Diff of the two buildlogs: -- --- b1/build.log 2023-04-12 14:00:50.336548460 +0000 +++ b2/build.log 2023-04-12 14:05:57.608712991 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 14 08:19:32 -12 2024 -I: pbuilder-time-stamp: 1715717972 +I: Current time: Thu Apr 13 04:00:54 +14 2023 +I: pbuilder-time-stamp: 1681308054 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 [./rdp-readseq_2.0.2.orig.tar.gz] I: copying [./rdp-readseq_2.0.2-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 6 02:31:13 2022 -12 +gpgv: Signature made Wed Dec 7 04:31:13 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -26,11 +26,20 @@ dpkg-source: info: unpacking rdp-readseq_2.0.2-9.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14248/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7347/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/7347/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7347/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' + 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' @@ -40,38 +49,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='14248' + PPID='7347' 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.x7F1VADM/pbuilderrc_Zgb7 --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.x7F1VADM/b1 --logfile b1/build.log rdp-readseq_2.0.2-9.dsc' + 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.x7F1VADM/pbuilderrc_N0Az --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.x7F1VADM/b2 --logfile b2/build.log --extrapackages usrmerge rdp-readseq_2.0.2-9.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink13-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 13 04:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14248/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 11 00:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/7347/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -400,7 +409,7 @@ Get: 271 http://deb.debian.org/debian bookworm/main arm64 libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 272 http://deb.debian.org/debian bookworm/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 273 http://deb.debian.org/debian bookworm/main arm64 libjaxb-java all 2.3.0.1-10.1 [1973 kB] -Fetched 382 MB in 52s (7368 kB/s) +Fetched 382 MB in 1min 21s (4701 kB/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 ... 19616 files and directories currently installed.) @@ -1692,8 +1701,17 @@ 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/rdp-readseq-2.0.2/ && 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 > ../rdp-readseq_2.0.2-9_source.changes +I: user script /srv/workspace/pbuilder/7347/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/7347/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/rdp-readseq-2.0.2/ && 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 > ../rdp-readseq_2.0.2-9_source.changes dpkg-buildpackage: info: source package rdp-readseq dpkg-buildpackage: info: source version 2.0.2-9 dpkg-buildpackage: info: source distribution unstable @@ -1703,16 +1721,16 @@ debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt binnengegaan rm -rf lib build *.jar junit-tmp.xml TEST-*.xml (test -e test && find test -name '*.class' -delete) || true -make[1]: Leaving directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt verlaten jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt binnengegaan dh_clean rm -f debian/*.log -make[1]: Leaving directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt verlaten debian/rules binary dh binary --with javahelper dh_update_autotools_config @@ -1720,7 +1738,7 @@ dh_auto_configure jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt binnengegaan jh_build --javacopts="-encoding UTF8" rdp-readseq.jar src warning: [options] bootstrap class path not set in conjunction with -source 7 warning: [options] source value 7 is obsolete and will be removed in a future release @@ -1769,9 +1787,9 @@ ^ 9 warnings cd src ; jar uf ../rdp-readseq.jar data -make[1]: Leaving directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/rdp-readseq-2.0.2' +make[1]: Map '/build/rdp-readseq-2.0.2' wordt binnengegaan cp debian/junit.xml ./junit-tmp.xml ant -f junit-tmp.xml junit Buildfile: /build/rdp-readseq-2.0.2/junit-tmp.xml @@ -1782,45 +1800,45 @@ [javac] Note: /build/rdp-readseq-2.0.2/test/edu/msu/cme/rdp/readseq/utils/gbregion/JoinRegionTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [junit] Running edu.msu.cme.rdp.readseq.IndexedSeqReaderTest - [junit] Indexed 5 sequences in 0 ms - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.452 sec + [junit] Indexed 5 sequences in 1 ms + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.616 sec [junit] Running edu.msu.cme.rdp.readseq.SequenceParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.667 sec [junit] Running edu.msu.cme.rdp.readseq.readers.QSeqReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.777 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.656 sec [junit] Running edu.msu.cme.rdp.readseq.readers.SeqFileReaderTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.892 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.057 sec [junit] Running edu.msu.cme.rdp.readseq.readers.core.FastqCoreTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.673 sec [junit] Running edu.msu.cme.rdp.readseq.utils.BarcodeUtilsTest [junit] Barcode aaa (test2) is a prefix of barcode aaaa (test1) [junit] Barcode for test1 and test2 are both aaaa - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.528 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.601 sec [junit] Running edu.msu.cme.rdp.readseq.utils.ProtTranslTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.687 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.653 sec [junit] Running edu.msu.cme.rdp.readseq.utils.SequenceFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.642 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.728 sec [junit] Running edu.msu.cme.rdp.readseq.utils.SequenceTrimmerTest [junit] ACT-..-- - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.558 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.639 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.ComplementRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.668 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.JoinRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.457 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.715 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.RegionParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.SimpleRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.51 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.783 sec [junit] Running edu.msu.cme.rdp.readseq.utils.kmermatch.NuclSeqMatchTest [junit] findTopKMatch - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.596 sec [junit] Running edu.msu.cme.rdp.readseq.utils.kmermatch.ProteinSeqMatchTest [junit] findTopKMatch - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.207 sec BUILD SUCCESSFUL -Total time: 42 seconds -make[1]: Leaving directory '/build/rdp-readseq-2.0.2' +Total time: 46 seconds +make[1]: Map '/build/rdp-readseq-2.0.2' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rdp-readseq/ @@ -1846,7 +1864,7 @@ dpkg-gencontrol: warning: Depends field of package rdp-readseq: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'rdp-readseq' in '../rdp-readseq_2.0.2-9_all.deb'. +dpkg-deb: pakket 'rdp-readseq' wordt gebouwd in '../rdp-readseq_2.0.2-9_all.deb'. dpkg-genbuildinfo --build=binary -O../rdp-readseq_2.0.2-9_arm64.buildinfo dpkg-genchanges --build=binary -O../rdp-readseq_2.0.2-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1854,12 +1872,14 @@ 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/7347/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7347/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/14248 and its subdirectories -I: Current time: Tue May 14 08:23:49 -12 2024 -I: pbuilder-time-stamp: 1715718229 +I: removing directory /srv/workspace/pbuilder/7347 and its subdirectories +I: Current time: Thu Apr 13 04:05:56 +14 2023 +I: pbuilder-time-stamp: 1681308356