Diff of the two buildlogs: -- --- b1/build.log 2023-06-05 14:34:59.173513169 +0000 +++ b2/build.log 2023-06-05 15:05:47.132514798 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 7 08:24:18 -12 2024 -I: pbuilder-time-stamp: 1720383858 +I: Current time: Tue Jun 6 04:35:02 +14 2023 +I: pbuilder-time-stamp: 1685975702 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./python-skbio_0.5.8.orig.tar.gz] I: copying [./python-skbio_0.5.8-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Feb 11 22:42:23 2023 -12 +gpgv: Signature made Mon Feb 13 00:42:23 2023 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.8-4.dsc: no acceptable signature found @@ -33,52 +33,84 @@ dpkg-source: info: applying numpy-1.24.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18110/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28081/tmp/hooks/D01_modify_environment starting +debug: Running on codethink12-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 Jun 6 04:35 /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/28081/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28081/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8 ' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='18110' - PS1='# ' - PS2='> ' + 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=28081 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.1m7ScUpA/pbuilderrc_odRT --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1m7ScUpA/b1 --logfile b1/build.log python-skbio_0.5.8-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.1m7ScUpA/pbuilderrc_0cTI --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1m7ScUpA/b2 --logfile b2/build.log --extrapackages usrmerge python-skbio_0.5.8-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink9-arm64 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jul 5 04:49 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18110/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 4 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/28081/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -389,7 +421,7 @@ Get: 223 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB] Get: 224 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB] Get: 225 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx-bootstrap-theme all 0.8.1-1 [422 kB] -Fetched 173 MB in 6s (27.6 MB/s) +Fetched 173 MB in 4s (42.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19611 files and directories currently installed.) @@ -1326,8 +1358,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/python-skbio-0.5.8/ && 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_0.5.8-4_source.changes +I: user script /srv/workspace/pbuilder/28081/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/28081/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/python-skbio-0.5.8/ && 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_0.5.8-4_source.changes dpkg-buildpackage: info: source package python-skbio dpkg-buildpackage: info: source version 0.5.8-4 dpkg-buildpackage: info: source distribution unstable @@ -2235,7 +2276,7 @@ http_proxy='127.0.0.1:9' \ python3 `which sphinx-build` -b html -d doc/build/doctrees doc/source doc/build/html Running Sphinx v5.3.0 -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-smpsezn_ 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 config/cache directory at /tmp/matplotlib-_wm_fsvz 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, index.rst, io.rst, metadata.rst, sequence.rst, stats.rst, tree.rst, util.rst, workflow.rst [autosummary] generating autosummary for: /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.AlignmentStructure.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.StripedSmithWaterman.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.TabularMSA.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.global_pairwise_align.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.global_pairwise_align_nucleotide.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.global_pairwise_align_protein.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.local_pairwise_align.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.local_pairwise_align_nucleotide.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.local_pairwise_align_protein.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.alignment.local_pairwise_align_ssw.rst, ..., /build/python-skbio-0.5.8/doc/source/generated/skbio.util.assert_data_frame_almost_equal.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.assert_ordination_results_equal.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.cardinal_to_ordinal.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.classproperty.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.find_duplicates.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.get_data_path.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.util.safe_md5.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.workflow.Workflow.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.workflow.method.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.workflow.requires.rst @@ -2243,16 +2284,16 @@ [autosummary] generating autosummary for: /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__eq__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__ge__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__getstate__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__gt__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__hash__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__le__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__lt__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__ne__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.__str__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.io.registry.Format.reader.rst, ..., /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__getstate__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__gt__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__hash__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__le__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__lt__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__ne__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.__str__.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.plot.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.read.rst, /build/python-skbio-0.5.8/doc/source/generated/skbio.stats.ordination.OrdinationResults.write.rst loading intersphinx inventory from /usr/share/doc/python3.11/html/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... -WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'http://docs.scipy.org/doc/numpy/objects.inv' not fetchable due to : HTTPConnectionPool(host='127.0.0.1', port=9): Max retries exceeded with url: http://docs.scipy.org/doc/numpy/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from /usr/share/doc/python-scipy-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 from http://matplotlib.org/objects.inv... -WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'http://matplotlib.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='127.0.0.1', port=9): Max retries exceeded with url: http://matplotlib.org/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from /usr/share/doc/python-pandas-doc/html/objects.inv... loading intersphinx inventory from /usr/share/doc/python-biom-format-doc/html/objects.inv... +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'http://docs.scipy.org/doc/numpy/objects.inv' not fetchable due to : HTTPConnectionPool(host='127.0.0.1', port=9): Max retries exceeded with url: http://docs.scipy.org/doc/numpy/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'http://matplotlib.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='127.0.0.1', port=9): Max retries exceeded with url: http://matplotlib.org/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date building [html]: targets for 13 source files that are out of date updating environment: [new config] 839 added, 0 changed, 0 removed @@ -4195,7 +4236,7 @@ self._coords = self._coords.loc[sample_ids] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -========== 2352 passed, 30 skipped, 68 warnings in 308.87s (0:05:08) =========== +========== 2352 passed, 30 skipped, 68 warnings in 312.09s (0:05:12) =========== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -5388,11 +5429,11 @@ /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/js/jquery-1.12.4.min.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/bootstrap-sphinx.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/js/jquery-fix.js -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/bootstrap-sphinx.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/bootstrap-3.4.1/js/bootstrap.min.js -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-skbio-doc/usr/share/doc/python-skbio-doc/html/_static/js/jquery-1.12.4.min.js make[1]: Leaving directory '/build/python-skbio-0.5.8' dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -5422,12 +5463,14 @@ 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/28081/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28081/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/18110 and its subdirectories -I: Current time: Sun Jul 7 08:57:57 -12 2024 -I: pbuilder-time-stamp: 1720385877 +I: removing directory /srv/workspace/pbuilder/28081 and its subdirectories +I: Current time: Tue Jun 6 05:05:45 +14 2023 +I: pbuilder-time-stamp: 1685977545