Diff of the two buildlogs: -- --- b1/build.log 2024-05-01 23:15:20.213295738 +0000 +++ b2/build.log 2024-05-01 23:18:45.400555132 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 3 17:36:34 -12 2025 -I: pbuilder-time-stamp: 1749015394 +I: Current time: Thu May 2 13:15:24 +14 2024 +I: pbuilder-time-stamp: 1714605324 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying libdata_libpbihdf.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2641766/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4089285/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 May 1 23:15 /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/4089285/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4089285/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='97fb3cfb25e246e5b5b148583a565d99' - 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='2641766' - PS1='# ' - PS2='> ' + INVOCATION_ID=b58fa14556c14670b47ae3a6d84be5d6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=4089285 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.jR9na3dn/pbuilderrc_q0AY --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.jR9na3dn/b1 --logfile b1/build.log pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.jR9na3dn/pbuilderrc_4z4V --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.jR9na3dn/b2 --logfile b2/build.log pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 3 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2641766/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 1 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4089285/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +260,7 @@ Get: 94 http://deb.debian.org/debian unstable/main amd64 libpbihdf-dev amd64 5.3.5+dfsg-6+b3 [47.2 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libpbseq-dev amd64 5.3.5+dfsg-6+b3 [5032 B] Get: 96 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b1 [3360 kB] -Fetched 60.2 MB in 4s (14.3 MB/s) +Fetched 60.2 MB in 5s (12.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19694 files and directories currently installed.) @@ -557,8 +589,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jun 4 05:37:09 UTC 2025. -Universal Time is now: Wed Jun 4 05:37:09 UTC 2025. +Local time is now: Wed May 1 23:16:49 UTC 2024. +Universal Time is now: Wed May 1 23:16:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -640,7 +672,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+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 > ../pbdagcon_0.3+git20180411.c14c422+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/4089285/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4089285/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+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 > ../pbdagcon_0.3+git20180411.c14c422+dfsg-8_source.changes dpkg-buildpackage: info: source package pbdagcon dpkg-buildpackage: info: source version 0.3+git20180411.c14c422+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -650,7 +686,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp clean make[2]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' @@ -699,7 +735,7 @@ """ make[1]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j20 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp make[2]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' @@ -728,7 +764,7 @@ make[2]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make[1]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_auto_test - make -j42 check + make -j20 check make[1]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp make[2]: Entering directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' @@ -764,7 +800,9 @@ g++ -o test-alignment gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlignmentTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o test-simple_aligner gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o SimpleAlignerTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o test-target_hit gtest-all.o gtest_main.o DB.o QV.o align.o Alignment.o DazAlnProvider.o TargetHitTest.o -Wl,-z,relro -L /usr/lib/x86_64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread +LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-target_hit --gtest_output=xml:xml/test-target_hit.xml +LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 3 tests from 1 test suite. [----------] Global test environment set-up. @@ -778,7 +816,6 @@ [----------] 3 tests from TargetHitTest (0 ms total) [----------] Global test environment tear-down -LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml [==========] 3 tests from 1 test suite ran. (0 ms total) [ PASSED ] 3 tests. Running main() from /usr/src/googletest/googletest/src/gtest_main.cc @@ -786,16 +823,32 @@ [----------] Global test environment set-up. [----------] 2 tests from AlnGraphBoostTest [ RUN ] AlnGraphBoostTest.RawConsensus +Running main() from /usr/src/googletest/googletest/src/gtest_main.cc +[==========] Running 4 tests from 1 test suite. +[----------] Global test environment set-up. +[----------] 4 tests from Alignment +[ RUN ] Alignment.Normalize +[ OK ] Alignment.Normalize (0 ms) [ OK ] AlnGraphBoostTest.RawConsensus (0 ms) [ RUN ] AlnGraphBoostTest.DanglingNodes [ OK ] AlnGraphBoostTest.DanglingNodes (0 ms) [----------] 2 tests from AlnGraphBoostTest (0 ms total) [----------] Global test environment tear-down +[ RUN ] Alignment.ParseBasic +[ OK ] Alignment.ParseBasic (0 ms) +[ RUN ] Alignment.ParseQuery +[ OK ] Alignment.ParseQuery (0 ms) +[ RUN ] Alignment.Trim +[ OK ] Alignment.Trim (0 ms) [==========] 2 tests from 1 test suite ran. (0 ms total) [ PASSED ] 2 tests. +[----------] 4 tests from Alignment (0 ms total) + +[----------] Global test environment tear-down +[==========] 4 tests from 1 test suite ran. (0 ms total) +[ PASSED ] 4 tests. LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml -LD_LIBRARY_PATH=::::/usr/lib/x86_64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. @@ -807,23 +860,6 @@ [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (0 ms total) [ PASSED ] 1 test. -Running main() from /usr/src/googletest/googletest/src/gtest_main.cc -[==========] Running 4 tests from 1 test suite. -[----------] Global test environment set-up. -[----------] 4 tests from Alignment -[ RUN ] Alignment.Normalize -[ OK ] Alignment.Normalize (0 ms) -[ RUN ] Alignment.ParseBasic -[ OK ] Alignment.ParseBasic (0 ms) -[ RUN ] Alignment.ParseQuery -[ OK ] Alignment.ParseQuery (0 ms) -[ RUN ] Alignment.Trim -[ OK ] Alignment.Trim (0 ms) -[----------] 4 tests from Alignment (0 ms total) - -[----------] Global test environment tear-down -[==========] 4 tests from 1 test suite ran. (0 ms total) -[ PASSED ] 4 tests. make[2]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp' make[1]: Leaving directory '/build/reproducible-path/pbdagcon-0.3+git20180411.c14c422+dfsg' create-stamp debian/debhelper-build-stamp @@ -848,8 +884,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.deb'. dpkg-deb: building package 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_amd64.deb'. +dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -857,12 +893,14 @@ 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/4089285/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4089285/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/2641766 and its subdirectories -I: Current time: Tue Jun 3 17:38:17 -12 2025 -I: pbuilder-time-stamp: 1749015497 +I: removing directory /srv/workspace/pbuilder/4089285 and its subdirectories +I: Current time: Thu May 2 13:18:44 +14 2024 +I: pbuilder-time-stamp: 1714605524