Diff of the two buildlogs: -- --- b1/build.log 2025-03-09 06:56:39.948106653 +0000 +++ b2/build.log 2025-03-09 06:59:15.905061716 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 11 01:18:15 -12 2026 -I: pbuilder-time-stamp: 1775913495 +I: Current time: Sun Mar 9 20:56:43 +14 2025 +I: pbuilder-time-stamp: 1741503403 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying missing_obj_files.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1060539/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2549414/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Mar 9 06:56 /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/2549414/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2549414/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(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='71e710229b0b4cf1b2dc917c3a734dbe' - 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='1060539' - PS1='# ' - PS2='> ' + INVOCATION_ID=1997298294fd43f994760637af3e06ae + 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=2549414 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.EhwtGSyh/pbuilderrc_1jNV --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.EhwtGSyh/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-3.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.EhwtGSyh/pbuilderrc_WCEI --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.EhwtGSyh/b2 --logfile b2/build.log gatk-bwamem_1.0.4+dfsg2-3.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 codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1060539/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2549414/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -296,7 +328,7 @@ Get: 166 http://deb.debian.org/debian trixie/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-2 [467 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 232 MB in 1s (282 MB/s) +Fetched 232 MB in 1s (199 MB/s) Preconfiguring packages ... 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 ... 19914 files and directories currently installed.) @@ -1184,7 +1216,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/ && 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-bwamem_1.0.4+dfsg2-3_source.changes +I: user script /srv/workspace/pbuilder/2549414/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2549414/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/ && 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-bwamem_1.0.4+dfsg2-3_source.changes dpkg-buildpackage: info: source package gatk-bwamem dpkg-buildpackage: info: source version 1.0.4+dfsg2-3 dpkg-buildpackage: info: source distribution unstable @@ -1243,18 +1279,18 @@ 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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 1.031 secs. -The client will now receive all logging from the daemon (pid: 1072739). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-1072739.out.log +An attempt to start the daemon took 2.451 secs. +The client will now receive all logging from the daemon (pid: 2571207). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-2571207.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. Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e4e3576 -Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e4e3576 -Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@16f4168d +Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e457d97 +Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e457d97 +Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@30196629 Starting Build Compiling initialization script '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@61cf78fc +Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3d77c186 Compiling initialization script '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using BuildScriptTransformer. @@ -1271,23 +1307,23 @@ 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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@631ef84e +Creating new cache for annotation-processors, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7562faee Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@16f4168d -Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@5c029972 -Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@f2308a7 +Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@30196629 +Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@6d335cad +Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4be4da3c :compileJava (Thread[#50,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.008 secs. -Up-to-date check for task ':compileJava' took 0.037 secs. It is not up-to-date because: +Putting task artifact state for task ':compileJava' into context took 0.013 secs. +Up-to-date check for task ':compileJava' took 0.079 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[#50,Task worker for ':',5,main]) completed. Took 1.11 secs. +:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 2.266 secs. :buildBwaLib (Thread[#50,Task worker for ':',5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. -Up-to-date check for task ':buildBwaLib' took 0.001 secs. It is not up-to-date because: +Up-to-date check for task ':buildBwaLib' took 0.008 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-21-openjdk-arm64 -> /usr/lib/jvm/java-21-openjdk-arm64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c Command: make @@ -1340,7 +1376,7 @@ make[2]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c/bwaComponent' gcc -Wl,-z,relro -Wl,-z,now -ggdb -dynamiclib -shared -o libbwa.so org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o jnibwa.o bwaComponent/libbwa.a -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c' -:buildBwaLib (Thread[#50,Task worker for ':',5,main]) completed. Took 9.038 secs. +:buildBwaLib (Thread[#50,Task worker for ':',5,main]) completed. Took 10.452 secs. :processResources (Thread[#50,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. @@ -1351,22 +1387,22 @@ :classes (Thread[#50,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.001 secs. +:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. :debianMavenPom (Thread[#50,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 0.001 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.005 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/debian/gatk-bwamem-jni.pom -:debianMavenPom (Thread[#50,Task worker for ':',5,main]) completed. Took 0.156 secs. +:debianMavenPom (Thread[#50,Task worker for ':',5,main]) completed. Took 0.242 secs. :jar (Thread[#50,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 0.008 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.026 secs. It is not up-to-date because: No history is available. -:jar (Thread[#50,Task worker for ':',5,main]) completed. Took 0.06 secs. +:jar (Thread[#50,Task worker for ':',5,main]) completed. Took 0.122 secs. -BUILD SUCCESSFUL in 15s +BUILD SUCCESSFUL in 24s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' @@ -1382,17 +1418,17 @@ 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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 1.066 secs. -The client will now receive all logging from the daemon (pid: 1075214). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-1075214.out.log +An attempt to start the daemon took 1.935 secs. +The client will now receive all logging from the daemon (pid: 2577670). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-2577670.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. Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d8909de -Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d8909de -Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@31f46324 +Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b7aa8ca +Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@3b7aa8ca +Creating new cache for fileHashes, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@175d64d7 Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@744be030 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@8f4268a Settings evaluated using settings file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build.gradle'. Included projects: [root project 'gatk-bwamem-jni'] @@ -1404,64 +1440,64 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : -Creating new cache for annotation-processors, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@51f65a9b +Creating new cache for annotation-processors, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4c7163f2 Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@31f46324 -Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@49657f2c -Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@3af3be88 -:compileJava (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@175d64d7 +Creating new cache for taskHistory, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@34702b61 +Creating new cache for outputFiles, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@19828e19 +:compileJava (Thread[#50,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.004 secs. -Skipping task ':compileJava' as it is up-to-date (took 0.06 secs). +Putting task artifact state for task ':compileJava' into context took 0.005 secs. +Skipping task ':compileJava' as it is up-to-date (took 0.093 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.134 secs. -:buildBwaLib (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 0.309 secs. +:buildBwaLib (Thread[#50,Task worker for ':',5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. -Skipping task ':buildBwaLib' as it is up-to-date (took 0.003 secs). +Skipping task ':buildBwaLib' as it is up-to-date (took 0.002 secs). :buildBwaLib UP-TO-DATE -:buildBwaLib (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.01 secs. -:processResources (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:buildBwaLib (Thread[#50,Task worker for ':',5,main]) completed. Took 0.011 secs. +:processResources (Thread[#50,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.004 secs. -:classes (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:processResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.008 secs. +:classes (Thread[#50,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.001 secs. -:compileTestJava (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[#50,Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@431a0461 +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@57add72f Loading the Maven rules... Replacing org.testng:testng:jar:6.9.6 -> org.testng:testng:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian -Up-to-date check for task ':compileTestJava' took 0.498 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.909 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. -:compileTestJava (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 1.516 secs. -:processTestResources (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:compileTestJava (Thread[#50,Task worker for ':',5,main]) completed. Took 2.771 secs. +:processTestResources (Thread[#50,Task worker for ':',5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.015 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.032 secs. -:testClasses (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:processTestResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.086 secs. +:testClasses (Thread[#50,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 0.0 secs. -:test (Thread[#54,Task worker for ':' Thread 5,5,main]) started. +:testClasses (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. +:test (Thread[#50,Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.06 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.184 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2 Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath68950270735512173txt -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' +Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2 Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4328815802628727407txt -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. [M::bwa_idx_load_from_disk] read 0 ALT contigs @@ -1471,12 +1507,12 @@ [M::mem_pestat] skip orientation RR as there are not enough pairs Gradle Test Executor 1 finished executing tests. Results: SUCCESS (7 tests, 7 successes, 0 failures, 0 skipped) -Finished generating test XML results (0.017 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test +Finished generating test XML results (0.024 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... -Finished generating test html results (0.032 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test -:test (Thread[#54,Task worker for ':' Thread 5,5,main]) completed. Took 1.013 secs. +Finished generating test html results (0.052 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test +:test (Thread[#50,Task worker for ':',5,main]) completed. Took 2.143 secs. -BUILD SUCCESSFUL in 8s +BUILD SUCCESSFUL in 14s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' create-stamp debian/debhelper-build-stamp @@ -1505,9 +1541,9 @@ dpkg-gencontrol: warning: Depends field of package libgatk-bwamem-java: substitution variable ${java:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_arm64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_arm64.deb'. +dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_arm64.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1515,12 +1551,14 @@ 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/2549414/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2549414/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/1060539 and its subdirectories -I: Current time: Sat Apr 11 01:19:37 -12 2026 -I: pbuilder-time-stamp: 1775913577 +I: removing directory /srv/workspace/pbuilder/2549414 and its subdirectories +I: Current time: Sun Mar 9 20:59:14 +14 2025 +I: pbuilder-time-stamp: 1741503554