Diff of the two buildlogs: -- --- b1/build.log 2024-10-24 06:16:48.111585269 +0000 +++ b2/build.log 2024-10-24 06:19:27.597897090 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 23 18:15:41 -12 2024 -I: pbuilder-time-stamp: 1729750541 +I: Current time: Thu Nov 27 02:39:51 +14 2025 +I: pbuilder-time-stamp: 1764160791 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2647906/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1662885/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Nov 26 12:39 /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/1662885/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1662885/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='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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='803ba677907744f7bf0c49d1f348b29a' - 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='2647906' - PS1='# ' - PS2='> ' + INVOCATION_ID=cddda43e04184f8499e32c0eea7877fc + 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=1662885 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.vsNNLo7R/pbuilderrc_CTvX --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vsNNLo7R/b1 --logfile b1/build.log iva_1.0.11+ds-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.vsNNLo7R/pbuilderrc_S4Z6 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vsNNLo7R/b2 --logfile b2/build.log iva_1.0.11+ds-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2647906/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1662885/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -275,7 +307,7 @@ Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13 [105 kB] -Fetched 189 MB in 1s (184 MB/s) +Fetched 189 MB in 2s (119 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 21997 files and directories currently installed.) @@ -708,8 +740,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Oct 24 06:16:08 UTC 2024. -Universal Time is now: Thu Oct 24 06:16:08 UTC 2024. +Local time is now: Wed Nov 26 12:40:49 UTC 2025. +Universal Time is now: Wed Nov 26 12:40:49 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libio-string-perl (1.08-4) ... @@ -1010,7 +1042,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/iva-1.0.11+ds/ && 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 > ../iva_1.0.11+ds-5_source.changes +I: user script /srv/workspace/pbuilder/1662885/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1662885/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/iva-1.0.11+ds/ && 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 > ../iva_1.0.11+ds-5_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable @@ -1055,15 +1091,15 @@ chmod a+x scripts/* javac -verbose /build/reproducible-path/iva-1.0.11+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.java]] -[parsing completed 79ms] +[parsing completed 134ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] -[parsing completed 7ms] +[parsing completed 17ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] -[parsing completed 4ms] +[parsing completed 2ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] -[parsing completed 11ms] +[parsing completed 22ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] -[parsing completed 14ms] +[parsing completed 37ms] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/java.xml/module-info.class] @@ -1247,7 +1283,7 @@ [checking getScaffoldStats] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.class] -[total 993ms] +[total 2752ms] Note: /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. dh_auto_build -- @@ -1510,7 +1546,7 @@ s = re.sub('\^.', '', s) ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 - /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'} + /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'} __version__ = Distribution().from_name('pyfastaq').version iva/external_progs.py:33 @@ -1546,7 +1582,7 @@ class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -======================= 160 passed, 10 warnings in 5.24s ======================= +====================== 160 passed, 10 warnings in 12.20s ======================= make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1744,12 +1780,14 @@ 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/1662885/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1662885/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/2647906 and its subdirectories -I: Current time: Wed Oct 23 18:16:46 -12 2024 -I: pbuilder-time-stamp: 1729750607 +I: removing directory /srv/workspace/pbuilder/1662885 and its subdirectories +I: Current time: Thu Nov 27 02:42:25 +14 2025 +I: pbuilder-time-stamp: 1764160945