Diff of the two buildlogs: -- --- b1/build.log 2023-05-09 23:25:28.171379896 +0000 +++ b2/build.log 2023-05-09 23:28:15.528055588 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 9 11:19:46 -12 2023 -I: pbuilder-time-stamp: 1683674386 +I: Current time: Tue Jun 11 19:48:31 +14 2024 +I: pbuilder-time-stamp: 1718084911 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./gatk-bwamem_1.0.4+dfsg2.orig.tar.xz] I: copying [./gatk-bwamem_1.0.4+dfsg2-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Jul 22 17:28:48 2022 -12 +gpgv: Signature made Sat Jul 23 19:28:48 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gatk-bwamem_1.0.4+dfsg2-2.dsc: no acceptable signature found @@ -38,52 +38,84 @@ 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/25366/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15333/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 11 19:48 /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/15333/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15333/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='25366' - 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=15333 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.Ei7z5wfq/pbuilderrc_aX1h --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.Ei7z5wfq/b1 --logfile b1/build.log gatk-bwamem_1.0.4+dfsg2-2.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.Ei7z5wfq/pbuilderrc_lEC4 --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.Ei7z5wfq/b2 --logfile b2/build.log --extrapackages usrmerge gatk-bwamem_1.0.4+dfsg2-2.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 codethink14-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 6 22:27 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/25366/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 11 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/15333/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -311,7 +343,7 @@ Get: 178 http://deb.debian.org/debian bookworm/main arm64 gradle-debian-helper all 2.4 [24.5 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 373 MB in 30s (12.6 MB/s) +Fetched 373 MB in 29s (13.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -1232,8 +1264,17 @@ 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-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+dfsg2-2_source.changes +I: user script /srv/workspace/pbuilder/15333/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/15333/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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+dfsg2-2_source.changes dpkg-buildpackage: info: source package gatk-bwamem dpkg-buildpackage: info: source version 1.0.4+dfsg2-2 dpkg-buildpackage: info: source distribution unstable @@ -1292,18 +1333,18 @@ 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/gatk-bwamem-1.0.4+dfsg2/.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 7.566 secs. -The client will now receive all logging from the daemon (pid: 27121). The daemon log file: /build/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-27121.out.log +An attempt to start the daemon took 2.338 secs. +The client will now receive all logging from the daemon (pid: 22482). The daemon log file: /build/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-22482.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. -Daemon will be stopped at the end of the build stopping after processing Using 8 worker leases. -Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6255b89d -Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6255b89d -Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7adb6efd +Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@31ae1563 +Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@31ae1563 +Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7176ad80 Starting Build Compiling initialization script '/build/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@732ffe23 +Creating new cache for metadata-1.1/results, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@25c56480 Compiling initialization script '/build/gatk-bwamem-1.0.4+dfsg2/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/gatk-bwamem-1.0.4+dfsg2/settings.gradle' using BuildScriptTransformer. @@ -1320,23 +1361,23 @@ 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/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@495f2423 +Creating new cache for annotation-processors, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@70e94ca6 Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7adb6efd -Creating new cache for taskHistory, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@22a2519d -Creating new cache for outputFiles, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@77eb52e0 -:compileJava (Thread[Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7176ad80 +Creating new cache for taskHistory, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@9841af2 +Creating new cache for outputFiles, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7b89d9b1 +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.095 secs. -Up-to-date check for task ':compileJava' took 0.351 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 0.108 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 11.527 secs. -:buildBwaLib (Thread[Task worker for ':',5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 3.538 secs. +:buildBwaLib (Thread[Task worker for ':' Thread 2,5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. -Up-to-date check for task ':buildBwaLib' took 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':buildBwaLib' took 0.004 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-17-openjdk-arm64 -> /usr/lib/jvm/java-17-openjdk-arm64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/gatk-bwamem-1.0.4+dfsg2/src/main/c Command: make @@ -1366,33 +1407,33 @@ make[2]: Leaving directory '/build/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/gatk-bwamem-1.0.4+dfsg2/src/main/c' -:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 32.336 secs. -:processResources (Thread[Task worker for ':' Thread 4,5,main]) started. +:buildBwaLib (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 24.704 secs. +:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/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[Task worker for ':' Thread 4,5,main]) completed. Took 0.031 secs. -:classes (Thread[Task worker for ':' Thread 4,5,main]) started. +:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.005 secs. +:classes (Thread[Task worker for ':' Thread 2,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.035 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 4,5,main]) started. +:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.003 secs. +:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.007 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/gatk-bwamem-1.0.4+dfsg2/build/debian/gatk-bwamem-jni.pom -:debianMavenPom (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 1.721 secs. -:jar (Thread[Task worker for ':' Thread 4,5,main]) started. +:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.223 secs. +:jar (Thread[Task worker for ':' Thread 2,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.118 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.016 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.999 secs. +:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.128 secs. -BUILD SUCCESSFUL in 1m 42s +BUILD SUCCESSFUL in 42s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/gatk-bwamem-1.0.4+dfsg2' @@ -1408,17 +1449,17 @@ 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/gatk-bwamem-1.0.4+dfsg2/.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 9.854 secs. -The client will now receive all logging from the daemon (pid: 21736). The daemon log file: /build/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-21736.out.log +An attempt to start the daemon took 2.343 secs. +The client will now receive all logging from the daemon (pid: 27049). The daemon log file: /build/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-27049.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 8 worker leases. -Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1d368ae3 -Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1d368ae3 -Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@66dfaae6 +Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@51746c0f +Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@51746c0f +Creating new cache for fileHashes, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7ec08578 Starting Build -Creating new cache for metadata-1.1/results, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@760e7428 +Creating new cache for metadata-1.1/results, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3f9e676 Settings evaluated using settings file '/build/gatk-bwamem-1.0.4+dfsg2/settings.gradle'. Projects loaded. Root project using build file '/build/gatk-bwamem-1.0.4+dfsg2/build.gradle'. Included projects: [root project 'gatk-bwamem-jni'] @@ -1430,64 +1471,64 @@ 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/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@66f6e93b +Creating new cache for annotation-processors, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f8e0710 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/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@66dfaae6 -Creating new cache for taskHistory, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a7ede9f -Creating new cache for outputFiles, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@72bdcdde +Creating new cache for resourceHashesCache, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7ec08578 +Creating new cache for taskHistory, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@235e2e7d +Creating new cache for outputFiles, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5a6c54ce :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.135 secs. -Skipping task ':compileJava' as it is up-to-date (took 0.645 secs). +Putting task artifact state for task ':compileJava' into context took 0.029 secs. +Skipping task ':compileJava' as it is up-to-date (took 0.124 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 1.332 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.291 secs. :buildBwaLib (Thread[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 0.029 secs). +Skipping task ':buildBwaLib' as it is up-to-date (took 0.008 secs). :buildBwaLib UP-TO-DATE -:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 0.134 secs. +:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 0.021 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-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[Task worker for ':',5,main]) completed. Took 0.052 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.012 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 0.024 secs. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.005 secs. :compileTestJava (Thread[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/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@165790ed +Creating new cache for metadata-2.36/module-metadata, path /build/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4c269860 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 7.47 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 1.598 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[Task worker for ':',5,main]) completed. Took 18.556 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 4.453 secs. :processTestResources (Thread[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 0.057 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.017 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.239 secs. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.081 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.018 secs. +:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.021 secs. :test (Thread[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 0.877 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.229 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/gatk-bwamem-1.0.4+dfsg2 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath5085657095739438487txt -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/gatk-bwamem-1.0.4+dfsg2 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath15671332939633202519txt -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 @@ -1501,12 +1542,12 @@ WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release Results: SUCCESS (7 tests, 7 successes, 0 failures, 0 skipped) -Finished generating test XML results (0.124 secs) into: /build/gatk-bwamem-1.0.4+dfsg2/build/test-results/test +Finished generating test XML results (0.026 secs) into: /build/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... -Finished generating test html results (0.135 secs) into: /build/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test -:test (Thread[Task worker for ':',5,main]) completed. Took 7.979 secs. +Finished generating test html results (0.048 secs) into: /build/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test +:test (Thread[Task worker for ':',5,main]) completed. Took 2.459 secs. -BUILD SUCCESSFUL in 1m 30s +BUILD SUCCESSFUL in 20s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/build/gatk-bwamem-1.0.4+dfsg2' create-stamp debian/debhelper-build-stamp @@ -1531,9 +1572,9 @@ 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+dfsg2-2_all.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-2_arm64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-2_arm64.deb'. +dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1541,12 +1582,14 @@ 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/15333/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15333/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/25366 and its subdirectories -I: Current time: Tue May 9 11:25:26 -12 2023 -I: pbuilder-time-stamp: 1683674726 +I: removing directory /srv/workspace/pbuilder/15333 and its subdirectories +I: Current time: Tue Jun 11 19:51:14 +14 2024 +I: pbuilder-time-stamp: 1718085074