Diff of the two buildlogs: -- --- b1/build.log 2024-12-13 09:42:35.738547429 +0000 +++ b2/build.log 2024-12-13 09:54:27.174258561 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 15 03:49:41 -12 2026 -I: pbuilder-time-stamp: 1768492181 +I: Current time: Fri Dec 13 23:42:38 +14 2024 +I: pbuilder-time-stamp: 1734082958 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying 45127698e270024bacb670cdd0bd2e4850104b6f.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2532106/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1174948/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 Dec 13 09:42 /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/1174948/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1174948/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='323f29272594467f9e34abbef2133af1' - 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='2532106' - PS1='# ' - PS2='> ' + INVOCATION_ID=bd35af446d704c419e4a2e3ea5908a99 + 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=1174948 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.GcZie8bU/pbuilderrc_fkTu --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GcZie8bU/b1 --logfile b1/build.log python-skbio_0.6.2-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GcZie8bU/pbuilderrc_ZQbO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GcZie8bU/b2 --logfile b2/build.log python-skbio_0.6.2-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2532106/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1174948/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -425,7 +457,7 @@ Get: 244 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-design all 0.6.1-1 [883 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1+b1 [2087 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels all 0.14.4+dfsg-1 [4825 kB] -Fetched 183 MB in 2s (119 MB/s) +Fetched 183 MB in 2s (87.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal: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 ... 20082 files and directories currently installed.) @@ -1222,8 +1254,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 15 15:51:00 UTC 2026. -Universal Time is now: Thu Jan 15 15:51:00 UTC 2026. +Local time is now: Fri Dec 13 09:44:17 UTC 2024. +Universal Time is now: Fri Dec 13 09:44:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1453,7 +1485,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-skbio-0.6.2/ && 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 > ../python-skbio_0.6.2-4_source.changes +I: user script /srv/workspace/pbuilder/1174948/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1174948/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-skbio-0.6.2/ && 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 > ../python-skbio_0.6.2-4_source.changes dpkg-buildpackage: info: source package python-skbio dpkg-buildpackage: info: source version 0.6.2-4 dpkg-buildpackage: info: source distribution unstable @@ -2480,7 +2516,7 @@ python3 `which sphinx-build` -b html -d doc/build/doctrees doc/source doc/build/html Running Sphinx v7.4.7 loading translations [en]... done -Matplotlib created a temporary cache directory at /tmp/matplotlib-r5y627pk because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary cache directory at /tmp/matplotlib-lszt06lo because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. making output directory... done [autosummary] generating autosummary for: alignment.rst, diversity.rst, embedding.rst, index.rst, io.rst, metadata.rst, sequence.rst, stats.rst, table.rst, tree.rst, util.rst, workflow.rst [autosummary] generating autosummary for: /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.AlignPath.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.AlignmentStructure.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.PairAlignPath.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.StripedSmithWaterman.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.TabularMSA.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.global_pairwise_align.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.global_pairwise_align_nucleotide.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.global_pairwise_align_protein.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.local_pairwise_align.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.alignment.local_pairwise_align_nucleotide.rst, ..., /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.assert_data_frame_almost_equal.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.assert_ordination_results_equal.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.cardinal_to_ordinal.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.classproperty.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.find_duplicates.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.get_data_path.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.util.safe_md5.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.workflow.Workflow.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.workflow.method.rst, /build/reproducible-path/python-skbio-0.6.2/doc/source/generated/skbio.workflow.requires.rst @@ -2489,15 +2525,15 @@ loading intersphinx inventory 'python' from /usr/share/doc/python3/html/objects.inv... loading intersphinx inventory 'numpy' from /usr/share/doc/python-numpy/html/objects.inv... loading intersphinx inventory 'scipy' from /usr/share/doc/python-scipy-doc/html/objects.inv... +loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv... +loading intersphinx inventory 'pandas' from /usr/share/doc/python-pandas-doc/html/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory '/usr/share/doc/python-scipy-doc/html/objects.inv' not fetchable due to : [Errno 2] No such file or directory: '/usr/share/doc/python-scipy-doc/html/objects.inv' -loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'matplotlib.org' ([Errno -3] Temporary failure in name resolution)")) -loading intersphinx inventory 'pandas' from /usr/share/doc/python-pandas-doc/html/objects.inv... +intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'matplotlib.org' ([Errno -3] Temporary failure in name resolution)")) loading intersphinx inventory 'biom-format' from /usr/share/doc/python-biom-format-doc/html/objects.inv... The version switcher "https://scikit.bio/versions.json" file cannot be read due to the following error: -ConnectionError(MaxRetryError('HTTPSConnectionPool(host=\'scikit.bio\', port=443): Max retries exceeded with url: /versions.json (Caused by NameResolutionError(": Failed to resolve \'scikit.bio\' ([Errno -3] Temporary failure in name resolution)"))')) +ConnectionError(MaxRetryError('HTTPSConnectionPool(host=\'scikit.bio\', port=443): Max retries exceeded with url: /versions.json (Caused by NameResolutionError(": Failed to resolve \'scikit.bio\' ([Errno -3] Temporary failure in name resolution)"))')) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 12 source files that are out of date @@ -5065,7 +5101,7 @@ warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -========== 2763 passed, 30 skipped, 70 warnings in 380.56s (0:06:20) =========== +========== 2763 passed, 30 skipped, 70 warnings in 166.69s (0:02:46) =========== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -6473,11 +6509,11 @@ /usr/share/javascript/mathjax/MathJax.js \ /usr/share/doc/python-skbio-doc/html/_static/MathJax.js dh_sphinxdoc --package=python-skbio-doc -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/MathJax.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/design-tabs.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/copybutton_funcs.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/copybutton.js -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/design-tabs.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/clipboard.min.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/MathJax.js make[1]: Leaving directory '/build/reproducible-path/python-skbio-0.6.2' dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -6512,12 +6548,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1174948/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1174948/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/2532106 and its subdirectories -I: Current time: Thu Jan 15 04:05:34 -12 2026 -I: pbuilder-time-stamp: 1768493134 +I: removing directory /srv/workspace/pbuilder/1174948 and its subdirectories +I: Current time: Fri Dec 13 23:54:26 +14 2024 +I: pbuilder-time-stamp: 1734083666