Running as unit: rb-build-arm64_3-121905.service; invocation ID: 37c85d51aa47420ca8aafb35aeb7cd7a ==================================================================================== Sat Nov 1 09:54:48 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_3) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Sat Nov 1 09:54:48 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-Anzk8bwC" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 09:54:49 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Nov 1 09:54:49 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-3U5JVi' Sat Nov 1 09:54:49 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 09:54:49 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-haWRql' ok, let's check if parsnp is building anywhere yet… ok, parsnp is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of parsnp in unstable on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Sat Nov 1 09:55:06 UTC 2025 I: starting to build parsnp/unstable/arm64 on jenkins on '2025-11-01 09:54' Sat Nov 1 09:55:06 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/121905/console.log 1761990906 arm64 unstable parsnp Sat Nov 1 09:55:06 UTC 2025 I: Downloading source for unstable/parsnp=2.1.3+dfsg-1 --2025-11-01 09:55:07-- http://deb.debian.org/debian/pool/main/p/parsnp/parsnp_2.1.3%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2246 (2.2K) [text/prs.lines.tag] Saving to: ‘parsnp_2.1.3+dfsg-1.dsc’ 0K .. 100% 252M=0s 2025-11-01 09:55:07 (252 MB/s) - ‘parsnp_2.1.3+dfsg-1.dsc’ saved [2246/2246] --2025-11-01 09:55:07-- http://deb.debian.org/debian/pool/main/p/parsnp/parsnp_2.1.3%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2246 (2.2K) [text/prs.lines.tag] Saving to: ‘parsnp_2.1.3+dfsg-1.dsc’ 0K .. 100% 252M=0s 2025-11-01 09:55:07 (252 MB/s) - ‘parsnp_2.1.3+dfsg-1.dsc’ saved [2246/2246] Sat Nov 1 09:55:07 UTC 2025 I: parsnp_2.1.3+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: parsnp Binary: parsnp Architecture: any Version: 2.1.3+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/parsnp Vcs-Git: https://salsa.debian.org/med-team/parsnp.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev Package-List: parsnp deb science optional arch=any Checksums-Sha1: 60c6898d93366d880548bdd6c596eac173caebec 142932 parsnp_2.1.3+dfsg.orig.tar.xz 67eba54d65d745a8f4bd17609df9798b58334fd8 10300 parsnp_2.1.3+dfsg-1.debian.tar.xz Checksums-Sha256: 9d654f2300fe6ace7450ffaf1f49c7fe742e0261ef53990dad4e87129dcecf82 142932 parsnp_2.1.3+dfsg.orig.tar.xz 783c1f0dcb74e0486c9207538cdcdcab700478593ac182fb773de95a6a05dd4e 10300 parsnp_2.1.3+dfsg-1.debian.tar.xz Files: d08f5861ba25b6be832b5919fbad252a 142932 parsnp_2.1.3+dfsg.orig.tar.xz 86639c08feae78f52067fc4e25ca9fd1 10300 parsnp_2.1.3+dfsg-1.debian.tar.xz Dgit: b03c932df9c1c340123ab19056a27844b4bd1b9f debian archive/debian/2.1.3+dfsg-1 https://git.dgit.debian.org/parsnp -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmfDVu4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpoog/7Bg8UQvBKj+nQ+o/abcJObXswTABt GaW2LwmvL/wc7T5SHseIFeWdhxhuZ31SX4t6Wl9EAB8IENNOo89q2vCgFAhSm3jH 9G4sMAiOTlbLxcqMh1SeRD5zu176te9jvSEX1Ig/O6SRz+ms8RiTIdbPcGgVkpZT fpzotsnX44IqnsOIPd3DTf0y2kPFjzFWLHBGX67skWkYZemcuTPL8iP2QX75s5U+ oSYLzdYhldh0MRVOVNdu6eFmc5ctdM53RfaGOeYYRrCXCiLq/N/6Kc0G5ZHD2vdF qsGfsElYZkhws/3B4I89qZlPLc14rJ6NNJjbsH6lIFGPyzj77NIpqG/gukWW8sLE vjYtyGhKQ7b8nbtiJ3idGVFpr64iRxrLRAZiyH8EWrHyY8uMdkKAC8K2V5e8C8vq LolrAejDjT12k10voyjA3ls9S2vFT9e1DGldYmlmPe94XCtb5MXnl451waiCzCPT KkhYTNTAdiamoCwVCtUS0eS6Bk8NQzeGfsqwleZY3yQDj9cnKnY3aQGN4NWa+6JG lKZ3IglwZKtdi54p8FVjBK2xJRyIGiG7Qapis3YxP6XnVvsGDfc1Fb/E3uyCZsjP 1SrBWUtN2cQavroHs1BvuRwSFGiUbnsoZsQbAAPT1D7faDcmxc5Cs/NUGG8KBp8q yDXzgAWcRNwyydw= =hCfq -----END PGP SIGNATURE----- Sat Nov 1 09:55:07 UTC 2025 I: Checking whether the package is not for us Sat Nov 1 09:55:07 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sat Nov 1 09:55:07 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sat Nov 1 09:55:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Nov 1 09:55:07 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-IPJVbO' ==================================================================================== Fri Dec 4 16:18:08 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 parsnp unstable /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b 2.1.3+dfsg-1" as arguments. Fri Dec 4 16:18:08 UTC 2026 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-U9179QTE" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Dec 4 16:18:08 UTC 2026 I: Downloading source for unstable/parsnp=2.1.3+dfsg-1 Reading package lists... NOTICE: 'parsnp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/parsnp.git Please use: git clone https://salsa.debian.org/med-team/parsnp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (dsc) [2246 B] Get:2 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (tar) [143 kB] Get:3 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (diff) [10.3 kB] Fetched 155 kB in 0s (2297 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'parsnp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/parsnp.git Please use: git clone https://salsa.debian.org/med-team/parsnp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (dsc) [2246 B] Get:2 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (tar) [143 kB] Get:3 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (diff) [10.3 kB] Fetched 155 kB in 0s (2297 kB/s) Download complete and in download only mode ============================================================================= Building parsnp in unstable on arm64 on codethink03-arm64 now. Date: Fri Dec 4 16:18:08 GMT 2026 Date UTC: Fri Dec 4 16:18:08 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 4 04:18:08 -12 2026 I: pbuilder-time-stamp: 1796401088 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 [parsnp_2.1.3+dfsg-1.dsc] I: copying [./parsnp_2.1.3+dfsg.orig.tar.xz] I: copying [./parsnp_2.1.3+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./parsnp_2.1.3+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting parsnp in parsnp-2.1.3+dfsg dpkg-source: info: unpacking parsnp_2.1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking parsnp_2.1.3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_missing_interpreter_line.patch dpkg-source: info: applying proper_calls_to_tools.patch dpkg-source: info: applying drop_m64.patch dpkg-source: info: applying fix_build_with_as-needed.patch dpkg-source: info: applying non-versioned-libs.patch dpkg-source: info: applying blhc-fix.patch dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1105788/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='badf657bdea14ba9b37e5bc2da4380be' 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='1105788' 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.QwO8rD4b/pbuilderrc_ZqHM --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.QwO8rD4b/b1 --logfile b1/build.log parsnp_2.1.3+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1105788/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), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libjs-sphinxdoc{a} libmagic-mgc{a} libmagic1t64{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 30.1 MB of archives. After unpacking 128 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libmuscle1 arm64 3.7+4565-8+b1 [236 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libmuscle-dev arm64 3.7+4565-8+b1 [296 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 30.1 MB in 0s (82.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../55-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmuscle1 (3.7+4565-8+b1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 4 16:18:24 UTC 2026. Universal Time is now: Fri Dec 4 16:18:24 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.3-1) ... Setting up libmuscle-dev (3.7+4565-8+b1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-8) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libpython3.13:arm64 (3.13.9-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:arm64 (3.13.9-1) ... Setting up cython3 (3.1.6+dfsg-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.9-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up python3-inflect (7.5.0-1) ... Setting up libpython3-all-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/parsnp-2.1.3+dfsg/ && 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 > ../parsnp_2.1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 2.1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 configure.ac:23: warning: AC_OUTPUT should be used without arguments. configure.ac:23: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory, src/Makefile.am:4: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. src/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for libMUSCLE/muscle.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector&)': parsnp.cpp:955:28: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~ parsnp.cpp:955:27: note: directive argument in the range [-2147483647, 2147483647] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from parsnp.hh:14, from parsnp.cpp:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'void Aligner::writeOutput(std::string, std::vector&)' at parsnp.cpp:955:24: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_test make -j12 check TESTSUITEFLAGS="-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ make -j12 install DESTDIR=/build/reproducible-path/parsnp-2.1.3\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' /usr/bin/install -c parsnp_core '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/parsnp/usr/bin/parsnp dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_fixperms chmod -x debian/parsnp/usr/share/parsnp/template.ini make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsnp' in '../parsnp_2.1.3+dfsg-1_arm64.deb'. dpkg-deb: building package 'parsnp-dbgsym' in '../parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsnp_2.1.3+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../parsnp_2.1.3+dfsg-1_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: including full 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/1105788 and its subdirectories I: Current time: Fri Dec 4 04:19:00 -12 2026 I: pbuilder-time-stamp: 1796401141 Fri Dec 4 16:19:01 UTC 2026 I: Signing ./b1/parsnp_2.1.3+dfsg-1_arm64.buildinfo as parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc Fri Dec 4 16:19:01 UTC 2026 I: Signed ./b1/parsnp_2.1.3+dfsg-1_arm64.buildinfo as ./b1/parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc Fri Dec 4 16:19:01 UTC 2026 - build #1 for parsnp/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Fri Dec 4 16:19:01 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-U9179QTE, removing. /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 09:56 b1 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 09:55 b2 -rw-rw-r-- 1 jenkins jenkins 2246 Mar 1 2025 parsnp_2.1.3+dfsg-1.dsc -rw------- 1 jenkins jenkins 3376 Nov 1 09:55 rbuildlog.3Lqia9F /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b1: total 1604 -rw-r--r-- 1 jenkins jenkins 47860 Nov 1 09:56 build.log -rw-r--r-- 1 jenkins jenkins 1204788 Nov 1 09:56 parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 10300 Nov 1 09:56 parsnp_2.1.3+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2246 Nov 1 09:56 parsnp_2.1.3+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 6066 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6948 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1508 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 196664 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1652 Nov 1 09:56 parsnp_2.1.3+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 142932 Nov 1 09:56 parsnp_2.1.3+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b2: total 0 Sat Nov 1 09:56:01 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 4 04:18:08 -12 2026 I: pbuilder-time-stamp: 1796401088 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 [parsnp_2.1.3+dfsg-1.dsc] I: copying [./parsnp_2.1.3+dfsg.orig.tar.xz] I: copying [./parsnp_2.1.3+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./parsnp_2.1.3+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting parsnp in parsnp-2.1.3+dfsg dpkg-source: info: unpacking parsnp_2.1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking parsnp_2.1.3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_missing_interpreter_line.patch dpkg-source: info: applying proper_calls_to_tools.patch dpkg-source: info: applying drop_m64.patch dpkg-source: info: applying fix_build_with_as-needed.patch dpkg-source: info: applying non-versioned-libs.patch dpkg-source: info: applying blhc-fix.patch dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1105788/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='badf657bdea14ba9b37e5bc2da4380be' 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='1105788' 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.QwO8rD4b/pbuilderrc_ZqHM --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.QwO8rD4b/b1 --logfile b1/build.log parsnp_2.1.3+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1105788/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), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libjs-sphinxdoc{a} libmagic-mgc{a} libmagic1t64{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 30.1 MB of archives. After unpacking 128 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libmuscle1 arm64 3.7+4565-8+b1 [236 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libmuscle-dev arm64 3.7+4565-8+b1 [296 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 30.1 MB in 0s (82.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_arm64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:arm64 (3.13.9-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20298 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.3-3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (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 ... 21313 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cython3. Preparing to unpack .../16-cython3_3.1.6+dfsg-2_arm64.deb ... Unpacking cython3 (3.1.6+dfsg-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. 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Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../26-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ... Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package dh-python. Preparing to unpack .../31-dh-python_6.20250414_all.deb ... Unpacking dh-python (6.20250414) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../32-libexpat1-dev_2.7.3-1_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.7.3-1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../33-libjs-sphinxdoc_8.2.3-8_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-8) ... Selecting previously unselected package libmuscle1. Preparing to unpack .../34-libmuscle1_3.7+4565-8+b1_arm64.deb ... Unpacking libmuscle1 (3.7+4565-8+b1) ... Selecting previously unselected package libmuscle-dev. Preparing to unpack .../35-libmuscle-dev_3.7+4565-8+b1_arm64.deb ... Unpacking libmuscle-dev (3.7+4565-8+b1) ... Selecting previously unselected package libpython3.13:arm64. Preparing to unpack .../36-libpython3.13_3.13.9-1_arm64.deb ... Unpacking libpython3.13:arm64 (3.13.9-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../37-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.13-dev:arm64. Preparing to unpack .../38-libpython3.13-dev_3.13.9-1_arm64.deb ... Unpacking libpython3.13-dev:arm64 (3.13.9-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../39-libpython3-dev_3.13.7-1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.13.7-1) ... Selecting previously unselected package libpython3-all-dev:arm64. Preparing to unpack .../40-libpython3-all-dev_3.13.7-1_arm64.deb ... Unpacking libpython3-all-dev:arm64 (3.13.7-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../41-python3-all_3.13.7-1_arm64.deb ... Unpacking python3-all (3.13.7-1) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../42-python3.13-dev_3.13.9-1_arm64.deb ... Unpacking python3.13-dev (3.13.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../43-python3-dev_3.13.7-1_arm64.deb ... Unpacking python3-dev (3.13.7-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../44-python3-all-dev_3.13.7-1_arm64.deb ... Unpacking python3-all-dev (3.13.7-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../45-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../46-python3-more-itertools_10.8.0-1_all.deb ... Unpacking python3-more-itertools (10.8.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../47-python3-typing-extensions_4.15.0-1_all.deb ... Unpacking python3-typing-extensions (4.15.0-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../48-python3-typeguard_4.4.4-1_all.deb ... Unpacking python3-typeguard (4.4.4-1) ... 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Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../55-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmuscle1 (3.7+4565-8+b1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 4 16:18:24 UTC 2026. Universal Time is now: Fri Dec 4 16:18:24 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.3-1) ... Setting up libmuscle-dev (3.7+4565-8+b1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-8) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libpython3.13:arm64 (3.13.9-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:arm64 (3.13.9-1) ... Setting up cython3 (3.1.6+dfsg-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.9-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up python3-inflect (7.5.0-1) ... Setting up libpython3-all-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/parsnp-2.1.3+dfsg/ && 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 > ../parsnp_2.1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 2.1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 configure.ac:23: warning: AC_OUTPUT should be used without arguments. configure.ac:23: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory, src/Makefile.am:4: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. src/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for libMUSCLE/muscle.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector&)': parsnp.cpp:955:28: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~ parsnp.cpp:955:27: note: directive argument in the range [-2147483647, 2147483647] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from parsnp.hh:14, from parsnp.cpp:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'void Aligner::writeOutput(std::string, std::vector&)' at parsnp.cpp:955:24: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_test make -j12 check TESTSUITEFLAGS="-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ make -j12 install DESTDIR=/build/reproducible-path/parsnp-2.1.3\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' /usr/bin/install -c parsnp_core '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/parsnp/usr/bin/parsnp dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_fixperms chmod -x debian/parsnp/usr/share/parsnp/template.ini make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsnp' in '../parsnp_2.1.3+dfsg-1_arm64.deb'. dpkg-deb: building package 'parsnp-dbgsym' in '../parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsnp_2.1.3+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../parsnp_2.1.3+dfsg-1_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: including full 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/1105788 and its subdirectories I: Current time: Fri Dec 4 04:19:00 -12 2026 I: pbuilder-time-stamp: 1796401141 Sat Nov 1 09:56:02 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sat Nov 1 09:56:02 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sat Nov 1 09:56:02 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Nov 1 09:56:02 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-JaI1Iu' ==================================================================================== Sat Nov 1 09:56:03 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 parsnp unstable /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b 2.1.3+dfsg-1" as arguments. Sat Nov 1 09:56:03 UTC 2025 - actually running "reproducible_build.sh" (md5sum bcb6fe1b50cf4e8eedacd0971a9eb63f) as "/tmp/jenkins-script-bBvF0SVa" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Nov 1 09:56:03 UTC 2025 I: Downloading source for unstable/parsnp=2.1.3+dfsg-1 Reading package lists... NOTICE: 'parsnp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/parsnp.git Please use: git clone https://salsa.debian.org/med-team/parsnp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (dsc) [2246 B] Get:2 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (tar) [143 kB] Get:3 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (diff) [10.3 kB] Fetched 155 kB in 0s (8194 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'parsnp' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/parsnp.git Please use: git clone https://salsa.debian.org/med-team/parsnp.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 155 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (dsc) [2246 B] Get:2 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (tar) [143 kB] Get:3 http://deb.debian.org/debian unstable/main parsnp 2.1.3+dfsg-1 (diff) [10.3 kB] Fetched 155 kB in 0s (8194 kB/s) Download complete and in download only mode ============================================================================= Re-Building parsnp in unstable on arm64 on codethink04-arm64 now. Date: Sat Nov 1 09:56:03 GMT 2025 Date UTC: Sat Nov 1 09:56:03 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/pbuilderrc_JBAz + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' parsnp = debian-installer -o parsnp = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' parsnp = u-boot ']' + case "${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.QwO8rD4b/pbuilderrc_JBAz --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.QwO8rD4b/b2 --logfile b2/build.log parsnp_2.1.3+dfsg-1.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: Sat Nov 1 23:56:03 +14 2025 I: pbuilder-time-stamp: 1761990963 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 [parsnp_2.1.3+dfsg-1.dsc] I: copying [./parsnp_2.1.3+dfsg.orig.tar.xz] I: copying [./parsnp_2.1.3+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./parsnp_2.1.3+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting parsnp in parsnp-2.1.3+dfsg dpkg-source: info: unpacking parsnp_2.1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking parsnp_2.1.3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_missing_interpreter_line.patch dpkg-source: info: applying proper_calls_to_tools.patch dpkg-source: info: applying drop_m64.patch dpkg-source: info: applying fix_build_with_as-needed.patch dpkg-source: info: applying non-versioned-libs.patch dpkg-source: info: applying blhc-fix.patch dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 1 09:56 /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/1026073/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1026073/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.3.3(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 nocheck' 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=ea67c9664131484383432e1e408cb59c 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=1026073 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.QwO8rD4b/pbuilderrc_JBAz --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.QwO8rD4b/b2 --logfile b2/build.log parsnp_2.1.3+dfsg-1.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins 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 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1026073/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), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libjs-sphinxdoc{a} libmagic-mgc{a} libmagic1t64{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 30.1 MB of archives. After unpacking 128 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libmuscle1 arm64 3.7+4565-8+b1 [236 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libmuscle-dev arm64 3.7+4565-8+b1 [296 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Fetched 30.1 MB in 0s (94.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_arm64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:arm64 (3.13.9-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20298 files and directories currently installed.) 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../55-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmuscle1 (3.7+4565-8+b1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Nov 1 09:56:20 UTC 2025. Universal Time is now: Sat Nov 1 09:56:20 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.3-1) ... Setting up libmuscle-dev (3.7+4565-8+b1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-8) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libpython3.13:arm64 (3.13.9-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:arm64 (3.13.9-1) ... Setting up cython3 (3.1.6+dfsg-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.9-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up python3-inflect (7.5.0-1) ... Setting up libpython3-all-dev:arm64 (3.13.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/parsnp-2.1.3+dfsg/ && 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 > ../parsnp_2.1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 2.1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 configure.ac:23: warning: AC_OUTPUT should be used without arguments. configure.ac:23: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory, src/Makefile.am:4: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibility. src/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7 ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for libMUSCLE/muscle.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector&)': parsnp.cpp:955:28: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~ parsnp.cpp:955:27: note: directive argument in the range [-2147483647, 2147483647] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from parsnp.hh:14, from parsnp.cpp:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'void Aligner::writeOutput(std::string, std::vector&)' at parsnp.cpp:955:24: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.1.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ make -j12 install DESTDIR=/build/reproducible-path/parsnp-2.1.3\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' /usr/bin/install -c parsnp_core '/build/reproducible-path/parsnp-2.1.3+dfsg/debian/parsnp../bin' make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/parsnp/usr/bin/parsnp dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_fixperms chmod -x debian/parsnp/usr/share/parsnp/template.ini make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsnp' in '../parsnp_2.1.3+dfsg-1_arm64.deb'. dpkg-deb: building package 'parsnp-dbgsym' in '../parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../parsnp_2.1.3+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../parsnp_2.1.3+dfsg-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1026073/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/1026073 and its subdirectories I: Current time: Sat Nov 1 23:57:03 +14 2025 I: pbuilder-time-stamp: 1761991023 + false + set +x Sat Nov 1 09:57:03 UTC 2025 I: Signing ./b2/parsnp_2.1.3+dfsg-1_arm64.buildinfo as parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc Sat Nov 1 09:57:03 UTC 2025 I: Signed ./b2/parsnp_2.1.3+dfsg-1_arm64.buildinfo as ./b2/parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc Sat Nov 1 09:57:03 UTC 2025 - build #2 for parsnp/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sat Nov 1 09:57:03 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-bBvF0SVa, removing. /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b: total 68 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 09:56 b1 drwxrwxr-x 2 jenkins jenkins 4096 Nov 1 09:57 b2 -rw-rw-r-- 1 jenkins jenkins 2246 Mar 1 2025 parsnp_2.1.3+dfsg-1.dsc -rw------- 1 jenkins jenkins 51537 Nov 1 09:56 rbuildlog.3Lqia9F /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b1: total 1616 -rw-r--r-- 1 jenkins jenkins 47860 Nov 1 09:56 build.log -rw-r--r-- 1 jenkins jenkins 1204788 Nov 1 09:56 parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 10300 Nov 1 09:56 parsnp_2.1.3+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2246 Nov 1 09:56 parsnp_2.1.3+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 6066 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6948 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1508 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 196664 Nov 1 09:56 parsnp_2.1.3+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1652 Nov 1 09:56 parsnp_2.1.3+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 142932 Nov 1 09:56 parsnp_2.1.3+dfsg.orig.tar.xz /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b2: total 1608 -rw-rw-r-- 1 jenkins jenkins 49281 Nov 1 09:57 build.log -rw-r--r-- 1 jenkins jenkins 1204788 Nov 1 09:57 parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 10300 Nov 1 09:57 parsnp_2.1.3+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2246 Nov 1 09:57 parsnp_2.1.3+dfsg-1.dsc -rw-rw-r-- 1 jenkins jenkins 6074 Nov 1 09:57 parsnp_2.1.3+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 6956 Nov 1 09:57 parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1508 Nov 1 09:57 parsnp_2.1.3+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 196664 Nov 1 09:57 parsnp_2.1.3+dfsg-1_arm64.deb -rw-rw-r-- 1 jenkins jenkins 1652 Nov 1 09:57 parsnp_2.1.3+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 142932 Nov 1 09:57 parsnp_2.1.3+dfsg.orig.tar.xz Sat Nov 1 09:57:04 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sat Nov 1 09:57:04 UTC 2025 I: parsnp_2.1.3+dfsg-1_arm64.changes: Format: 1.8 Date: Sat, 01 Mar 2025 19:19:00 +0100 Source: parsnp Binary: parsnp parsnp-dbgsym Architecture: arm64 Version: 2.1.3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: parsnp - rapid core genome multi-alignment Changes: parsnp (2.1.3+dfsg-1) unstable; urgency=medium . * New upstream version 2.1.3+dfsg * proper_calls_to_tools.patch: refresh patch. * py3-parsnp-libs.patch: unfuzz patch. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: 4b53c6527f958c55d4c0168ae71129471ecef01f 1204788 parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb 811438e3fbdc7669af203bfb2963a4dbc9698322 6066 parsnp_2.1.3+dfsg-1_arm64.buildinfo baee1289e2862edb9ede66c7ea42187698de6e91 196664 parsnp_2.1.3+dfsg-1_arm64.deb Checksums-Sha256: 5d6e6de60cee4608b3c3c9b926bc9570938824535f0e6d0803932404fb786e8d 1204788 parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb e89f181295ba32d14da886a269fa92823fe1fae1527ef6e2ac7ff5b1f5027d34 6066 parsnp_2.1.3+dfsg-1_arm64.buildinfo 44a5c141eb3b0cb770fa6ec9153301e868d9b816ffa629e4bfeafedd16b9cfa3 196664 parsnp_2.1.3+dfsg-1_arm64.deb Files: c2313d3df92a1de03daf1e8f62acf575 1204788 debug optional parsnp-dbgsym_2.1.3+dfsg-1_arm64.deb 40ed720fa3d28f9c50335d0b86f23ce1 6066 science optional parsnp_2.1.3+dfsg-1_arm64.buildinfo ef3951b99fa9a2bd7688ddaa2c2c9125 196664 science optional parsnp_2.1.3+dfsg-1_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/parsnp_2.1.3+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/parsnp_2.1.3+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/parsnp_2.1.3+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/parsnp_2.1.3+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/parsnp_2.1.3+dfsg-1_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/parsnp_2.1.3+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-11-01 09:56:01.654181248 +0000 +++ b2/build.log 2025-11-01 09:57:04.046253131 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 4 04:18:08 -12 2026 -I: pbuilder-time-stamp: 1796401088 +I: Current time: Sat Nov 1 23:56:03 +14 2025 +I: pbuilder-time-stamp: 1761990963 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1105788/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 1 09:56 /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/1026073/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1026073/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' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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 nocheck' + 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='badf657bdea14ba9b37e5bc2da4380be' - 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='1105788' - PS1='# ' - PS2='> ' + INVOCATION_ID=ea67c9664131484383432e1e408cb59c + 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=1026073 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.QwO8rD4b/pbuilderrc_ZqHM --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.QwO8rD4b/b1 --logfile b1/build.log parsnp_2.1.3+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.QwO8rD4b/pbuilderrc_JBAz --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.QwO8rD4b/b2 --logfile b2/build.log parsnp_2.1.3+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1105788/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -191,7 +223,7 @@ Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] -Fetched 30.1 MB in 0s (82.7 MB/s) +Fetched 30.1 MB in 0s (94.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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.) @@ -427,8 +459,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Dec 4 16:18:24 UTC 2026. -Universal Time is now: Fri Dec 4 16:18:24 UTC 2026. +Local time is now: Sat Nov 1 09:56:20 UTC 2025. +Universal Time is now: Sat Nov 1 09:56:20 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -494,7 +526,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/parsnp-2.1.3+dfsg/ && 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 > ../parsnp_2.1.3+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/parsnp-2.1.3+dfsg/ && 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 > ../parsnp_2.1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 2.1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -538,8 +574,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for gcc... gcc checking whether the C compiler works... yes @@ -621,17 +657,7 @@ make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' - dh_auto_test - make -j12 check TESTSUITEFLAGS="-j12 --verbose" VERBOSE=1 -make[1]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' -Making check in src -make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' -make[2]: Nothing to be done for 'check'. -make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg/src' -make[2]: Entering directory '/build/reproducible-path/parsnp-2.1.3+dfsg' -make[2]: Nothing to be done for 'check-am'. -make[2]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' -make[1]: Leaving directory '/build/reproducible-path/parsnp-2.1.3+dfsg' +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ @@ -690,12 +716,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1026073/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1026073/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/1105788 and its subdirectories -I: Current time: Fri Dec 4 04:19:00 -12 2026 -I: pbuilder-time-stamp: 1796401141 +I: removing directory /srv/workspace/pbuilder/1026073 and its subdirectories +I: Current time: Sat Nov 1 23:57:03 +14 2025 +I: pbuilder-time-stamp: 1761991023 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/parsnp_2.1.3+dfsg-1.diff: 67.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/parsnp_2.1.3+dfsg-1.diff.gz b2/build.log: 79.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 80.5% -- replaced with stdout Sat Nov 1 09:57:05 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_parsnp_unstable_arm64_1761991025 + touch /var/log/reproducible-builds/diffoscope_stamp_parsnp_unstable_arm64_1761991025 + RESULT=0 + systemd-run '--description=diffoscope on parsnp/2.1.3+dfsg-1 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_3-121905 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b --run-session -c jenkins-reproducible-unstable-diffoscope-a16f592b-5867-4be4-81ac-17b9ae68386b -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/dbd-tmp-aSDUhuO ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b1/parsnp_2.1.3+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b2/parsnp_2.1.3+dfsg-1_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_3-121905.service; invocation ID: 44d9e81a1fa44542a6cda1cc51660682 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/parsnp_2.1.3+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b1/parsnp_2.1.3+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QwO8rD4b/b2/parsnp_2.1.3+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 202ms CPU time consumed: 164ms Memory peak: 17.6M (swap: 0B) _ __ __ _ _ __ ___ _ __ _ __ | '_ \ / _` | '__/ __| '_ \| '_ \ | |_) | (_| | | \__ \ | | | |_) | | .__/ \__,_|_| |___/_| |_| .__/ |_| |_| Sat Nov 1 09:57:05 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Sat Nov 1 09:57:05 UTC 2025 I: parsnp from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-11-01 09:57:06] INFO: Starting at 2025-11-01 09:57:06.274919 [2025-11-01 09:57:06] INFO: Generating the pages of 1 package(s) [2025-11-01 09:57:06] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/parsnp didn't produce a buildlog, even though it has been built. [2025-11-01 09:57:06] INFO: Finished at 2025-11-01 09:57:06.546975, took: 0:00:00.272059 Sat Nov 1 09:57:06 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/parsnp.html Sat Nov 1 09:57:06 UTC 2025 I: Removing signed parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc files: removed './b1/parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc' removed './b2/parsnp_2.1.3+dfsg-1_arm64.buildinfo.asc' 1761991026 arm64 unstable parsnp Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/parsnp_2.1.3+dfsg-1.rbuild.log: 77.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/parsnp_2.1.3+dfsg-1.rbuild.log.gz [2025-11-01 09:57:06] INFO: Starting at 2025-11-01 09:57:06.856606 [2025-11-01 09:57:06] INFO: Generating the pages of 1 package(s) [2025-11-01 09:57:07] INFO: Finished at 2025-11-01 09:57:07.112271, took: 0:00:00.255668 All cleanup done. Sat Nov 1 09:57:07 UTC 2025 - total duration: 0h 2m 17s. Sat Nov 1 09:57:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Anzk8bwC, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 2min 18.285s CPU time consumed: 3.030s Memory peak: 42.3M (swap: 0B)