Diff of the two buildlogs: -- --- b1/build.log 2024-04-29 20:17:48.375483874 +0000 +++ b2/build.log 2024-04-29 20:28:45.699477307 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 29 08:09:20 -12 2024 -I: pbuilder-time-stamp: 1714421360 +I: Current time: Tue Apr 30 10:18:01 +14 2024 +I: pbuilder-time-stamp: 1714421881 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/6918/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22968/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 Apr 29 20:18 /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/22968/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22968/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a2fad1d49e87441c995c2dfe6afd3bb0' - 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='6918' - PS1='# ' - PS2='> ' + INVOCATION_ID=3c8c70a57d9a45e0b1bf1603d9ed3a48 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=22968 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.b1H9Jeyc/pbuilderrc_HwKH --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.b1H9Jeyc/b1 --logfile b1/build.log rdp-readseq_2.0.2-9.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.b1H9Jeyc/pbuilderrc_LNHd --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.b1H9Jeyc/b2 --logfile b2/build.log rdp-readseq_2.0.2-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 6.1.0-20-armmp #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 25 07:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6918/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 25 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/22968/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -412,7 +444,7 @@ Get: 283 http://deb.debian.org/debian unstable/main armhf libtxw2-java all 2.3.0.1-10.1 [134 kB] Get: 284 http://deb.debian.org/debian unstable/main armhf libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 285 http://deb.debian.org/debian unstable/main armhf libjaxb-java all 2.3.0.1-10.1 [1973 kB] -Fetched 220 MB in 22s (10.0 MB/s) +Fetched 220 MB in 9s (23.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:armhf. (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 ... 19440 files and directories currently installed.) @@ -1341,8 +1373,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 29 20:13:09 UTC 2024. -Universal Time is now: Mon Apr 29 20:13:09 UTC 2024. +Local time is now: Mon Apr 29 20:24:45 UTC 2024. +Universal Time is now: Mon Apr 29 20:24:45 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1773,7 +1805,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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/22968/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/22968/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -1806,15 +1842,15 @@ warning: [options] source value 7 is obsolete and will be removed in a future release warning: [options] target value 7 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. -src/edu/msu/cme/rdp/readseq/utils/ProteinUtils.java:105: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal - currTable = new Integer(m.group(1)); - ^ src/edu/msu/cme/rdp/readseq/utils/gbregion/RegionParser.java:178: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rangeStart = new Integer(buf.toString()); ^ src/edu/msu/cme/rdp/readseq/utils/gbregion/RegionParser.java:211: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rangeEnd = new Integer(buf.toString()); ^ +src/edu/msu/cme/rdp/readseq/utils/ProteinUtils.java:105: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal + currTable = new Integer(m.group(1)); + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. @@ -1862,44 +1898,44 @@ [javac] Note: /build/reproducible-path/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 3 ms - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.101 sec + [junit] Indexed 5 sequences in 2 ms + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.842 sec [junit] Running edu.msu.cme.rdp.readseq.SequenceParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.105 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 sec [junit] Running edu.msu.cme.rdp.readseq.readers.QSeqReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.265 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.627 sec [junit] Running edu.msu.cme.rdp.readseq.readers.SeqFileReaderTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.715 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 sec [junit] Running edu.msu.cme.rdp.readseq.readers.core.FastqCoreTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.177 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.618 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: 1.015 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.667 sec [junit] Running edu.msu.cme.rdp.readseq.utils.ProtTranslTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.471 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 sec [junit] Running edu.msu.cme.rdp.readseq.utils.SequenceFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.137 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.762 sec [junit] Running edu.msu.cme.rdp.readseq.utils.SequenceTrimmerTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.099 sec [junit] ACT-..-- + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.ComplementRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.075 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.725 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.JoinRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.123 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.185 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.RegionParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.054 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 sec [junit] Running edu.msu.cme.rdp.readseq.utils.gbregion.SimpleRegionTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.114 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.898 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: 1.024 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.472 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: 1.458 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.741 sec BUILD SUCCESSFUL -Total time: 1 minute 17 seconds +Total time: 44 seconds make[1]: Leaving directory '/build/reproducible-path/rdp-readseq-2.0.2' create-stamp debian/debhelper-build-stamp dh_prep @@ -1934,12 +1970,14 @@ 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/22968/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22968/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/6918 and its subdirectories -I: Current time: Mon Apr 29 08:17:43 -12 2024 -I: pbuilder-time-stamp: 1714421863 +I: removing directory /srv/workspace/pbuilder/22968 and its subdirectories +I: Current time: Tue Apr 30 10:28:41 +14 2024 +I: pbuilder-time-stamp: 1714422521