Diff of the two buildlogs: -- --- b1/build.log 2024-05-26 12:26:04.607379713 +0000 +++ b2/build.log 2024-05-26 12:31:00.982769692 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 28 06:44:11 -12 2025 -I: pbuilder-time-stamp: 1751136251 +I: Current time: Mon May 27 02:26:08 +14 2024 +I: pbuilder-time-stamp: 1716726368 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -40,51 +40,83 @@ 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/1723854/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 May 26 12:26 /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/656546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='af4a758e9bcb4cd5ab6de5423e3988e7' - 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='1723854' - PS1='# ' - PS2='> ' + INVOCATION_ID=8f0861d69afc42c1b94ba6442f01489b + 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=656546 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.k2AGKRRd/pbuilderrc_6XLC --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.k2AGKRRd/b1 --logfile b1/build.log jalview_2.11.3.1+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k2AGKRRd/pbuilderrc_uIPa --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.k2AGKRRd/b2 --logfile b2/build.log jalview_2.11.3.1+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 28 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1723854/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 26 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -624,7 +656,7 @@ Get: 430 http://deb.debian.org/debian unstable/main amd64 libmockito-java all 2.23.0-2 [479 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 libvamsas-client-java all 0.2+dfsg-2 [584 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 varna all 3-93+ds-5 [803 kB] -Fetched 366 MB in 5s (80.1 MB/s) +Fetched 366 MB in 4s (84.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19718 files and directories currently installed.) @@ -2029,8 +2061,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jun 28 18:46:32 UTC 2025. -Universal Time is now: Sat Jun 28 18:46:32 UTC 2025. +Local time is now: Sun May 26 12:28:23 UTC 2024. +Universal Time is now: Sun May 26 12:28:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2581,7 +2613,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jalview-2.11.3.1+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_2.11.3.1+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jalview-2.11.3.1+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_2.11.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package jalview dpkg-buildpackage: info: source version 2.11.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2637,18 +2673,18 @@ 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-2.11.3.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 0.772 secs. -The client will now receive all logging from the daemon (pid: 1738985). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-1738985.out.log +An attempt to start the daemon took 1.237 secs. +The client will now receive all logging from the daemon (pid: 672031). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-672031.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-2.11.3.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9 -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9 -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b6ec4e1 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b6ec4e1 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@8ac3632 Starting Build Compiling initialization script '/build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d96c56b +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3f7c8578 Compiling initialization script '/build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.3.1+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.3.1+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2675,73 +2711,73 @@ 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-2.11.3.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@459fc9ef +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@25c2f4cb 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-2.11.3.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@634efa85 -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@73b42a94 -:copyHelp (Thread[Task worker for ':' Thread 2,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@8ac3632 +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@5baa7006 +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1e275ae +: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 0.13 secs. It is not up-to-date because: +Putting task artifact state for task ':copyHelp' into context took 0.0 secs. +Up-to-date check for task ':copyHelp' took 0.091 secs. It is not up-to-date because: No history is available. -:copyHelp (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.539 secs. -:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.447 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 0.095 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.093 secs. It is not up-to-date because: No history is available. -Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.3.1+dfsg/classes:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.jar com.sun.java.help.search.Indexer html +Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.3.1+dfsg/classes:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java'' -:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.946 secs. -:copyResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 0.944 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 0.021 secs. It is not up-to-date because: +Up-to-date check for task ':copyResources' took 0.016 secs. It is not up-to-date because: No history is available. -:copyResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.053 secs. -:copyChannelResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.051 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 0.006 secs. It is not up-to-date because: +Up-to-date check for task ':copyChannelResources' took 0.005 secs. It is not up-to-date because: No history is available. -:copyChannelResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.025 secs. -:createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.025 secs. +:createBuildProperties (Thread[Task worker for ':',5,main]) started. :createBuildProperties 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-2.11.3.1+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 0.144 secs. -:buildResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.156 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. -Up-to-date check for task ':copyDocs' took 0.011 secs. It is not up-to-date because: +Up-to-date check for task ':copyDocs' took 0.01 secs. It is not up-to-date because: No history is available. -:copyDocs (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.057 secs. -:convertMdFiles (Thread[Task worker for ':' Thread 2,5,main]) started. +:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.063 secs. +:convertMdFiles (Thread[Task worker for ':',5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. -:convertMdFiles (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[Task worker for ':' Thread 2,5,main]) started. +:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[Task worker for ':',5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. -: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-2.11.3.1+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 1.371 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.834 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'. @@ -2774,14 +2810,14 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class synchronized (firing) ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal + InputStream is = System.getSecurityManager().getClass() + ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter; allFeatures = sf.getAllFeatures(null); ^ cast to String for a varargs call cast to String[] for a non-varargs call and to suppress this warning -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal - InputStream is = System.getSecurityManager().getClass() - ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/gui/FeatureEditor.java:313: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start.setValue(new Integer(sf.getBegin())); ^ @@ -2799,32 +2835,32 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 15 warnings -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 13.275 secs. -:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 13.51 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 0.038 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.173 secs. -:classes (Thread[Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.211 secs. +:classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/jalview-2.11.3.1+dfsg/build/debian/jalview.pom -:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.05 secs. -:jar (Thread[Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.065 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 0.048 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.045 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.865 secs. +:jar (Thread[Task worker for ':',5,main]) completed. Took 0.975 secs. -BUILD SUCCESSFUL in 21s +BUILD SUCCESSFUL in 23s 10 actionable tasks: 10 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jalview-2.11.3.1+dfsg' @@ -2846,8 +2882,8 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 0.772 secs. -The client will now receive all logging from the daemon (pid: 1741278). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-1741278.out.log +An attempt to start the daemon took 0.895 secs. +The client will now receive all logging from the daemon (pid: 674388). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-674388.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. @@ -2876,33 +2912,33 @@ 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-2.11.3.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@531cb0e6 +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2c15c91c 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 ':testTask0', task ':testTask1', task ':testTask2', task ':testTask3', task ':test'] Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@67456c59 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@2f16ab5b -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@6720ba8c +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@768c49cc +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7c7ee06 :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 0.125 secs). +Skipping task ':copyHelp' as it is up-to-date (took 0.11 secs). :copyHelp UP-TO-DATE -:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.135 secs. +:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.125 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 0.255 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.273 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar has been removed. Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/apache-mime4j-core.jar has been removed. -Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.3.1+dfsg/classes:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.jar com.sun.java.help.search.Indexer html +Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.3.1+dfsg/classes:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/mockito-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/java'' -:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 1.112 secs. +:buildIndices (Thread[Task worker for ':',5,main]) completed. Took 1.116 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 0.017 secs). +Skipping task ':copyResources' as it is up-to-date (took 0.025 secs). :copyResources UP-TO-DATE -:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.02 secs. +:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.028 secs. :copyChannelResources (Thread[Task worker for ':',5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. @@ -2911,12 +2947,12 @@ :copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.006 secs. :createBuildProperties (Thread[Task worker for ':',5,main]) started. :createBuildProperties -Putting task artifact state for task ':createBuildProperties' into context took 0.0 secs. +Putting task artifact state for task ':createBuildProperties' into context took 0.002 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-2.11.3.1+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.147 secs. +:createBuildProperties (Thread[Task worker for ':',5,main]) completed. Took 0.203 secs. :buildResources (Thread[Task worker for ':',5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. @@ -2926,7 +2962,7 @@ Putting task artifact state for task ':copyDocs' into context took 0.0 secs. Skipping task ':copyDocs' as it is up-to-date (took 0.007 secs). :copyDocs UP-TO-DATE -:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.009 secs. +:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.01 secs. :convertMdFiles (Thread[Task worker for ':',5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. @@ -2946,7 +2982,7 @@ Putting task artifact state for task ':compileJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 1.197 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.401 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/classes/com/stevesoft/pat/AmpersandRule.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.3.1+dfsg/classes/com/stevesoft/pat/Any.class has been added. @@ -2980,14 +3016,14 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class synchronized (firing) ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal + InputStream is = System.getSecurityManager().getClass() + ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/analysis/Finder.java:609: warning: non-varargs call of varargs method with inexact argument type for last parameter; allFeatures = sf.getAllFeatures(null); ^ cast to String for a varargs call cast to String[] for a non-varargs call and to suppress this warning -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal - InputStream is = System.getSecurityManager().getClass() - ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/gui/FeatureEditor.java:313: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start.setValue(new Integer(sf.getBegin())); ^ @@ -3005,13 +3041,13 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 15 warnings -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 13.033 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 13.322 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-2.11.3.1+dfsg/src/test/java', not found file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/test/java', not found -Up-to-date check for task ':compileTestJava' took 0.069 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.073 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'. @@ -3021,13 +3057,13 @@ 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 ':',5,main]) completed. Took 3.951 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 3.37 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 0.042 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.035 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.295 secs. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.168 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. @@ -3035,9 +3071,9 @@ :testTask0 (Thread[Task worker for ':',5,main]) started. :testTask0 Putting task artifact state for task ':testTask0' into context took 0.0 secs. -Up-to-date check for task ':testTask0' took 0.043 secs. It is not up-to-date because: +Up-to-date check for task ':testTask0' took 0.039 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath13661783496111729809txt -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-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath12397202770064673620txt -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. Gradle Test Executor 1 finished executing tests. @@ -3045,16 +3081,16 @@ 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 -Finished generating test XML results (0.122 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask0 +Finished generating test XML results (0.05 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask0 Generating HTML test report... -Finished generating test html results (0.133 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0 -:testTask0 (Thread[Task worker for ':',5,main]) completed. Took 7.371 secs. +Finished generating test html results (0.095 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0 +:testTask0 (Thread[Task worker for ':',5,main]) completed. Took 4.513 secs. :testTask1 (Thread[Task worker for ':',5,main]) started. :testTask1 Putting task artifact state for task ':testTask1' into context took 0.0 secs. -Up-to-date check for task ':testTask1' took 0.01 secs. It is not up-to-date because: +Up-to-date check for task ':testTask1' took 0.011 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath8812493186313834406txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' +Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath14822895742395518334txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' Successfully started process 'Gradle Test Executor 2' Gradle Test Executor 2 started executing tests. WARNING: A terminally deprecated method in java.lang.System has been called @@ -3066,13 +3102,13 @@ Generating HTML test report... Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask1 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask1/index.html -:testTask1 (Thread[Task worker for ':',5,main]) completed. Took 1.68 secs. +:testTask1 (Thread[Task worker for ':',5,main]) completed. Took 1.798 secs. :testTask2 (Thread[Task worker for ':',5,main]) started. :testTask2 Putting task artifact state for task ':testTask2' into context took 0.0 secs. -Up-to-date check for task ':testTask2' took 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':testTask2' took 0.012 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4595932358947838210txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' +Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9276772276175368697txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' Successfully started process 'Gradle Test Executor 3' Gradle Test Executor 3 started executing tests. WARNING: A terminally deprecated method in java.lang.System has been called @@ -3080,17 +3116,17 @@ 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 3 finished executing tests. -Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask2 +Finished generating test XML results (0.0 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask2 Generating HTML test report... Finished generating test html results (0.002 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask2 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask2/index.html -:testTask2 (Thread[Task worker for ':',5,main]) completed. Took 1.647 secs. +:testTask2 (Thread[Task worker for ':',5,main]) completed. Took 1.583 secs. :testTask3 (Thread[Task worker for ':',5,main]) started. :testTask3 Putting task artifact state for task ':testTask3' into context took 0.0 secs. -Up-to-date check for task ':testTask3' took 0.013 secs. It is not up-to-date because: +Up-to-date check for task ':testTask3' took 0.011 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 4'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath1835137043895609331txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 4' +Starting process 'Gradle Test Executor 4'. Working directory: /build/reproducible-path/jalview-2.11.3.1+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9003696751783746026txt -Xmx1024m -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 4' Successfully started process 'Gradle Test Executor 4' Gradle Test Executor 4 started executing tests. WARNING: A terminally deprecated method in java.lang.System has been called @@ -3098,34 +3134,34 @@ 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 4 finished executing tests. -Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask3 +Finished generating test XML results (0.0 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask3 Generating HTML test report... -Finished generating test html results (0.002 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3 +Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3/index.html -:testTask3 (Thread[Task worker for ':',5,main]) completed. Took 1.659 secs. -:test (Thread[Task worker for ':' Thread 4,5,main]) started. +:testTask3 (Thread[Task worker for ':',5,main]) completed. Took 1.675 secs. +:test (Thread[Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Skipping task ':test' as it has no source files and no previous output files. :test NO-SOURCE -:test (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.003 secs. +:test (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. -BUILD SUCCESSFUL in 35s +BUILD SUCCESSFUL in 32s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.115 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.684 seconds│ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.619 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.735 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask1/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.595 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.525 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask2/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.600 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.622 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 9.929 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 7.566 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3232,22 +3268,22 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 35s +BUILD FAILED in 32s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.115 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.684 seconds│ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.619 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.735 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask1/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.595 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.525 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask2/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.600 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.622 seconds │ │Report file: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 9.929 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 7.566 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3350,7 +3386,7 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 35s +BUILD FAILED in 32s 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=jalview -Dfile.encoding=UTF-8 --parallel --max-workers=12 test returned exit code 1 echo "------------------------------" ------------------------------ @@ -3403,12 +3439,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/656546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/656546/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/1723854 and its subdirectories -I: Current time: Sat Jun 28 06:49:03 -12 2025 -I: pbuilder-time-stamp: 1751136543 +I: removing directory /srv/workspace/pbuilder/656546 and its subdirectories +I: Current time: Mon May 27 02:31:00 +14 2024 +I: pbuilder-time-stamp: 1716726660