Diff of the two buildlogs: -- --- b1/build.log 2023-06-09 10:21:38.233470471 +0000 +++ b2/build.log 2023-06-09 10:28:54.294394196 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 11 04:33:59 -12 2024 -I: pbuilder-time-stamp: 1720715639 +I: Current time: Sat Jun 10 00:21:41 +14 2023 +I: pbuilder-time-stamp: 1686306101 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 [./adapterremoval_2.3.3.orig.tar.gz] I: copying [./adapterremoval_2.3.3-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Nov 25 18:53:14 2022 -12 +gpgv: Signature made Sat Nov 26 20:53:14 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -26,52 +26,84 @@ dpkg-source: info: unpacking adapterremoval_2.3.3-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30423/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17701/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 10 00:21 /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/17701/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17701/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='30423' - 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=17701 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.BvKtXIK7/pbuilderrc_fPiX --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.BvKtXIK7/b1 --logfile b1/build.log adapterremoval_2.3.3-2.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.BvKtXIK7/pbuilderrc_7ryW --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.BvKtXIK7/b2 --logfile b2/build.log --extrapackages usrmerge adapterremoval_2.3.3-2.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 codethink15-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 9 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30423/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 00:26 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/17701/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -150,7 +182,7 @@ Get: 33 http://deb.debian.org/debian bookworm/main arm64 libgtest-dev arm64 1.12.1-0.2 [231 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 markdown all 1.0.1-12 [17.7 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 20.0 MB in 1s (37.9 MB/s) +Fetched 20.0 MB in 0s (45.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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.) @@ -304,8 +336,17 @@ 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/adapterremoval-2.3.3/ && 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 > ../adapterremoval_2.3.3-2_source.changes +I: user script /srv/workspace/pbuilder/17701/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/17701/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/adapterremoval-2.3.3/ && 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 > ../adapterremoval_2.3.3-2_source.changes dpkg-buildpackage: info: source package adapterremoval dpkg-buildpackage: info: source version 2.3.3-2 dpkg-buildpackage: info: source distribution unstable @@ -319,9 +360,9 @@ make[1]: Entering directory '/build/adapterremoval-2.3.3' Building AdapterRemoval with coverage instrumentation: no Building AdapterRemoval with debug information: no -Cleaning tests ... -Cleaning documentation ... -Cleaning ... +\033[0;32mCleaning tests ...\033[0m +\033[0;32mCleaning documentation ...\033[0m +\033[0;32mCleaning ...\033[0m make[1]: Leaving directory '/build/adapterremoval-2.3.3' dh_clean debian/rules binary @@ -336,33 +377,33 @@ make[2]: Entering directory '/build/adapterremoval-2.3.3' Building AdapterRemoval with coverage instrumentation: no Building AdapterRemoval with debug information: no -Building build/main/adapterset.o from src/adapterset.cpp -Building build/main/alignment.o from src/alignment.cpp -Building build/main/alignment_tables.o from src/alignment_tables.cpp -Building build/main/argparse.o from src/argparse.cpp -Building build/main/barcode_table.o from src/barcode_table.cpp -Building build/main/debug.o from src/debug.cpp -Building build/main/demultiplex.o from src/demultiplex.cpp -Building build/main/fastq.o from src/fastq.cpp +\033[0;36mBuilding build/main/adapterset.o from src/adapterset.cpp\033[0m +\033[0;36mBuilding build/main/alignment.o from src/alignment.cpp\033[0m +\033[0;36mBuilding build/main/alignment_tables.o from src/alignment_tables.cpp\033[0m +\033[0;36mBuilding build/main/argparse.o from src/argparse.cpp\033[0m +\033[0;36mBuilding build/main/barcode_table.o from src/barcode_table.cpp\033[0m +\033[0;36mBuilding build/main/debug.o from src/debug.cpp\033[0m +\033[0;36mBuilding build/main/demultiplex.o from src/demultiplex.cpp\033[0m +\033[0;36mBuilding build/main/fastq.o from src/fastq.cpp\033[0m +\033[0;36mBuilding build/main/fastq_enc.o from src/fastq_enc.cpp\033[0m src/alignment.cpp:66:2: warning: #warning SEE optimizations disabled! [-Wcpp] 66 | #warning SEE optimizations disabled! | ^~~~~~~ -Building build/main/fastq_enc.o from src/fastq_enc.cpp -Building build/main/fastq_io.o from src/fastq_io.cpp -Building build/main/linereader.o from src/linereader.cpp -Building build/main/linereader_joined.o from src/linereader_joined.cpp -Building build/main/main_adapter_id.o from src/main_adapter_id.cpp -Building build/main/main_adapter_rm.o from src/main_adapter_rm.cpp -Building build/main/main_demultiplex.o from src/main_demultiplex.cpp -Building build/main/managed_writer.o from src/managed_writer.cpp -Building build/main/scheduler.o from src/scheduler.cpp -Building build/main/strutils.o from src/strutils.cpp -Building build/main/threads.o from src/threads.cpp -Building build/main/timer.o from src/timer.cpp -Building build/main/trimmed_reads.o from src/trimmed_reads.cpp -Building build/main/userconfig.o from src/userconfig.cpp -Building build/main/main.o from src/main.cpp -Linking executable build/AdapterRemoval +\033[0;36mBuilding build/main/fastq_io.o from src/fastq_io.cpp\033[0m +\033[0;36mBuilding build/main/linereader.o from src/linereader.cpp\033[0m +\033[0;36mBuilding build/main/linereader_joined.o from src/linereader_joined.cpp\033[0m +\033[0;36mBuilding build/main/main_adapter_id.o from src/main_adapter_id.cpp\033[0m +\033[0;36mBuilding build/main/main_adapter_rm.o from src/main_adapter_rm.cpp\033[0m +\033[0;36mBuilding build/main/main_demultiplex.o from src/main_demultiplex.cpp\033[0m +\033[0;36mBuilding build/main/managed_writer.o from src/managed_writer.cpp\033[0m +\033[0;36mBuilding build/main/scheduler.o from src/scheduler.cpp\033[0m +\033[0;36mBuilding build/main/strutils.o from src/strutils.cpp\033[0m +\033[0;36mBuilding build/main/threads.o from src/threads.cpp\033[0m +\033[0;36mBuilding build/main/timer.o from src/timer.cpp\033[0m +\033[0;36mBuilding build/main/trimmed_reads.o from src/trimmed_reads.cpp\033[0m +\033[0;36mBuilding build/main/userconfig.o from src/userconfig.cpp\033[0m +\033[0;36mBuilding build/main/main.o from src/main.cpp\033[0m +\033[0;32mLinking executable build/AdapterRemoval\033[0m make[2]: Leaving directory '/build/adapterremoval-2.3.3' markdown README.md > README.html make[1]: Leaving directory '/build/adapterremoval-2.3.3' @@ -373,26 +414,26 @@ make[2]: Entering directory '/build/adapterremoval-2.3.3' Building AdapterRemoval with coverage instrumentation: no Building AdapterRemoval with debug information: no -Building build/tests/main_test.o from tests/unit/main_test.cpp -Building build/tests/debug.o from src/debug.cpp -Building build/tests/alignment.o from src/alignment.cpp +\033[0;36mBuilding build/tests/main_test.o from tests/unit/main_test.cpp\033[0m +\033[0;36mBuilding build/tests/debug.o from src/debug.cpp\033[0m +\033[0;36mBuilding build/tests/alignment.o from src/alignment.cpp\033[0m src/alignment.cpp:66:2: warning: #warning SEE optimizations disabled! [-Wcpp] 66 | #warning SEE optimizations disabled! | ^~~~~~~ -Building build/tests/alignment_tables.o from src/alignment_tables.cpp -Building build/tests/alignment_test.o from tests/unit/alignment_test.cpp -Building build/tests/argparse.o from src/argparse.cpp -Building build/tests/argparse_test.o from tests/unit/argparse_test.cpp -Building build/tests/barcodes_test.o from tests/unit/barcodes_test.cpp -Building build/tests/barcode_table.o from src/barcode_table.cpp -Building build/tests/fastq.o from src/fastq.cpp -Building build/tests/fastq_test.o from tests/unit/fastq_test.cpp -Building build/tests/fastq_enc.o from src/fastq_enc.cpp -Building build/tests/fastq_enc_test.o from tests/unit/fastq_enc_test.cpp -Building build/tests/strutils.o from src/strutils.cpp -Building build/tests/strutils_test.o from tests/unit/strutils_test.cpp -Linking executable build/tests/main -Running unit tests +\033[0;36mBuilding build/tests/alignment_tables.o from src/alignment_tables.cpp\033[0m +\033[0;36mBuilding build/tests/alignment_test.o from tests/unit/alignment_test.cpp\033[0m +\033[0;36mBuilding build/tests/argparse.o from src/argparse.cpp\033[0m +\033[0;36mBuilding build/tests/argparse_test.o from tests/unit/argparse_test.cpp\033[0m +\033[0;36mBuilding build/tests/barcodes_test.o from tests/unit/barcodes_test.cpp\033[0m +\033[0;36mBuilding build/tests/barcode_table.o from src/barcode_table.cpp\033[0m +\033[0;36mBuilding build/tests/fastq.o from src/fastq.cpp\033[0m +\033[0;36mBuilding build/tests/fastq_test.o from tests/unit/fastq_test.cpp\033[0m +\033[0;36mBuilding build/tests/fastq_enc.o from src/fastq_enc.cpp\033[0m +\033[0;36mBuilding build/tests/fastq_enc_test.o from tests/unit/fastq_enc_test.cpp\033[0m +\033[0;36mBuilding build/tests/strutils.o from src/strutils.cpp\033[0m +\033[0;36mBuilding build/tests/strutils_test.o from tests/unit/strutils_test.cpp\033[0m +\033[0;32mLinking executable build/tests/main\033[0m +\033[0;32mRunning unit tests\033[0m =============================================================================== All tests passed (827 assertions in 268 test cases) @@ -401,7 +442,7 @@ make[2]: Entering directory '/build/adapterremoval-2.3.3' Building AdapterRemoval with coverage instrumentation: no Building AdapterRemoval with debug information: no -Cleaning tests ... +\033[0;32mCleaning tests ...\033[0m removed 'build/tests/main' removed 'build/tests/strutils_test.deps' removed 'build/tests/strutils_test.o' @@ -473,9 +514,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'adapterremoval-dbgsym' in '../adapterremoval-dbgsym_2.3.3-2_arm64.deb'. dpkg-deb: building package 'adapterremoval-examples' in '../adapterremoval-examples_2.3.3-2_all.deb'. dpkg-deb: building package 'adapterremoval' in '../adapterremoval_2.3.3-2_arm64.deb'. -dpkg-deb: building package 'adapterremoval-dbgsym' in '../adapterremoval-dbgsym_2.3.3-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../adapterremoval_2.3.3-2_arm64.buildinfo dpkg-genchanges --build=binary -O../adapterremoval_2.3.3-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -483,12 +524,14 @@ 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/17701/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17701/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/30423 and its subdirectories -I: Current time: Thu Jul 11 04:44:28 -12 2024 -I: pbuilder-time-stamp: 1720716268 +I: removing directory /srv/workspace/pbuilder/17701 and its subdirectories +I: Current time: Sat Jun 10 00:28:52 +14 2023 +I: pbuilder-time-stamp: 1686306532