Diff of the two buildlogs: -- --- b1/build.log 2024-05-16 01:52:59.531655806 +0000 +++ b2/build.log 2024-05-16 01:56:09.831555777 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 15 13:50:29 -12 2024 -I: pbuilder-time-stamp: 1715824229 +I: Current time: Wed Jun 18 22:16:02 +14 2025 +I: pbuilder-time-stamp: 1750234562 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -38,51 +38,83 @@ 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/1062564/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/369521/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 18 08:16 /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/369521/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/369521/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='amd64' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='425bb14bd2a1432c8b9fcf97580f20d6' - 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='1062564' - PS1='# ' - PS2='> ' + INVOCATION_ID=228eaf9db4114bf58e2f9c2b24278a33 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=369521 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.klnq0Ptn/pbuilderrc_jmrk --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.klnq0Ptn/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' + 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.klnq0Ptn/pbuilderrc_uOm6 --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.klnq0Ptn/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' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 14 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1062564/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 16 03:15 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/369521/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -292,7 +324,7 @@ Get: 160 http://deb.debian.org/debian unstable/main amd64 gradle-debian-helper all 2.4 [24.5 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] -Fetched 219 MB in 3s (79.5 MB/s) +Fetched 219 MB in 3s (72.0 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 ... 19701 files and directories currently installed.) @@ -1149,7 +1181,11 @@ 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/369521/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/369521/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 @@ -1208,18 +1244,18 @@ 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-17-openjdk-amd64/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 1.326 secs. -The client will now receive all logging from the daemon (pid: 1077357). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-1077357.out.log +An attempt to start the daemon took 2.043 secs. +The client will now receive all logging from the daemon (pid: 383843). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-383843.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@1316b211 -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@1316b211 -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@6483e21d +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@33205c2c +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@33205c2c +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@3cfee424 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@775a3975 +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@678f6ea6 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. @@ -1236,23 +1272,23 @@ 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@46930f90 +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@5406907d 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@6483e21d -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@6aadd05c -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@21c84e1d -:compileJava (Thread[Task worker for ':' Thread 2,5,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@3cfee424 +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@22fff082 +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@515d71c4 +:compileJava (Thread[Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.004 secs. -Up-to-date check for task ':compileJava' took 0.03 secs. It is not up-to-date because: +Putting task artifact state for task ':compileJava' into context took 0.007 secs. +Up-to-date check for task ':compileJava' took 0.053 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 ':' Thread 2,5,main]) completed. Took 1.076 secs. -:buildBwaLib (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 2.102 secs. +:buildBwaLib (Thread[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 0.0 secs. It is not up-to-date because: +Up-to-date check for task ':buildBwaLib' took 0.003 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-17-openjdk-amd64 -> /usr/lib/jvm/java-17-openjdk-amd64 as JAVA_HOME Starting process 'command 'make''. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/src/main/c Command: make @@ -1305,33 +1341,33 @@ 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[Task worker for ':' Thread 2,5,main]) completed. Took 7.716 secs. -:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 10.329 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/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[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs. -:classes (Thread[Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.002 secs. +:classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 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[Task worker for ':' Thread 2,5,main]) completed. Took 0.08 secs. -:jar (Thread[Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.158 secs. +:jar (Thread[Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.011 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.051 secs. +:jar (Thread[Task worker for ':',5,main]) completed. Took 0.068 secs. -BUILD SUCCESSFUL in 14s +BUILD SUCCESSFUL in 23s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gatk-bwamem-1.0.4+dfsg2' @@ -1347,8 +1383,8 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/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 0.91 secs. -The client will now receive all logging from the daemon (pid: 1080375). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-1080375.out.log +An attempt to start the daemon took 1.699 secs. +The client will now receive all logging from the daemon (pid: 388587). The daemon log file: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/daemon/4.4.1/daemon-388587.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. @@ -1376,57 +1412,57 @@ 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@62e6f6cd :compileJava (Thread[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 0.037 secs). +Putting task artifact state for task ':compileJava' into context took 0.007 secs. +Skipping task ':compileJava' as it is up-to-date (took 0.061 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.069 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.118 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 0.002 secs). +Skipping task ':buildBwaLib' as it is up-to-date (took 0.004 secs). :buildBwaLib UP-TO-DATE -:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 0.004 secs. +:buildBwaLib (Thread[Task worker for ':',5,main]) completed. Took 0.014 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/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[Task worker for ':',5,main]) completed. Took 0.002 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.006 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 0.001 secs. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.002 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/reproducible-path/gatk-bwamem-1.0.4+dfsg2/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5fe1adbb +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@5214192e 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 0.437 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.959 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 1.323 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 2.776 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 0.004 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.023 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.031 secs. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.1 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 0.0 secs. +:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.006 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 0.054 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.152 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-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17824608649022549495txt -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-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3897292169624962127txt -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 @@ -1440,12 +1476,12 @@ 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 (0.016 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test +Finished generating test XML results (0.014 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/test-results/test Generating HTML test report... -Finished generating test html results (0.029 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test -:test (Thread[Task worker for ':',5,main]) completed. Took 1.295 secs. +Finished generating test html results (0.038 secs) into: /build/reproducible-path/gatk-bwamem-1.0.4+dfsg2/build/reports/tests/test +:test (Thread[Task worker for ':',5,main]) completed. Took 1.911 secs. -BUILD SUCCESSFUL in 6s +BUILD SUCCESSFUL in 12s 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 @@ -1470,9 +1506,9 @@ 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-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb'. dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in '../libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb'. 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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo dpkg-genchanges --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1480,12 +1516,14 @@ 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/369521/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/369521/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/1062564 and its subdirectories -I: Current time: Wed May 15 13:52:58 -12 2024 -I: pbuilder-time-stamp: 1715824378 +I: removing directory /srv/workspace/pbuilder/369521 and its subdirectories +I: Current time: Wed Jun 18 22:19:08 +14 2025 +I: pbuilder-time-stamp: 1750234748