Diff of the two buildlogs: -- --- b1/build.log 2025-01-01 09:32:30.654782512 +0000 +++ b2/build.log 2025-01-01 09:37:26.537205332 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 31 21:27:58 -12 2024 -I: pbuilder-time-stamp: 1735723678 +I: Current time: Wed Jan 1 23:32:41 +14 2025 +I: pbuilder-time-stamp: 1735723961 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/30623/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20685/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +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 Jan 1 09:32 /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/20685/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20685/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7e86103ea37c42928978f2173d73e84f' - 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='30623' - PS1='# ' - PS2='> ' + INVOCATION_ID=93f49d309e9d4eb8b1414b7f48c0dd31 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=20685 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.3OlSVBuc/pbuilderrc_KxlU --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.3OlSVBuc/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-3.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.3OlSVBuc/pbuilderrc_nBKr --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.3OlSVBuc/b2 --logfile b2/build.log gatk-bwamem_1.0.4+dfsg2-3.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64a 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30623/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/20685/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +329,7 @@ Get: 167 http://deb.debian.org/debian unstable/main armhf gradle-debian-helper all 2.4 [24.5 kB] Get: 168 http://deb.debian.org/debian unstable/main armhf libsimde-dev all 0.8.2-2 [467 kB] Get: 169 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] -Fetched 223 MB in 4s (55.1 MB/s) +Fetched 223 MB in 4s (57.7 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 ... 19572 files and directories currently installed.) @@ -1189,7 +1221,11 @@ 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/20685/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/20685/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 @@ -1240,7 +1276,7 @@ dh_auto_build mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=3 jar + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-Debian-1, mixed mode, sharing) @@ -1248,18 +1284,18 @@ 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-armhf/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 3.064 secs. -The client will now receive all logging from the daemon (pid: 4633). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-4633.out.log +An attempt to start the daemon took 3.31 secs. +The client will now receive all logging from the daemon (pid: 30775). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-30775.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 3 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@1419659 -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@1419659 -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@115ec4f +Using 4 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@13c7b76 +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@13c7b76 +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@53d8f2 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@12be14a +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@183c4f 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. @@ -1276,19 +1312,19 @@ 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@574243 +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@1bde86e 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@115ec4f -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@17d5837 -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@116b46f +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@53d8f2 +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@db28db +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@1917711 :compileJava (Thread[#41,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.013 secs. -Up-to-date check for task ':compileJava' took 0.071 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 0.074 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[#41,Task worker for ':',5,main]) completed. Took 3.888 secs. +:compileJava (Thread[#41,Task worker for ':',5,main]) completed. Took 4.228 secs. :buildBwaLib (Thread[#41,Task worker for ':',5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. @@ -1393,14 +1429,14 @@ 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[#41,Task worker for ':',5,main]) completed. Took 27.002 secs. +:buildBwaLib (Thread[#41,Task worker for ':',5,main]) completed. Took 28.39 secs. :processResources (Thread[#41,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[#41,Task worker for ':',5,main]) completed. Took 0.005 secs. +:processResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.007 secs. :classes (Thread[#41,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. @@ -1408,18 +1444,18 @@ :debianMavenPom (Thread[#41,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 0.002 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.003 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[#41,Task worker for ':',5,main]) completed. Took 0.195 secs. +:debianMavenPom (Thread[#41,Task worker for ':',5,main]) completed. Took 0.229 secs. :jar (Thread[#41,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 0.015 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.02 secs. It is not up-to-date because: No history is available. -:jar (Thread[#41,Task worker for ':',5,main]) completed. Took 0.118 secs. +:jar (Thread[#41,Task worker for ':',5,main]) completed. Took 0.144 secs. -BUILD SUCCESSFUL in 48s +BUILD SUCCESSFUL in 52s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' @@ -1427,7 +1463,7 @@ LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$(readlink -f src/main/c)" dh_auto_test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=3 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=4 test openjdk version "21.0.5" 2024-10-15 OpenJDK Runtime Environment (build 21.0.5+11-Debian-1) OpenJDK Server VM (build 21.0.5+11-Debian-1, mixed mode, sharing) @@ -1435,17 +1471,17 @@ 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-armhf/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 3.055 secs. -The client will now receive all logging from the daemon (pid: 5011). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-5011.out.log +An attempt to start the daemon took 3.284 secs. +The client will now receive all logging from the daemon (pid: 32522). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-32522.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 3 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@13c7b76 -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@13c7b76 -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@53d8f2 +Using 4 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@1be5d8c +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@1be5d8c +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@7d9719 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@192e98 +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@1debac7 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'] @@ -1457,64 +1493,64 @@ 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@1ba4845 +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@1afeb95 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@53d8f2 -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@652bc5 -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@5781a2 +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@7d9719 +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@189130e +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@1c4f308 :compileJava (Thread[#41,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.013 secs. -Skipping task ':compileJava' as it is up-to-date (took 0.093 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.095 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#41,Task worker for ':',5,main]) completed. Took 0.197 secs. +:compileJava (Thread[#41,Task worker for ':',5,main]) completed. Took 0.199 secs. :buildBwaLib (Thread[#41,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 0.005 secs). +Skipping task ':buildBwaLib' as it is up-to-date (took 0.018 secs). :buildBwaLib UP-TO-DATE -:buildBwaLib (Thread[#41,Task worker for ':',5,main]) completed. Took 0.015 secs. +:buildBwaLib (Thread[#41,Task worker for ':',5,main]) completed. Took 0.033 secs. :processResources (Thread[#41,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[#41,Task worker for ':',5,main]) completed. Took 0.007 secs. +:processResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.01 secs. :classes (Thread[#41,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#41,Task worker for ':',5,main]) completed. Took 0.003 secs. +:classes (Thread[#41,Task worker for ':',5,main]) completed. Took 0.007 secs. :compileTestJava (Thread[#41,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@1c11d72 +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@1b230f9 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 1.919 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 2.251 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[#41,Task worker for ':',5,main]) completed. Took 5.274 secs. +:compileTestJava (Thread[#41,Task worker for ':',5,main]) completed. Took 5.963 secs. :processTestResources (Thread[#41,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 0.024 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.022 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.087 secs. :testClasses (Thread[#41,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#41,Task worker for ':',5,main]) completed. Took 0.002 secs. +:testClasses (Thread[#41,Task worker for ':',5,main]) completed. Took 0.001 secs. :test (Thread[#41,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 0.342 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.316 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-armhf/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9687715406838525176txt -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-armhf/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9485317860448665953txt -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 @@ -1524,12 +1560,12 @@ [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 (0.026 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test +Finished generating test XML results (0.028 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... -Finished generating test html results (0.053 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test -:test (Thread[#41,Task worker for ':',5,main]) completed. Took 3.29 secs. +Finished generating test html results (0.086 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test +:test (Thread[#41,Task worker for ':',5,main]) completed. Took 3.472 secs. -BUILD SUCCESSFUL in 25s +BUILD SUCCESSFUL in 28s 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 @@ -1559,8 +1595,8 @@ 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' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_armhf.deb'. +dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_armhf.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1568,12 +1604,14 @@ 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/20685/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20685/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/30623 and its subdirectories -I: Current time: Tue Dec 31 21:32:26 -12 2024 -I: pbuilder-time-stamp: 1735723946 +I: removing directory /srv/workspace/pbuilder/20685 and its subdirectories +I: Current time: Wed Jan 1 23:37:22 +14 2025 +I: pbuilder-time-stamp: 1735724242