main arm64 libbio-perl-run-perl all 1.7.3-13 [528 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 paml arm64 4.9j+dfsg-5+b1 [663 kB] -Fetched 24.5 MB in 0s (94.0 MB/s) +Fetched 24.5 MB in 0s (160 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 ... 19964 files and directories currently installed.) @@ -325,7 +357,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes +I: user script /srv/workspace/pbuilder/815311/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/815311/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/ && 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-phylo-paml-perl_1.7.3-4_source.changes dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl dpkg-buildpackage: info: source version 1.7.3-4 dpkg-buildpackage: info: source distribution unstable @@ -355,14 +391,14 @@ dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' +cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm +cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm +cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm +cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm +cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm -cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm -cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm -cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm -cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm -cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks Manifying 1 pod document @@ -680,7 +716,7 @@ 1..29 ok All tests successful. -Files=8, Tests=293, 2 wallclock secs ( 0.03 usr 0.02 sys + 1.44 cusr 0.15 csys = 1.64 CPU) +Files=8, Tests=293, 3 wallclock secs ( 0.09 usr 0.02 sys + 2.20 cusr 0.24 csys = 2.55 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' create-stamp debian/debhelper-build-stamp @@ -690,14 +726,14 @@ make[1]: Entering directory '/build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents -Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm -Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm +Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm +Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm -Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm +Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm Installing /build/reproducible-path/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm @@ -736,12 +772,14 @@ 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/815311/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/815311/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/3923641 and its subdirectories -I: Current time: Wed Jan 22 08:05:24 -12 2025 -I: pbuilder-time-stamp: 1737576324 +I: removing directory /srv/workspace/pbuilder/815311 and its subdirectories +I: Current time: Wed Feb 25 16:28:57 +14 2026 +I: pbuilder-time-stamp: 1771986537 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.diff: 73.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.diff.gz b2/build.log: 76.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 76.8% -- replaced with stdout Wed Jan 22 20:05:59 UTC 2025 I: diffoscope 285 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libbio-tools-phylo-paml-perl_unstable_arm64_1737576359 + touch /var/log/reproducible-builds/diffoscope_stamp_libbio-tools-phylo-paml-perl_unstable_arm64_1737576359 + RESULT=0 + systemd-run '--description=diffoscope on libbio-tools-phylo-paml-perl/1.7.3-4 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_12-79215 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy --run-session -c jenkins-reproducible-unstable-diffoscope-9a861193-8a23-46c4-906e-febffabda9ea -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/dbd-tmp-nl5LQL8 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_12-79215.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ToWrpYBy/b2/libbio-tools-phylo-paml-perl_1.7.3-4_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 abc.DotChangesFile ## main (total time: 0.370s) 0.370s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 688ms CPU time consumed: 688ms _ _ _ _ _ _ _ _ _ | (_) |__ | |__ (_) ___ | |_ ___ ___ | |___ _ __ | |__ _ _| | | | | '_ \| '_ \| |/ _ \ _____| __/ _ \ / _ \| / __|_____| '_ \| '_ \| | | | | | | | |_) | |_) | | (_) |_____| || (_) | (_) | \__ \_____| |_) | | | | |_| | | |_|_|_.__/|_.__/|_|\___/ \__\___/ \___/|_|___/ | .__/|_| |_|\__, |_| |_| |___/ _ _ ___ _ __ __ _ _ __ ___ | | _ __ ___ _ __| | / _ \ _____| '_ \ / _` | '_ ` _ \| |_____| '_ \ / _ \ '__| | | (_) |_____| |_) | (_| | | | | | | |_____| |_) | __/ | | | \___/ | .__/ \__,_|_| |_| |_|_| | .__/ \___|_| |_| |_| |_| Wed Jan 22 20:06:00 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Wed Jan 22 20:06:00 UTC 2025 I: libbio-tools-phylo-paml-perl from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-22 20:06:01] INFO: Starting at 2025-01-22 20:06:01.457920 [2025-01-22 20:06:01] INFO: Generating the pages of 1 package(s) [2025-01-22 20:06:01] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libbio-tools-phylo-paml-perl didn't produce a buildlog, even though it has been built. [2025-01-22 20:06:01] INFO: Finished at 2025-01-22 20:06:01.854119, took: 0:00:00.396208 Wed Jan 22 20:06:01 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libbio-tools-phylo-paml-perl.html Wed Jan 22 20:06:01 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Jan 22 20:06:01 UTC 2025 I: Submitting 8.0K b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc https://buildinfo.debian.net/370f8e22a685dba4b1eeeba4840a8c9e98a27c6c/libbio-tools-phylo-paml-perl_1.7.3-4_all Wed Jan 22 20:06:02 UTC 2025 I: Submitting 8.0K b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc https://buildinfo.debian.net/db38d2617d879f65ec831f06b7c4334bfa9b931c/libbio-tools-phylo-paml-perl_1.7.3-4_all Wed Jan 22 20:06:03 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jan 22 20:06:03 UTC 2025 I: Done submitting .buildinfo files. Wed Jan 22 20:06:03 UTC 2025 I: Removing signed libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc files: removed './b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc' removed './b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc' 1737576363 arm64 unstable libbio-tools-phylo-paml-perl Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.rbuild.log: 74.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libbio-tools-phylo-paml-perl_1.7.3-4.rbuild.log.gz [2025-01-22 20:06:03] INFO: Starting at 2025-01-22 20:06:03.805056 [2025-01-22 20:06:03] INFO: Generating the pages of 1 package(s) [2025-01-22 20:06:04] INFO: Finished at 2025-01-22 20:06:04.232720, took: 0:00:00.427672 All cleanup done. Wed Jan 22 20:06:04 UTC 2025 - total duration: 0h 1m 22s. Wed Jan 22 20:06:04 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Cm9olvd7, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1min 26.354s CPU time consumed: 7.250s