Diff of the two buildlogs: -- --- b1/build.log 2025-03-12 08:07:52.307637571 +0000 +++ b2/build.log 2025-03-12 08:19:16.948700578 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 14 02:21:44 -12 2026 -I: pbuilder-time-stamp: 1776176504 +I: Current time: Wed Mar 12 22:07:54 +14 2025 +I: pbuilder-time-stamp: 1741766874 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying openjdk-21.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2978142/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Mar 12 08:08 /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/868584/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/868584/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + 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='31bac4e62a2844d9a82b8216bc4c6c9e' - 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='2978142' - PS1='# ' - PS2='> ' + INVOCATION_ID=571b27338aea44e3817942b1e563c8a3 + 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=868584 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.XDnNLAQz/pbuilderrc_F5Rb --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.XDnNLAQz/b1 --logfile b1/build.log gkl_0.8.11+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.XDnNLAQz/pbuilderrc_g1DK --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.XDnNLAQz/b2 --logfile b2/build.log gkl_0.8.11+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2978142/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -546,7 +578,7 @@ Get: 410 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 yasm amd64 1.3.0-5 [412 kB] Get: 412 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 366 MB in 9s (39.3 MB/s) +Fetched 366 MB in 11s (32.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19783 files and directories currently installed.) @@ -1901,8 +1933,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 14 14:23:27 UTC 2026. -Universal Time is now: Tue Apr 14 14:23:27 UTC 2026. +Local time is now: Wed Mar 12 08:10:56 UTC 2025. +Universal Time is now: Wed Mar 12 08:10:56 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2454,7 +2486,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gkl-0.8.11+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gkl_0.8.11+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gkl-0.8.11+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gkl_0.8.11+dfsg-2_source.changes dpkg-buildpackage: info: source package gkl dpkg-buildpackage: info: source version 0.8.11+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2476,8 +2512,8 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* -Duplicate specification "unlink|u" for option "u" Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper dh_clean -O--buildsystem=gradle @@ -2506,12 +2542,12 @@ dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/gkl-0.8.11+dfsg' jh_linkjars -O--buildsystem=gradle -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" Duplicate specification "u=s" for option "u" dh_auto_build -O--buildsystem=gradle 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=gkl -Dfile.encoding=UTF-8 --parallel --max-workers=42 jar + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gkl -Dfile.encoding=UTF-8 --parallel --max-workers=20 jar openjdk version "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) @@ -2519,18 +2555,18 @@ 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/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 3.679 secs. -The client will now receive all logging from the daemon (pid: 3000920). The daemon log file: /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1/daemon-3000920.out.log +An attempt to start the daemon took 1.852 secs. +The client will now receive all logging from the daemon (pid: 912366). The daemon log file: /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1/daemon-912366.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 42 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6e35b1e7 -Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6e35b1e7 -Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@63841bec +Using 20 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cb02e07 +Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cb02e07 +Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e8f266f Starting Build Compiling initialization script '/build/reproducible-path/gkl-0.8.11+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@5acab510 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@ac9c177 Compiling initialization script '/build/reproducible-path/gkl-0.8.11+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/gkl-0.8.11+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/gkl-0.8.11+dfsg/settings.gradle) @@ -2549,15 +2585,15 @@ 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/gkl-0.8.11+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@59b193bd +Creating new cache for annotation-processors, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@185b68d0 Tasks to be executed: [task ':compileJava', task ':cmakeConfig', task ':cmakeBuild', task ':copyNativeLib', task ':processResources', task ':classes', task ':buildOnMac', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@63841bec -Creating new cache for taskHistory, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@48eaec1 -Creating new cache for outputFiles, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4123892e -:compileJava (Thread[#89,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e8f266f +Creating new cache for taskHistory, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@63aaa237 +Creating new cache for outputFiles, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@67de65e3 +:compileJava (Thread[#69,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.014 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3e4c4d7d +Putting task artifact state for task ':compileJava' into context took 0.02 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@7fb94bac Loading the Maven rules... Replacing commons-io:commons-io:jar:2.7 -> commons-io:commons-io:jar:debian Passing through org.apache.commons:commons-parent:jar:debian @@ -2634,22 +2670,22 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Up-to-date check for task ':compileJava' took 3.405 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 7.115 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[#89,Task worker for ':',5,main]) completed. Took 7.106 secs. -:cmakeConfig (Thread[#89,Task worker for ':',5,main]) started. +:compileJava (Thread[#69,Task worker for ':',5,main]) completed. Took 12.853 secs. +:cmakeConfig (Thread[#69,Task worker for ':',5,main]) started. :cmakeConfig Putting task artifact state for task ':cmakeConfig' into context took 0.0 secs. -Up-to-date check for task ':cmakeConfig' took 0.008 secs. It is not up-to-date because: +Up-to-date check for task ':cmakeConfig' took 0.099 secs. It is not up-to-date because: No history is available. Starting process 'command 'cmake''. Working directory: /build/reproducible-path/gkl-0.8.11+dfsg/build/native Command: cmake -Wno-dev /build/reproducible-path/gkl-0.8.11+dfsg Successfully started process 'command 'cmake'' -:cmakeConfig (Thread[#89,Task worker for ':',5,main]) completed. Took 5.414 secs. -:cmakeBuild (Thread[#89,Task worker for ':',5,main]) started. +:cmakeConfig (Thread[#69,Task worker for ':',5,main]) completed. Took 11.823 secs. +:cmakeBuild (Thread[#69,Task worker for ':',5,main]) started. :cmakeBuild -Putting task artifact state for task ':cmakeBuild' into context took 0.001 secs. +Putting task artifact state for task ':cmakeBuild' into context took 0.002 secs. Up-to-date check for task ':cmakeBuild' took 0.0 secs. It is not up-to-date because: Task has not declared any outputs. Starting process 'command 'make''. Working directory: /build/reproducible-path/gkl-0.8.11+dfsg/build/native Command: make install @@ -2688,44 +2724,44 @@ configure.ac:73: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:73: the top level -:cmakeBuild (Thread[#89,Task worker for ':',5,main]) completed. Took 2 mins 46.486 secs. -:copyNativeLib (Thread[#89,Task worker for ':',5,main]) started. +:cmakeBuild (Thread[#69,Task worker for ':',5,main]) completed. Took 2 mins 55.248 secs. +:copyNativeLib (Thread[#69,Task worker for ':',5,main]) started. :copyNativeLib Putting task artifact state for task ':copyNativeLib' into context took 0.0 secs. -Up-to-date check for task ':copyNativeLib' took 0.01 secs. It is not up-to-date because: +Up-to-date check for task ':copyNativeLib' took 0.016 secs. It is not up-to-date because: No history is available. -:copyNativeLib (Thread[#89,Task worker for ':',5,main]) completed. Took 0.044 secs. -:processResources (Thread[#89,Task worker for ':',5,main]) started. +:copyNativeLib (Thread[#69,Task worker for ':',5,main]) completed. Took 0.07 secs. +:processResources (Thread[#69,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/gkl-0.8.11+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[#89,Task worker for ':',5,main]) completed. Took 0.001 secs. -:classes (Thread[#89,Task worker for ':',5,main]) started. +:processResources (Thread[#69,Task worker for ':',5,main]) completed. Took 0.006 secs. +:classes (Thread[#69,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#89,Task worker for ':',5,main]) completed. Took 0.0 secs. -:buildOnMac (Thread[#89,Task worker for ':',5,main]) started. +:classes (Thread[#69,Task worker for ':',5,main]) completed. Took 0.0 secs. +:buildOnMac (Thread[#69,Task worker for ':',5,main]) started. :buildOnMac Skipping task ':buildOnMac' as task onlyIf is false. :buildOnMac SKIPPED -:buildOnMac (Thread[#89,Task worker for ':',5,main]) completed. Took 0.007 secs. -:debianMavenPom (Thread[#89,Task worker for ':',5,main]) started. +:buildOnMac (Thread[#69,Task worker for ':',5,main]) completed. Took 0.009 secs. +:debianMavenPom (Thread[#69,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: +Up-to-date check for task ':debianMavenPom' took 0.004 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/gkl-0.8.11+dfsg/build/debian/gkl.pom -:debianMavenPom (Thread[#89,Task worker for ':',5,main]) completed. Took 0.061 secs. -:jar (Thread[#89,Task worker for ':',5,main]) started. +:debianMavenPom (Thread[#69,Task worker for ':',5,main]) completed. Took 0.097 secs. +:jar (Thread[#69,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 0.008 secs. It is not up-to-date because: No history is available. -:jar (Thread[#89,Task worker for ':',5,main]) completed. Took 0.032 secs. +:jar (Thread[#69,Task worker for ':',5,main]) completed. Took 0.051 secs. -BUILD SUCCESSFUL in 3m 15s +BUILD SUCCESSFUL in 3m 37s 6 actionable tasks: 6 executed jh_build -O--buildsystem=gradle rm -f debian/libgkl-java.debhelper.log debian/libgkl-jni.debhelper.log @@ -2736,7 +2772,7 @@ LC_ALL=C LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:$(readlink -f build/native)" 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=gkl -Dfile.encoding=UTF-8 --parallel --max-workers=42 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gkl -Dfile.encoding=UTF-8 --parallel --max-workers=20 test openjdk version "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) @@ -2744,17 +2780,17 @@ 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/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-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 0.771 secs. -The client will now receive all logging from the daemon (pid: 3034457). The daemon log file: /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1/daemon-3034457.out.log -Daemon will be stopped at the end of the build stopping after processing +An attempt to start the daemon took 2.322 secs. +The client will now receive all logging from the daemon (pid: 952789). The daemon log file: /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/daemon/4.4.1/daemon-952789.out.log Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 42 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1b0672f6 -Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1b0672f6 -Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@47e1608d +Daemon will be stopped at the end of the build stopping after processing +Using 20 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@21f76a01 +Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@21f76a01 +Creating new cache for fileHashes, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5c91b336 Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3af4a19 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@16588182 Settings evaluated using settings file '/build/reproducible-path/gkl-0.8.11+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/gkl-0.8.11+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'gkl' instead of the name of the root directory 'gkl-0.8.11+dfsg' @@ -2770,15 +2806,15 @@ 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/gkl-0.8.11+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@a400b83 +Creating new cache for annotation-processors, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@553acca4 Tasks to be executed: [task ':compileJava', task ':cmakeConfig', task ':cmakeBuild', task ':copyNativeLib', task ':processResources', task ':classes', task ':buildOnMac', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@47e1608d -Creating new cache for taskHistory, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@7439ca10 -Creating new cache for outputFiles, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@53ff8771 -:compileJava (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5c91b336 +Creating new cache for taskHistory, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@37a5a313 +Creating new cache for outputFiles, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@70940123 +:compileJava (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.005 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@233e14c +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/gkl-0.8.11+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5f426156 Loading the Maven rules... Replacing commons-io:commons-io:jar:2.7 -> commons-io:commons-io:jar:debian Passing through org.apache.commons:commons-parent:jar:debian @@ -2807,76 +2843,76 @@ Passing through xerces:xercesImpl:jar:debian Passing through jaxen:jaxen:jar:debian Passing through xml-apis:xml-apis-1.4:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 0.32 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.686 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.338 secs. -:cmakeConfig (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.73 secs. +:cmakeConfig (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :cmakeConfig Putting task artifact state for task ':cmakeConfig' into context took 0.0 secs. -Up-to-date check for task ':cmakeConfig' took 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':cmakeConfig' took 0.009 secs. It is not up-to-date because: Input property '$1' file /build/reproducible-path/gkl-0.8.11+dfsg/build/native/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/CMakeLists.txt has been added. Starting process 'command 'cmake''. Working directory: /build/reproducible-path/gkl-0.8.11+dfsg/build/native Command: cmake -Wno-dev /build/reproducible-path/gkl-0.8.11+dfsg Successfully started process 'command 'cmake'' -:cmakeConfig (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.19 secs. -:cmakeBuild (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:cmakeConfig (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 1.542 secs. +:cmakeBuild (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :cmakeBuild Putting task artifact state for task ':cmakeBuild' into context took 0.001 secs. Up-to-date check for task ':cmakeBuild' took 0.0 secs. It is not up-to-date because: Task has not declared any outputs. Starting process 'command 'true''. Working directory: /build/reproducible-path/gkl-0.8.11+dfsg/build/native Command: true Successfully started process 'command 'true'' -:cmakeBuild (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.006 secs. -:copyNativeLib (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:cmakeBuild (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.011 secs. +:copyNativeLib (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :copyNativeLib Putting task artifact state for task ':copyNativeLib' into context took 0.0 secs. -Skipping task ':copyNativeLib' as it is up-to-date (took 0.003 secs). +Skipping task ':copyNativeLib' as it is up-to-date (took 0.005 secs). :copyNativeLib UP-TO-DATE -:copyNativeLib (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.005 secs. -:processResources (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:copyNativeLib (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.008 secs. +:processResources (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/reproducible-path/gkl-0.8.11+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:classes (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.002 secs. +:classes (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:buildOnMac (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:buildOnMac (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :buildOnMac Skipping task ':buildOnMac' as task onlyIf is false. :buildOnMac SKIPPED -:buildOnMac (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.005 secs. -:compileTestJava (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:buildOnMac (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.007 secs. +:compileTestJava (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Replacing org.testng:testng:jar:7.5.1 -> 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 0.197 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.49 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[#90,Task worker for ':' Thread 2,5,main]) completed. Took 1.21 secs. -:processTestResources (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:compileTestJava (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 2.977 secs. +:processTestResources (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.025 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.04 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.073 secs. -:testClasses (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:processTestResources (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.127 secs. +:testClasses (Thread[#72,Task worker for ':' Thread 4,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:test (Thread[#90,Task worker for ':' Thread 2,5,main]) started. +:testClasses (Thread[#72,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:test (Thread[#70,Task worker for ':' Thread 2,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.866 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 1.499 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/gkl-0.8.11+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=gkl -Dfile.separator=/ -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=:/build/reproducible-path/gkl-0.8.11+dfsg/build/native:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.6+7-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.6 -Djava.version.date=2025-01-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.6+7-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/gkl-0.8.11+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.12+bpo-amd64 -Dpath.separator=: -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/gkl-0.8.11+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 -Xcheck:jni -XX:+RestoreMXCSROnJNICalls @/tmp/gradle-worker-classpath5020612647381002004txt -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' + -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.1.0-31-amd64 -Dpath.separator=: -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/gkl-0.8.11+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 -Xcheck:jni -XX:+RestoreMXCSROnJNICalls @/tmp/gradle-worker-classpath11173322185714569653txt -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -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. @@ -2888,233 +2924,124 @@ Gradle suite > Gradle test > com.intel.gkl.compression.IntelDeflaterFactoryUnitTest.IntelDeflaterFactoryReturnsIntelDeflaterIfCompressionLevelIsNotOneOrTwoTest[1](1) SKIPPED Gradle suite > Gradle test > com.intel.gkl.compression.IntelDeflaterFactoryUnitTest.IntelDeflaterFactoryReturnsIntelDeflaterIfCompressionLevelIsNotOneOrTwoTest[2](2) SKIPPED + +Gradle suite > Gradle test > com.intel.gkl.smithwaterman.SmithWatermanUnitTest.inputDataTest FAILED + java.lang.UnsatisfiedLinkError: 'void com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative()' + at com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative(Native Method) + at com.intel.gkl.smithwaterman.IntelSmithWaterman.close(IntelSmithWaterman.java:185) + at com.intel.gkl.smithwaterman.SmithWatermanUnitTest.inputDataTest(SmithWatermanUnitTest.java:37) + +Gradle suite > Gradle test > com.intel.gkl.smithwaterman.SmithWatermanUnitTest.simpleTest FAILED + java.lang.UnsatisfiedLinkError: 'void com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative()' + at com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative(Native Method) + at com.intel.gkl.smithwaterman.IntelSmithWaterman.close(IntelSmithWaterman.java:185) + at com.intel.gkl.smithwaterman.SmithWatermanUnitTest.simpleTest(SmithWatermanUnitTest.java:215) + +Gradle suite > Gradle test > com.intel.gkl.smithwaterman.SmithWatermanUnitTest.singleElementSequencesAlignmentTest FAILED + java.lang.UnsatisfiedLinkError: 'void com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative()' + at com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative(Native Method) + at com.intel.gkl.smithwaterman.IntelSmithWaterman.close(IntelSmithWaterman.java:185) + at com.intel.gkl.smithwaterman.SmithWatermanUnitTest.singleElementSequencesAlignmentTest(SmithWatermanUnitTest.java:151) Gradle Test Executor 1 finished executing tests. -Results: SUCCESS (107 tests, 105 successes, 0 failures, 2 skipped) -Finished generating test XML results (0.053 secs) into: /build/reproducible-path/gkl-0.8.11+dfsg/build/test-results/test + +Gradle suite > Gradle test > com.intel.gkl.smithwaterman.SmithWatermanUnitTest.twoElementSequencesAlignmentTest FAILED + java.lang.UnsatisfiedLinkError: 'void com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative()' + at com.intel.gkl.smithwaterman.IntelSmithWaterman.doneNative(Native Method) + at com.intel.gkl.smithwaterman.IntelSmithWaterman.close(IntelSmithWaterman.java:185) + at com.intel.gkl.smithwaterman.SmithWatermanUnitTest.twoElementSequencesAlignmentTest(SmithWatermanUnitTest.java:167) +Results: FAILURE (107 tests, 101 successes, 4 failures, 2 skipped) + +107 tests completed, 4 failed, 2 skipped +Finished generating test XML results (0.038 secs) into: /build/reproducible-path/gkl-0.8.11+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.092 secs) into: /build/reproducible-path/gkl-0.8.11+dfsg/build/reports/tests/test -:test (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 2 mins 24.538 secs. +Finished generating test html results (0.063 secs) into: /build/reproducible-path/gkl-0.8.11+dfsg/build/reports/tests/test +:test FAILED +:test (Thread[#70,Task worker for ':' Thread 2,5,main]) completed. Took 3 mins 5.274 secs. + +FAILURE: Build failed with an exception. -BUILD SUCCESSFUL in 2m 30s +* What went wrong: +Execution failed for task ':test'. +> There were failing tests. See the report at: file:///build/reproducible-path/gkl-0.8.11+dfsg/build/reports/tests/test/index.html + +* Try: +Run with --debug option to get more log output. Run with --scan to get full insights. + +* Exception is: +org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':test'. + at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100) + at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70) + at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51) + at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62) + at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) + at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) + at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) + at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) + at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52) + at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) + at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54) + at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) + at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) + at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) + at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) + at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) + at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) + at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) + at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) + at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) + at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) + at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) + at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) + at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) + at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) + at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) + at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) + at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) + at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) + at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) +Caused by: org.gradle.api.GradleException: There were failing tests. See the report at: file:///build/reproducible-path/gkl-0.8.11+dfsg/build/reports/tests/test/index.html + at org.gradle.api.tasks.testing.AbstractTestTask.handleTestFailures(AbstractTestTask.java:547) + at org.gradle.api.tasks.testing.AbstractTestTask.executeTests(AbstractTestTask.java:464) + at org.gradle.api.tasks.testing.Test.executeTests(Test.java:530) + at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73) + at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46) + at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39) + at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26) + at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:780) + at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:747) + at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121) + at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) + at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) + at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) + at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) + at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110) + at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92) + ... 29 more + + +* Get more help at https://help.gradle.org + +BUILD FAILED in 3m 21s 7 actionable tasks: 5 executed, 2 up-to-date - rm -fr -- /tmp/dh-xdg-rundir-esfWWZcr + rm -fr -- /tmp/dh-xdg-rundir-cmaJMVbK +dh_auto_test: error: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gkl -Dfile.encoding=UTF-8 --parallel --max-workers=20 test returned exit code 1 +make[1]: *** [debian/rules:28: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/gkl-0.8.11+dfsg' - create-stamp debian/debhelper-build-stamp - dh_testroot -O--buildsystem=gradle - dh_prep -O--buildsystem=gradle - rm -f -- debian/libgkl-java.substvars debian/libgkl-jni.substvars - rm -fr -- debian/.debhelper/generated/libgkl-java/ debian/libgkl-java/ debian/tmp/ debian/.debhelper/generated/libgkl-jni/ debian/libgkl-jni/ - dh_auto_install -O--buildsystem=gradle - install -m0755 -d /build/reproducible-path/gkl-0.8.11\+dfsg/debian/tmp - dh_install -O--buildsystem=gradle - install -m0755 -d debian/libgkl-jni/usr/lib/jni - cp --reflink=auto -a ./build/native/libgkl_compression.so ./build/native/libgkl_pairhmm.so ./build/native/libgkl_pairhmm_omp.so ./build/native/libgkl_smithwaterman.so ./build/native/libgkl_utils.so debian/libgkl-jni/usr/lib/jni/ - jh_installjavadoc -O--buildsystem=gradle -Duplicate specification "A" for option "A" -Duplicate specification "A" for option "A" - dh_installdocs -O--buildsystem=gradle - install -m0755 -d debian/libgkl-java/usr/share/doc/libgkl-java - install -p -m0644 debian/README.Debian debian/libgkl-java/usr/share/doc/libgkl-java/README.Debian - install -p -m0644 debian/copyright debian/libgkl-java/usr/share/doc/libgkl-java/copyright - install -m0755 -d debian/libgkl-jni/usr/share/doc/libgkl-jni - install -p -m0644 debian/copyright debian/libgkl-jni/usr/share/doc/libgkl-jni/copyright - dh_installchangelogs -O--buildsystem=gradle - install -m0755 -d debian/libgkl-jni/usr/share/doc/libgkl-jni - install -p -m0644 debian/.debhelper/generated/libgkl-jni/dh_installchangelogs.dch.trimmed debian/libgkl-jni/usr/share/doc/libgkl-jni/changelog.Debian - install -m0755 -d debian/libgkl-java/usr/share/doc/libgkl-java - install -p -m0644 debian/.debhelper/generated/libgkl-java/dh_installchangelogs.dch.trimmed debian/libgkl-java/usr/share/doc/libgkl-java/changelog.Debian - dh_installsystemduser -O--buildsystem=gradle - dh_lintian -O--buildsystem=gradle - install -m0755 -d debian/libgkl-jni/usr/share/lintian/overrides - install -p -m0644 debian/libgkl-jni.lintian-overrides debian/libgkl-jni/usr/share/lintian/overrides/libgkl-jni - dh_perl -O--buildsystem=gradle - dh_link -O--buildsystem=gradle - jh_installlibs -O--buildsystem=gradle - install -m0755 -d debian/libgkl-java/usr/share/java - install -p -m0644 ./build/libs/gkl-0.8.11.jar debian/libgkl-java/usr/share/java/gkl-0.8.11.jar - rm -f debian/libgkl-java/usr/share/java/gkl.jar - ln -s gkl-0.8.11.jar debian/libgkl-java/usr/share/java/gkl.jar - jh_classpath -O--buildsystem=gradle - jh_manifest -plibgkl-java "--classpath=/usr/share/java/commons-io.jar /usr/share/java/htsjdk.jar /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/log4j-api.jar /usr/share/java/log4j-core.jar /usr/share/java/gatk-native-bindings.jar" debian/libgkl-java/usr/share/java/gkl.jar -Duplicate specification "V:s" for option "V" -Duplicate specification "version|V" for option "V" - Updating symlinked /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/gkl-0.8.11.jar (via debian/libgkl-java/usr/share/java/gkl.jar) - Reading manifest from /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/gkl-0.8.11.jar - Updating manifest in /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/gkl-0.8.11.jar - jh_manifest -O--buildsystem=gradle -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" - find debian/libgkl-java -name '*.jar' - Found symlink usr/share/java/gkl.jar - Found usr/share/java/gkl-0.8.11.jar - Reading manifest from debian/libgkl-java/usr/share/java/gkl-0.8.11.jar - No update of debian/libgkl-java/usr/share/java/gkl-0.8.11.jar required. - find debian/libgkl-jni -name '*.jar' - jh_exec -O--buildsystem=gradle - jh_depends -O--buildsystem=gradle -Searching /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java for libgkl-java -Searching /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/gkl-0.8.11.jar -Found Jars: /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/commons-io.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/htsjdk.jar /usr/share/java/log4j-api.jar /usr/share/java/log4j-core.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/lib/jvm/default-java/lib/tools.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/lib/jvm/default-java/lib/tools.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/commons-io-2.18.0.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/share/java/commons-io-2.18.0.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/gatk-native-bindings-1.0.0.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/share/java/gatk-native-bindings-1.0.0.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/htsjdk-4.1.3.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/share/java/htsjdk-4.1.3.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/log4j-api.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/share/java/log4j-api.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-java/usr/share/java/log4j-core.jar -Checking: /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni/usr/share/java/log4j-core.jar -Found Debs: libcommons-io-java libgatk-native-bindings-java libhtsjdk-java liblog4j2-java -Adding substvars: java:Depends=libcommons-io-java, libgatk-native-bindings-java, libhtsjdk-java, liblog4j2-java java:Recommends= -Searching /build/reproducible-path/gkl-0.8.11+dfsg/debian/libgkl-jni for libgkl-jni -Searching -Found Jars: -Found Debs: -Adding substvars: java:Depends= java:Recommends= - mh_installpoms -O--buildsystem=gradle - mh_installpom --package=libgkl-java --usj-name=gkl debian/pom-gkl.xml - mh_cleanpom --package=libgkl-java --rules=debian/maven.rules debian/pom-gkl.xml debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/pom.properties - mv debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/gkl-debian.pom - install -m 644 -D debian/.debhelper/.mh/gkl-0.8.11.pom debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.pom - install -m 644 -D debian/.debhelper/.mh/gkl-debian.pom debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/debian/gkl-debian.pom - mh_linkjars --skip-clean-poms -O--buildsystem=gradle - mh_linkjar --package=libgkl-java --skip-clean-pom debian/pom-gkl.xml /usr/share/java/gkl.jar - dh_link -plibgkl-java /usr/share/javagkl.jar usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.jar - rm -f debian/libgkl-java/usr/share/java/gkl.jar - ln -s gkl-0.8.11.jar debian/libgkl-java/usr/share/java/gkl.jar - install -m0755 -d debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11 - rm -f debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.jar - ln -s ../../../../../../java/gkl.jar debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.jar - dh_link -plibgkl-java /usr/share/javagkl.jar usr/share/maven-repo/com/intel/gkl/gkl/debian/gkl-debian.jar - rm -f debian/libgkl-java/usr/share/java/gkl.jar - ln -s gkl-0.8.11.jar debian/libgkl-java/usr/share/java/gkl.jar - rm -f debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.jar - ln -s ../../../../../../java/gkl.jar debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/0.8.11/gkl-0.8.11.jar - install -m0755 -d debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/debian - rm -f debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/debian/gkl-debian.jar - ln -s ../../../../../../java/gkl.jar debian/libgkl-java/usr/share/maven-repo/com/intel/gkl/gkl/debian/gkl-debian.jar - dh_strip_nondeterminism -O--buildsystem=gradle - Using 1702588020 as canonical time - Normalizing debian/libgkl-java/usr/share/java/gkl-0.8.11.jar using File::StripNondeterminism::handlers::jar - dh_compress -O--buildsystem=gradle - cd debian/libgkl-java - cd debian/libgkl-jni - chmod a-x usr/share/doc/libgkl-jni/changelog.Debian - chmod a-x usr/share/doc/libgkl-java/changelog.Debian - gzip -9nf usr/share/doc/libgkl-jni/changelog.Debian - gzip -9nf usr/share/doc/libgkl-java/changelog.Debian - cd '/build/reproducible-path/gkl-0.8.11+dfsg' - cd '/build/reproducible-path/gkl-0.8.11+dfsg' - dh_fixperms -O--buildsystem=gradle - find debian/libgkl-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/libgkl-jni ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/libgkl-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libgkl-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libgkl-jni/usr/share/doc -type f -a -true -a ! -regex 'debian/libgkl-jni/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libgkl-jni/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libgkl-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libgkl-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libgkl-jni/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libgkl-jni -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libgkl-jni/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w - dh_missing -O--buildsystem=gradle - dh_dwz -a -O--buildsystem=gradle - install -m0755 -d debian/libgkl-jni/usr/lib/debug/.dwz/x86_64-linux-gnu - dwz -mdebian/libgkl-jni/usr/lib/debug/.dwz/x86_64-linux-gnu/libgkl-jni.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libgkl-jni.debug -- debian/libgkl-jni/usr/lib/jni/libgkl_compression.so debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm.so debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm_omp.so debian/libgkl-jni/usr/lib/jni/libgkl_smithwaterman.so debian/libgkl-jni/usr/lib/jni/libgkl_utils.so - objcopy --compress-debug-sections debian/libgkl-jni/usr/lib/debug/.dwz/x86_64-linux-gnu/libgkl-jni.debug - chmod 0644 -- debian/libgkl-jni/usr/lib/debug/.dwz/x86_64-linux-gnu/libgkl-jni.debug - dh_strip -a -O--buildsystem=gradle - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/4b - objcopy --only-keep-debug --compress-debug-sections debian/libgkl-jni/usr/lib/jni/libgkl_compression.so debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/4b/e4137cdcbdddfa8d622bb25734ea02d358ce2d.debug - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/4b/e4137cdcbdddfa8d622bb25734ea02d358ce2d.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libgkl-jni/usr/lib/jni/libgkl_compression.so - objcopy --add-gnu-debuglink debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/4b/e4137cdcbdddfa8d622bb25734ea02d358ce2d.debug debian/libgkl-jni/usr/lib/jni/libgkl_compression.so - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/72 - objcopy --only-keep-debug --compress-debug-sections debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm_omp.so debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/72/70783a01bc783bcb7681427f9716158f1a5d18.debug - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/72/70783a01bc783bcb7681427f9716158f1a5d18.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm_omp.so - objcopy --add-gnu-debuglink debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/72/70783a01bc783bcb7681427f9716158f1a5d18.debug debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm_omp.so - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/31 - objcopy --only-keep-debug --compress-debug-sections debian/libgkl-jni/usr/lib/jni/libgkl_smithwaterman.so debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/31/9967bb27ba07cacc99ef4c13f4836e6f351ea9.debug - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/31/9967bb27ba07cacc99ef4c13f4836e6f351ea9.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libgkl-jni/usr/lib/jni/libgkl_smithwaterman.so - objcopy --add-gnu-debuglink debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/31/9967bb27ba07cacc99ef4c13f4836e6f351ea9.debug debian/libgkl-jni/usr/lib/jni/libgkl_smithwaterman.so - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/c9 - objcopy --only-keep-debug --compress-debug-sections debian/libgkl-jni/usr/lib/jni/libgkl_utils.so debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/c9/397b6eb8178f827ec3282037e7718a755e0bfb.debug - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/c9/397b6eb8178f827ec3282037e7718a755e0bfb.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libgkl-jni/usr/lib/jni/libgkl_utils.so - objcopy --add-gnu-debuglink debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/c9/397b6eb8178f827ec3282037e7718a755e0bfb.debug debian/libgkl-jni/usr/lib/jni/libgkl_utils.so - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/e0 - objcopy --only-keep-debug --compress-debug-sections debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm.so debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/e0/dc8e3def9e6e8b061b530e1ff8882ab091bbc0.debug - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/e0/dc8e3def9e6e8b061b530e1ff8882ab091bbc0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm.so - objcopy --add-gnu-debuglink debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.build-id/e0/dc8e3def9e6e8b061b530e1ff8882ab091bbc0.debug debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm.so - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.dwz - cp --reflink=auto -a debian/libgkl-jni/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/libgkl-jni/dbgsym-root/usr/lib/debug/.dwz - rm -fr debian/libgkl-jni/usr/lib/debug/.dwz - rmdir -p --ignore-fail-on-non-empty debian/libgkl-jni/usr/lib/debug - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/usr/share/doc - ln -s libgkl-jni debian/.debhelper/libgkl-jni/dbgsym-root/usr/share/doc/libgkl-jni-dbgsym - install -m0755 -d debian/.debhelper/libgkl-jni - dh_makeshlibs -a -O--buildsystem=gradle - rm -f debian/libgkl-jni/DEBIAN/shlibs - dh_shlibdeps -a -O--buildsystem=gradle - install -m0755 -d debian/libgkl-jni/DEBIAN - dpkg-shlibdeps -Tdebian/libgkl-jni.substvars debian/libgkl-jni/usr/lib/jni/libgkl_compression.so debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm_omp.so debian/libgkl-jni/usr/lib/jni/libgkl_smithwaterman.so debian/libgkl-jni/usr/lib/jni/libgkl_utils.so debian/libgkl-jni/usr/lib/jni/libgkl_pairhmm.so -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged - dh_installdeb -O--buildsystem=gradle - install -m0755 -d debian/libgkl-java/DEBIAN - install -m0755 -d debian/libgkl-jni/DEBIAN - dh_gencontrol -O--buildsystem=gradle - install -m0755 -d debian/libgkl-java/DEBIAN - echo misc:Depends= >> debian/libgkl-java.substvars - echo misc:Pre-Depends= >> debian/libgkl-java.substvars - dpkg-gencontrol -plibgkl-java -ldebian/changelog -Tdebian/libgkl-java.substvars -cdebian/control -Pdebian/libgkl-java - install -m0755 -d debian/libgkl-jni/DEBIAN - echo misc:Depends= >> debian/libgkl-jni.substvars - echo misc:Pre-Depends= >> debian/libgkl-jni.substvars - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/DEBIAN - dpkg-gencontrol -plibgkl-jni -ldebian/changelog -Tdebian/libgkl-jni.substvars -cdebian/control -Pdebian/.debhelper/libgkl-jni/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libgkl-jni-dbgsym "-DDepends=libgkl-jni (= \${binary:Version})" "-DDescription=debug symbols for libgkl-jni" "-DBuild-Ids=319967bb27ba07cacc99ef4c13f4836e6f351ea9 4be4137cdcbdddfa8d622bb25734ea02d358ce2d 7270783a01bc783bcb7681427f9716158f1a5d18 c9397b6eb8178f827ec3282037e7718a755e0bfb e0dc8e3def9e6e8b061b530e1ff8882ab091bbc0" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/DEBIAN/control - dpkg-gencontrol -plibgkl-jni -ldebian/changelog -Tdebian/libgkl-jni.substvars -cdebian/control -Pdebian/libgkl-jni -dpkg-gencontrol: warning: Depends field of package libgkl-java: substitution variable ${maven:Depends} used, but is not defined - chmod 0644 -- debian/libgkl-java/DEBIAN/control - chmod 0644 -- debian/libgkl-jni/DEBIAN/control - dh_md5sums -O--buildsystem=gradle - install -m0755 -d debian/libgkl-java/DEBIAN - cd debian/libgkl-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - install -m0755 -d debian/libgkl-jni/DEBIAN - cd debian/libgkl-jni >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/libgkl-java/DEBIAN/md5sums - chmod 0644 -- debian/libgkl-jni/DEBIAN/md5sums - install -m0755 -d debian/.debhelper/libgkl-jni/dbgsym-root/DEBIAN - cd debian/.debhelper/libgkl-jni/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/.debhelper/libgkl-jni/dbgsym-root/DEBIAN/md5sums - dh_builddeb -O--buildsystem=gradle - dpkg-deb --root-owner-group --build debian/libgkl-java .. - dpkg-deb --root-owner-group --build debian/libgkl-jni .. - dpkg-deb --root-owner-group --build debian/.debhelper/libgkl-jni/dbgsym-root .. -dpkg-deb: building package 'libgkl-java' in '../libgkl-java_0.8.11+dfsg-2_all.deb'. -dpkg-deb: building package 'libgkl-jni' in '../libgkl-jni_0.8.11+dfsg-2_amd64.deb'. -dpkg-deb: building package 'libgkl-jni-dbgsym' in '../libgkl-jni-dbgsym_0.8.11+dfsg-2_amd64.deb'. - dpkg-genbuildinfo --build=binary -O../gkl_0.8.11+dfsg-2_amd64.buildinfo - dpkg-genchanges --build=binary -O../gkl_0.8.11+dfsg-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +make: *** [debian/rules:11: binary] Error 2 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Wed Mar 12 08:19:11 UTC 2025 +Filesystem Size Used Avail Use% Mounted on +tmpfs 40G 0 40G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/868584/tmp/hooks/C01_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/2978142 and its subdirectories -I: Current time: Tue Apr 14 02:30:45 -12 2026 -I: pbuilder-time-stamp: 1776177045 +I: removing directory /srv/workspace/pbuilder/868584 and its subdirectories