Diff of the two buildlogs: -- --- b1/build.log 2024-01-08 12:05:45.297224665 +0000 +++ b2/build.log 2024-01-08 12:10:57.399705407 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 8 00:01:55 -12 2024 -I: pbuilder-time-stamp: 1704715315 +I: Current time: Mon Feb 10 08:28:48 +14 2025 +I: pbuilder-time-stamp: 1739125728 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -40,48 +39,81 @@ dpkg-source: info: applying deactivate_flatlaf.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2379138/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/859881/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 9 18:28 /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/859881/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/859881/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2379138' - PS1='# ' - PS2='> ' + INVOCATION_ID=055145a95437457f8ea923080ea12322 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=859881 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.SDebL9MH/pbuilderrc_UuLz --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SDebL9MH/b1 --logfile b1/build.log jalview_2.11.2.5+dfsg-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://192.168.101.104:3128' + 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.SDebL9MH/pbuilderrc_YiLA --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SDebL9MH/b2 --logfile b2/build.log jalview_2.11.2.5+dfsg-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink04-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -139,15 +171,15 @@ -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 9 18:28 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar - -rwxr-xr-x 1 root root 67904 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 Mar 23 2023 ulockmgr_server @@ -167,7 +199,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2379138/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/859881/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -693,7 +725,7 @@ Get: 418 http://deb.debian.org/debian bookworm/main arm64 libmockito-java all 2.23.0-2 [479 kB] Get: 419 http://deb.debian.org/debian bookworm/main arm64 libvamsas-client-java all 0.2+dfsg-2 [584 kB] Get: 420 http://deb.debian.org/debian bookworm/main arm64 varna all 3-93+ds-4 [790 kB] -Fetched 366 MB in 2s (164 MB/s) +Fetched 366 MB in 2s (154 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 18171 files and directories currently installed.) @@ -2584,7 +2616,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jalview-2.11.2.5+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 > ../jalview_2.11.2.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/859881/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/859881/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jalview-2.11.2.5+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 > ../jalview_2.11.2.5+dfsg-3_source.changes dpkg-buildpackage: info: source package jalview dpkg-buildpackage: info: source version 2.11.2.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -2594,7 +2630,7 @@ debian/rules clean dh clean --with javahelper --with maven_repo_helper debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt binnengegaan # Removing our handmade pom. rm -f pom.xml # Removing the jars we gathered for the build and the tests. @@ -2603,7 +2639,7 @@ sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/reproducible-path/jalview-2.11.2.5\+dfsg/.gradle /build/reproducible-path/jalview-2.11.2.5\+dfsg/buildSrc/.gradle .m2 -make[1]: Leaving directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt verlaten jh_clean dh_clean debian/rules binary @@ -2611,7 +2647,7 @@ dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt binnengegaan # Placing pom.xml at root, with a hack to put the package version number # inside the pom. sed 's/\(VERSION_PACKAGE\)/\12.11.2.5+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/pom.xml > pom.xml @@ -2622,7 +2658,7 @@ cp $F cpJars; \ done dh_auto_configure -make[1]: Leaving directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt verlaten jh_linkjars dh_auto_build mkdir -p .gradle/init.d @@ -2635,18 +2671,18 @@ 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/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 1.809 secs. -The client will now receive all logging from the daemon (pid: 2403353). The daemon log file: /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1/daemon-2403353.out.log +An attempt to start the daemon took 2.33 secs. +The client will now receive all logging from the daemon (pid: 879128). The daemon log file: /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1/daemon-879128.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/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f7d0cdf -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4f7d0cdf -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@551d8a0a +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@726ca91 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@726ca91 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4d0d3ab8 Starting Build Compiling initialization script '/build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@12002b16 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@17d18a60 Compiling initialization script '/build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.2.5+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.2.5+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2669,37 +2705,37 @@ 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/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@57a1098d +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a574066 Tasks to be executed: [task ':copyHelp', task ':buildIndices', task ':copyResources', task ':copyChannelResources', task ':createBuildProperties', task ':buildResources', task ':copyDocs', task ':convertMdFiles', task ':releasesTemplates', task ':prepare', task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@551d8a0a -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4768802a -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@203c2ed3 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4d0d3ab8 +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@51b1fb23 +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4ada9ea7 :copyHelp (Thread[Task worker for ':',5,main]) started. :copyHelp -Putting task artifact state for task ':copyHelp' into context took 0.001 secs. -Up-to-date check for task ':copyHelp' took 0.463 secs. It is not up-to-date because: +Putting task artifact state for task ':copyHelp' into context took 0.009 secs. +Up-to-date check for task ':copyHelp' took 2.303 secs. It is not up-to-date because: No history is available. -:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 1.305 secs. +:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 3.313 secs. :buildIndices (Thread[Task worker for ':',5,main]) started. :buildIndices Putting task artifact state for task ':buildIndices' into context took 0.0 secs. -Up-to-date check for task ':buildIndices' took 0.136 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.178 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.2.5+dfsg/classes:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/apache-mime4j-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/java'' -:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 2.038 secs. +:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 2.481 secs. :copyResources (Thread[Task worker for ':',5,main]) started. :copyResources Putting task artifact state for task ':copyResources' into context took 0.0 secs. -Up-to-date check for task ':copyResources' took 0.037 secs. It is not up-to-date because: +Up-to-date check for task ':copyResources' took 0.042 secs. It is not up-to-date because: No history is available. -:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.085 secs. +:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.131 secs. :copyChannelResources (Thread[Task worker for ':',5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. -Up-to-date check for task ':copyChannelResources' took 0.021 secs. It is not up-to-date because: +Up-to-date check for task ':copyChannelResources' took 0.013 secs. It is not up-to-date because: No history is available. -:copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.05 secs. +:copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.049 secs. :createBuildProperties (Thread[Task worker for ':',5,main]) started. :createBuildProperties Putting task artifact state for task ':createBuildProperties' into context took 0.001 secs. @@ -2707,7 +2743,7 @@ Task has not declared any outputs. Starting process 'command 'sh''. Working directory: /build/reproducible-path/jalview-2.11.2.5+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.263 secs. +:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.374 secs. :buildResources (Thread[Task worker for ':',5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. @@ -2715,15 +2751,15 @@ :copyDocs (Thread[Task worker for ':',5,main]) started. :copyDocs Putting task artifact state for task ':copyDocs' into context took 0.0 secs. -Up-to-date check for task ':copyDocs' took 0.027 secs. It is not up-to-date because: +Up-to-date check for task ':copyDocs' took 0.337 secs. It is not up-to-date because: No history is available. -:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.099 secs. +:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.669 secs. :convertMdFiles (Thread[Task worker for ':',5,main]) started. :convertMdFiles Putting task artifact state for task ':convertMdFiles' into context took 0.0 secs. -Up-to-date check for task ':convertMdFiles' took 0.004 secs. It is not up-to-date because: +Up-to-date check for task ':convertMdFiles' took 0.009 secs. It is not up-to-date because: No history is available. -:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.005 secs. +:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.011 secs. :releasesTemplates (Thread[Task worker for ':',5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. @@ -2737,7 +2773,7 @@ Putting task artifact state for task ':compileJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 1.502 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 4.275 secs. It is not up-to-date because: No history is available. Setting target compatibility to 11 All input files are considered out-of-date for incremental task ':compileJava'. @@ -2790,13 +2826,13 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 21.701 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 31.454 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.094 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.082 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.301 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.538 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. @@ -2807,18 +2843,18 @@ 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/jalview-2.11.2.5+dfsg/build/debian/jalview.pom -:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.174 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.168 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 0.111 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.084 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':',5,main]) completed. Took 0.966 secs. +:jar (Thread[Task worker for ':',5,main]) completed. Took 1.026 secs. -BUILD SUCCESSFUL in 42s +BUILD SUCCESSFUL in 55s 11 actionable tasks: 11 executed debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt binnengegaan # Putting the additional jars needed for the tests in cpJars. for F in /usr/share/java/jaxb-impl.jar /usr/share/java/jcommander.jar /usr/share/java/junit4.jar /usr/share/java/mockito-core.jar /usr/share/java/testng.jar; do \ cp $F cpJars; \ @@ -2834,17 +2870,17 @@ 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/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 1.744 secs. -The client will now receive all logging from the daemon (pid: 2412720). The daemon log file: /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1/daemon-2412720.out.log +An attempt to start the daemon took 2.254 secs. +The client will now receive all logging from the daemon (pid: 882215). The daemon log file: /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/daemon/4.4.1/daemon-882215.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/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@fe9e904 -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@fe9e904 -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@11d9cc4 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@442318d2 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@442318d2 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@60cbe7bd Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@32102a5d +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@191cad1a Settings evaluated using settings file '/build/reproducible-path/jalview-2.11.2.5+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/jalview-2.11.2.5+dfsg/build.gradle'. Included projects: [root project 'jalview'] @@ -2860,80 +2896,80 @@ 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/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2a089fcf +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@23db6f8c Tasks to be executed: [task ':copyHelp', task ':buildIndices', task ':copyResources', task ':copyChannelResources', task ':createBuildProperties', task ':buildResources', task ':copyDocs', task ':convertMdFiles', task ':releasesTemplates', task ':prepare', task ':compileJava', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@11d9cc4 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@5cbd35ff -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7fb09ce4 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@60cbe7bd +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@7eeb0132 +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.2.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1799b957 :copyHelp (Thread[Task worker for ':',5,main]) started. :copyHelp Putting task artifact state for task ':copyHelp' into context took 0.001 secs. -Skipping task ':copyHelp' as it is up-to-date (took 0.387 secs). +Skipping task ':copyHelp' as it is up-to-date (took 0.597 secs). :copyHelp UP-TO-DATE -:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.416 secs. -:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.628 secs. +:buildIndices (Thread[Task worker for ':',5,main]) started. :buildIndices Putting task artifact state for task ':buildIndices' into context took 0.0 secs. -Up-to-date check for task ':buildIndices' took 0.546 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 2.464 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/Jmol.jar has been removed. Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/apache-mime4j-core.jar has been removed. Starting process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.2.5+dfsg/classes:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.2.5+dfsg/cpJars/apache-mime4j-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/java'' -:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 2.174 secs. -:copyResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 4.965 secs. +:copyResources (Thread[Task worker for ':',5,main]) started. :copyResources Putting task artifact state for task ':copyResources' into context took 0.0 secs. -Skipping task ':copyResources' as it is up-to-date (took 0.046 secs). +Skipping task ':copyResources' as it is up-to-date (took 0.044 secs). :copyResources UP-TO-DATE -:copyResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.048 secs. -:copyChannelResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.056 secs. +:copyChannelResources (Thread[Task worker for ':',5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. -Skipping task ':copyChannelResources' as it is up-to-date (took 0.056 secs). +Skipping task ':copyChannelResources' as it is up-to-date (took 0.012 secs). :copyChannelResources UP-TO-DATE -:copyChannelResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.07 secs. -:createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.015 secs. +:createBuildProperties (Thread[Task worker for ':',5,main]) started. :createBuildProperties -Putting task artifact state for task ':createBuildProperties' into context took 0.009 secs. +Putting task artifact state for task ':createBuildProperties' into context took 0.001 secs. Up-to-date check for task ':createBuildProperties' took 0.0 secs. It is not up-to-date because: Task has not declared any outputs. Starting process 'command 'sh''. Working directory: /build/reproducible-path/jalview-2.11.2.5+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.181 secs. -:buildResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.379 secs. +:buildResources (Thread[Task worker for ':',5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:copyDocs (Thread[Task worker for ':' Thread 2,5,main]) started. +:buildResources (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[Task worker for ':',5,main]) started. :copyDocs Putting task artifact state for task ':copyDocs' into context took 0.0 secs. -Skipping task ':copyDocs' as it is up-to-date (took 0.02 secs). +Skipping task ':copyDocs' as it is up-to-date (took 0.17 secs). :copyDocs UP-TO-DATE -:copyDocs (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.024 secs. -:convertMdFiles (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.177 secs. +:convertMdFiles (Thread[Task worker for ':',5,main]) started. :convertMdFiles Putting task artifact state for task ':convertMdFiles' into context took 0.0 secs. -Up-to-date check for task ':convertMdFiles' took 0.011 secs. It is not up-to-date because: +Up-to-date check for task ':convertMdFiles' took 0.006 secs. It is not up-to-date because: Output property '$1$2' has been added for task ':convertMdFiles' Output property '$1$1' has been added for task ':convertMdFiles' Output property '$1$4' has been added for task ':convertMdFiles' -:convertMdFiles (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.014 secs. -:releasesTemplates (Thread[Task worker for ':' Thread 2,5,main]) started. +:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.009 secs. +:releasesTemplates (Thread[Task worker for ':',5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. :releasesTemplates UP-TO-DATE -:releasesTemplates (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:prepare (Thread[Task worker for ':' Thread 2,5,main]) started. +:releasesTemplates (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:prepare (Thread[Task worker for ':',5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. +:prepare (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 2.352 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 3.483 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/classes/com/stevesoft/pat/AmpersandRule.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.2.5+dfsg/classes/com/stevesoft/pat/Any.class has been added. @@ -2987,13 +3023,13 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 27.864 secs. -:compileTestJava (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 33.022 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/test/java', not found file or directory '/build/reproducible-path/jalview-2.11.2.5+dfsg/src/test/java', not found -Up-to-date check for task ':compileTestJava' took 0.373 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.136 secs. It is not up-to-date because: No history is available. Setting target compatibility to 11 All input files are considered out-of-date for incremental task ':compileTestJava'. @@ -3003,23 +3039,23 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileTestJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 8.662 secs. -:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 6.792 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 0.109 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.088 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.635 secs. -:testClasses (Thread[Task worker for ':' Thread 2,5,main]) started. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.449 secs. +:testClasses (Thread[Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:test (Thread[Task worker for ':' Thread 2,5,main]) started. +:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.0 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 0.09 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.131 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/jalview-2.11.2.5+dfsg Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7563374817918337240txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -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/jalview-2.11.2.5+dfsg Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9213886148975059522txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -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. @@ -8141,10 +8177,10 @@ Ensembl is DOWN or unreachable ******************* BAD! Gradle suite > Gradle test > jalview.math.MatrixTest.testFindMinMax_timing STANDARD_OUT - findMinMax for 1000 x 1000 took 6ms + findMinMax for 1000 x 1000 took 14ms Gradle suite > Gradle test > jalview.math.MatrixTest.testPreMultiply_timing STANDARD_OUT - 50x100 multiplications of double took 24ms + 50x100 multiplications of double took 26ms Gradle suite > Gradle test > jalview.datamodel.VisibleRowsIteratorTest STANDARD_OUT >SEQ1/1-20 @@ -8318,19 +8354,19 @@ Gradle suite > Gradle test > jalview.io.FileFormatsTest.testRegisterFileFormat STANDARD_ERROR Overwriting file format: mmCIF +Gradle Test Executor 1 finished executing tests. WARNING: A terminally deprecated method in java.lang.System has been called WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) 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 -Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.269 secs) into: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/test-results/test +Finished generating test XML results (0.251 secs) into: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.36 secs) into: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/reports/tests/test -:test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 11.786 secs. +Finished generating test html results (0.096 secs) into: /build/reproducible-path/jalview-2.11.2.5+dfsg/build/reports/tests/test +:test (Thread[Task worker for ':',5,main]) completed. Took 10.152 secs. -BUILD SUCCESSFUL in 1m 1s +BUILD SUCCESSFUL in 1m 9s 11 actionable tasks: 7 executed, 4 up-to-date -make[1]: Leaving directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/jalview/ @@ -8340,11 +8376,11 @@ dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples -make[1]: Entering directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt binnengegaan dh_installexamples # Providing an example at startup instead of having to load it from the Internet. cp examples/exampleFile_2_7.jar debian/jalview/usr/share/doc/jalview/examples/exampleFile_2_7.jvp -make[1]: Leaving directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt verlaten dh_installman dh_installdebconf dh_icons @@ -8358,17 +8394,17 @@ dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms -make[1]: Entering directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt binnengegaan # Setting the packaged example file as not executable. chmod a-x debian/jalview/usr/share/doc/jalview/examples/uniref50.fa dh_fixperms -make[1]: Leaving directory '/build/reproducible-path/jalview-2.11.2.5+dfsg' +make[1]: Map '/build/reproducible-path/jalview-2.11.2.5+dfsg' wordt verlaten dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'jalview' in '../jalview_2.11.2.5+dfsg-3_all.deb'. +dpkg-deb: pakket 'jalview' wordt gebouwd in '../jalview_2.11.2.5+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../jalview_2.11.2.5+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../jalview_2.11.2.5+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -8376,12 +8412,14 @@ 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/859881/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/859881/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/2379138 and its subdirectories -I: Current time: Mon Jan 8 00:05:44 -12 2024 -I: pbuilder-time-stamp: 1704715544 +I: removing directory /srv/workspace/pbuilder/859881 and its subdirectories +I: Current time: Mon Feb 10 08:33:55 +14 2025 +I: pbuilder-time-stamp: 1739126035