Diff of the two buildlogs: -- --- b1/build.log 2023-05-02 11:58:08.309082364 +0000 +++ b2/build.log 2023-05-02 12:01:27.932317186 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 1 23:54:22 -12 2023 -I: pbuilder-time-stamp: 1683028462 +I: Current time: Tue Jun 4 08:21:12 +14 2024 +I: pbuilder-time-stamp: 1717438872 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 [./gatk-native-bindings_1.0.0+dfsg.orig.tar.xz] I: copying [./gatk-native-bindings_1.0.0+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 27 21:42:37 2022 -12 +gpgv: Signature made Wed Dec 28 23:42:37 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gatk-native-bindings_1.0.0+dfsg-2.dsc: no acceptable signature found @@ -27,52 +27,84 @@ dpkg-source: info: applying fix_build_debian.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16774/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25065/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-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 4 08:21 /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/25065/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25065/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='16774' - 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=25065 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.ImBhbnui/pbuilderrc_bmCB --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.ImBhbnui/b1 --logfile b1/build.log gatk-native-bindings_1.0.0+dfsg-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.ImBhbnui/pbuilderrc_il8Z --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.ImBhbnui/b2 --logfile b2/build.log --extrapackages usrmerge gatk-native-bindings_1.0.0+dfsg-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 codethink10-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 1 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/16774/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 3 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/25065/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -373,7 +405,7 @@ Get: 253 http://deb.debian.org/debian bookworm/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 254 http://deb.debian.org/debian bookworm/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 255 http://deb.debian.org/debian bookworm/main arm64 javahelper all 0.78 [97.2 kB] -Fetched 401 MB in 36s (11.2 MB/s) +Fetched 401 MB in 32s (12.4 MB/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.) @@ -1596,8 +1628,17 @@ 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/gatk-native-bindings-1.0.0+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 > ../gatk-native-bindings_1.0.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/25065/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/25065/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/gatk-native-bindings-1.0.0+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 > ../gatk-native-bindings_1.0.0+dfsg-2_source.changes dpkg-buildpackage: info: source package gatk-native-bindings dpkg-buildpackage: info: source version 1.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1653,8 +1694,8 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 5.193 secs. -The client will now receive all logging from the daemon (pid: 5964). The daemon log file: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1/daemon-5964.out.log +An attempt to start the daemon took 4.638 secs. +The client will now receive all logging from the daemon (pid: 13966). The daemon log file: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1/daemon-13966.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. @@ -1684,45 +1725,45 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : -Creating new cache for annotation-processors, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2d70417 +Creating new cache for annotation-processors, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@3ce9b109 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7176ad80 -Creating new cache for taskHistory, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@22d9dac4 -Creating new cache for outputFiles, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@29214594 +Creating new cache for taskHistory, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4edd31d2 +Creating new cache for outputFiles, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@55ef7f40 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.12 secs. -Up-to-date check for task ':compileJava' took 0.171 secs. It is not up-to-date because: +Putting task artifact state for task ':compileJava' into context took 0.018 secs. +Up-to-date check for task ':compileJava' took 0.254 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 4.993 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 4.327 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/gatk-native-bindings-1.0.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.021 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.02 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.003 secs. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.007 secs. :debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.004 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.007 secs. It is not up-to-date because: No history is available. Generating pom file /build/gatk-native-bindings-1.0.0+dfsg/build/debian/gatk-native-bindings.pom -:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.442 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.438 secs. :jar (Thread[Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.047 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.043 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':',5,main]) completed. Took 0.27 secs. +:jar (Thread[Task worker for ':',5,main]) completed. Took 0.22 secs. -BUILD SUCCESSFUL in 37s +BUILD SUCCESSFUL in 30s 3 actionable tasks: 3 executed make[1]: Leaving directory '/build/gatk-native-bindings-1.0.0+dfsg' jh_build -O--buildsystem=gradle @@ -1743,8 +1784,8 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 5.051 secs. -The client will now receive all logging from the daemon (pid: 1303). The daemon log file: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1/daemon-1303.out.log +An attempt to start the daemon took 4.609 secs. +The client will now receive all logging from the daemon (pid: 15150). The daemon log file: /build/gatk-native-bindings-1.0.0+dfsg/.gradle/daemon/4.4.1/daemon-15150.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. @@ -1775,29 +1816,29 @@ Creating new cache for outputFiles, path /build/gatk-native-bindings-1.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a39ff93 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.057 secs. -Skipping task ':compileJava' as it is up-to-date (took 0.314 secs). +Putting task artifact state for task ':compileJava' into context took 0.037 secs. +Skipping task ':compileJava' as it is up-to-date (took 0.297 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.574 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.525 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources -Putting task artifact state for task ':processResources' into context took 0.009 secs. +Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/gatk-native-bindings-1.0.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.04 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.033 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.002 secs. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.01 secs. :compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. file or directory '/build/gatk-native-bindings-1.0.0+dfsg/src/test/java', not found Skipping task ':compileTestJava' as it has no source files and no previous output files. :compileTestJava NO-SOURCE -:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 0.038 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 0.027 secs. :processTestResources (Thread[Task worker for ':',5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. @@ -1809,15 +1850,15 @@ :testClasses Skipping task ':testClasses' as it has no actions. :testClasses UP-TO-DATE -:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.009 secs. +:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.016 secs. :test (Thread[Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Skipping task ':test' as it has no source files and no previous output files. :test NO-SOURCE -:test (Thread[Task worker for ':',5,main]) completed. Took 0.021 secs. +:test (Thread[Task worker for ':',5,main]) completed. Took 0.03 secs. -BUILD SUCCESSFUL in 28s +BUILD SUCCESSFUL in 25s 1 actionable task: 1 up-to-date make[1]: Leaving directory '/build/gatk-native-bindings-1.0.0+dfsg' create-stamp debian/debhelper-build-stamp @@ -1934,12 +1975,14 @@ 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/25065/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25065/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/16774 and its subdirectories -I: Current time: Mon May 1 23:58:07 -12 2023 -I: pbuilder-time-stamp: 1683028687 +I: removing directory /srv/workspace/pbuilder/25065 and its subdirectories +I: Current time: Tue Jun 4 08:24:26 +14 2024 +I: pbuilder-time-stamp: 1717439066