Thu May 18 13:41:35 UTC 2023 I: starting to build libbio-tools-phylo-paml-perl/bookworm/arm64 on jenkins on '2023-05-18 13:41' Thu May 18 13:41:35 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/6280/console.log Thu May 18 13:41:35 UTC 2023 I: Downloading source for bookworm/libbio-tools-phylo-paml-perl=1.7.3-4 --2023-05-18 13:41:35-- http://cdn-fastly.deb.debian.org/debian/pool/main/libb/libbio-tools-phylo-paml-perl/libbio-tools-phylo-paml-perl_1.7.3-4.dsc Connecting to 78.137.99.97:3128... 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% 38.2M=0s 2023-05-18 13:41:35 (38.2 MB/s) - ‘libbio-tools-phylo-paml-perl_1.7.3-4.dsc’ saved [2341/2341] Thu May 18 13:41:35 UTC 2023 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----- Thu May 18 13:41:35 UTC 2023 I: Checking whether the package is not for us Thu May 18 13:41:35 UTC 2023 I: Starting 1st build on remote node codethink10-arm64.debian.net. Thu May 18 13:41:35 UTC 2023 I: Preparing to do remote build '1' on codethink10-arm64.debian.net. Thu May 18 13:42:48 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 18 01:41:41 -12 2023 I: pbuilder-time-stamp: 1684417301 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 gpgv: Signature made Fri Oct 14 02:47:44 2022 -12 gpgv: using RSA key B23862C415D6565A4E86CBD7579C160D4C9E23E8 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: no acceptable signature found 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/27700/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8 ' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='27700' 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.RcEMNAnO/pbuilderrc_dzgO --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink10-arm64 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 16 22:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27700/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 ... 19616 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} libelf1{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} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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 22.8 MB of archives. After unpacking 89.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libbio-perl-run-perl all 1.7.3-9 [605 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B] Get: 39 http://deb.debian.org/debian bookworm/main arm64 paml arm64 4.9j+dfsg-4 [632 kB] Fetched 22.8 MB in 2s (10.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... 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_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... 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%3a1.17-1_arm64.deb ... Unpacking libio-pty-perl (1:1.17-1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../34-libipc-run-perl_20220807.0-1_all.deb ... Unpacking libipc-run-perl (20220807.0-1) ... 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_1.7.3-9_all.deb ... Unpacking libbio-perl-run-perl (1.7.3-9) ... 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-4_arm64.deb ... Unpacking paml (4.9j+dfsg-4) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libdevel-checkbin-perl (0.04-3) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up autoconf (2.71-3) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up paml (4.9j+dfsg-4) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... 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 (1.13.1-1) ... Setting up libbio-perl-run-perl (1.7.3-9) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/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 -ffile-prefix-map=/build/libbio-tools-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/libbio-tools-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j8 make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3' 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/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.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.pm blib/lib/Bio/Tools/Phylo/PAML.pm 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 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/libbio-tools-phylo-paml-perl-1.7.3' dh_auto_test make -j8 test TEST_VERBOSE=1 make[1]: Entering directory '/build/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, 8 wallclock secs ( 0.15 usr 0.04 sys + 6.50 cusr 0.53 csys = 7.22 CPU) Result: PASS make[1]: Leaving directory '/build/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 -j8 install DESTDIR=/build/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/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents Installing /build/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/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/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/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/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm Installing /build/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/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/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/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/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/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/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/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/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/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/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/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/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/libbio-tools-phylo-paml-perl-1.7.3' debian/rules override_dh_install make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3' dh_install sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/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/27700 and its subdirectories I: Current time: Thu May 18 01:42:46 -12 2023 I: pbuilder-time-stamp: 1684417366 Thu May 18 13:42:49 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Thu May 18 13:42:49 UTC 2023 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Thu May 18 13:43:51 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Thu May 18 13:43:51 UTC 2023 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: c9b2b0fcafbd28c5b9bdc6f1fb6f69f86e603b07 80832 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb 43f320d8cebf22ad4676c60934c4916256a12fe4 5240 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo Checksums-Sha256: 9de191c5e1bda8d1ea54d17e3e9ddbfc18baa62007849aa79a17b253348d39ed 80832 libbio-tools-phylo-paml-perl_1.7.3-4_all.deb 352725625a3e76eb486cdc71810de8e1a466755cd4fa0e8a37b11189b6ba6dd9 5240 libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo Files: 76349f03becd7b72ffc8b5c386584a9a 80832 science optional libbio-tools-phylo-paml-perl_1.7.3-4_all.deb 6d1df57837ba5d75a6b46b478e1ae310 5240 science optional libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo Thu May 18 13:43:53 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/libbio-tools-phylo-paml-perl_1.7.3-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/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: 0.303s) 0.303s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.015s) 0.015s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu May 18 13:43:54 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu May 18 13:43:54 UTC 2023 I: libbio-tools-phylo-paml-perl from bookworm built successfully and reproducibly on arm64. Thu May 18 13:43:55 UTC 2023 I: Submitting .buildinfo files to external archives: Thu May 18 13:43:55 UTC 2023 I: Submitting 8.0K b1/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Thu May 18 13:43:56 UTC 2023 I: Submitting 8.0K b2/libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo.asc Thu May 18 13:43:56 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 18 13:43:56 UTC 2023 I: Done submitting .buildinfo files. Thu May 18 13:43:56 UTC 2023 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'