Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 08:28:50.958145193 +0000 +++ b2/build.log 2024-04-30 08:31:47.098636423 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 29 20:22:04 -12 2024 -I: pbuilder-time-stamp: 1714465324 +I: Current time: Tue Jun 3 04:51:55 +14 2025 +I: pbuilder-time-stamp: 1748875915 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -40,52 +40,84 @@ 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/914194/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/582091/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 2 14:52 /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/582091/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/582091/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="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=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='95eaedc7822f4187906c067eae7850ab' - 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='914194' - PS1='# ' - PS2='> ' + INVOCATION_ID=29eb90c5f6db48e8935c7f31c52ad947 + 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=582091 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.eqjf25hY/pbuilderrc_NZaO --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eqjf25hY/b1 --logfile b1/build.log jalview_2.11.3.1+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.eqjf25hY/pbuilderrc_aw7e --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eqjf25hY/b2 --logfile b2/build.log jalview_2.11.3.1+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/914194/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 25 19:07 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/582091/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -939,7 +971,7 @@ Get: 433 http://deb.debian.org/debian trixie/main amd64 libmockito-java all 2.23.0-2 [479 kB] Get: 434 http://deb.debian.org/debian trixie/main amd64 libvamsas-client-java all 0.2+dfsg-2 [584 kB] Get: 435 http://deb.debian.org/debian trixie/main amd64 varna all 3-93+ds-5 [803 kB] -Fetched 393 MB in 16s (24.0 MB/s) +Fetched 393 MB in 5s (77.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. @@ -2366,8 +2398,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 30 08:25:24 UTC 2024. -Universal Time is now: Tue Apr 30 08:25:24 UTC 2024. +Local time is now: Mon Jun 2 14:53:10 UTC 2025. +Universal Time is now: Mon Jun 2 14:53:10 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2923,7 +2955,11 @@ 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/582091/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/582091/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 @@ -2971,7 +3007,7 @@ dh_auto_build mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=jalview -Dfile.encoding=UTF-8 --parallel --max-workers=20 jar + 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=42 jar openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing) @@ -2979,18 +3015,18 @@ 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 1.172 secs. -The client will now receive all logging from the daemon (pid: 953353). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-953353.out.log +An attempt to start the daemon took 0.709 secs. +The client will now receive all logging from the daemon (pid: 596915). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-596915.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 20 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@72f1f8b3 -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@72f1f8b3 -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@c2e9c0d +Using 42 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@28c8497b +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@28c8497b +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@52768cb8 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@74ce91da +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@13ae7c71 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. @@ -3017,87 +3053,78 @@ 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@101026fb +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@17ff6fdb 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@c2e9c0d -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@5e384e0f -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@55b78b8 -:copyHelp (Thread[Task worker for ':',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@52768cb8 +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@32da9e43 +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@5c82b757 +:copyHelp (Thread[Task worker for ':' Thread 4,5,main]) started. :copyHelp Putting task artifact state for task ':copyHelp' into context took 0.001 secs. -Up-to-date check for task ':copyHelp' took 0.263 secs. It is not up-to-date because: +Up-to-date check for task ':copyHelp' took 0.099 secs. It is not up-to-date because: No history is available. -:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.997 secs. -:buildIndices (Thread[Task worker for ':',5,main]) started. +:copyHelp (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.459 secs. +:buildIndices (Thread[Task worker for ':' Thread 4,5,main]) started. :buildIndices Putting task artifact state for task ':buildIndices' into context took 0.0 secs. -Up-to-date check for task ':buildIndices' took 0.107 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.075 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/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.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/axis.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/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/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.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/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.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/htsjdk.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/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.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/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.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/org.jfree.svg.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/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.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/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.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 1.821 secs. -:copyResources (Thread[Task worker for ':',5,main]) started. +:buildIndices (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.972 secs. +:copyResources (Thread[Task worker for ':' Thread 4,5,main]) started. :copyResources Putting task artifact state for task ':copyResources' into context took 0.0 secs. -Up-to-date check for task ':copyResources' took 0.019 secs. It is not up-to-date because: +Up-to-date check for task ':copyResources' took 0.012 secs. It is not up-to-date because: No history is available. -:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.058 secs. -:copyChannelResources (Thread[Task worker for ':',5,main]) started. +:copyResources (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.04 secs. +:copyChannelResources (Thread[Task worker for ':' Thread 4,5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. -Up-to-date check for task ':copyChannelResources' took 0.008 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 ':',5,main]) completed. Took 0.03 secs. -:createBuildProperties (Thread[Task worker for ':',5,main]) started. +:copyChannelResources (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.019 secs. +:createBuildProperties (Thread[Task worker for ':' Thread 4,5,main]) started. :createBuildProperties -Putting task artifact state for task ':createBuildProperties' into context took 0.001 secs. +Putting task artifact state for task ':createBuildProperties' into context took 0.0 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 0.365 secs. -:buildResources (Thread[Task worker for ':',5,main]) started. +:createBuildProperties (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.151 secs. +:buildResources (Thread[Task worker for ':' Thread 4,5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:copyDocs (Thread[Task worker for ':',5,main]) started. +:buildResources (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[Task worker for ':' Thread 4,5,main]) started. :copyDocs Putting task artifact state for task ':copyDocs' into context took 0.0 secs. -Up-to-date check for task ':copyDocs' took 0.157 secs. It is not up-to-date because: +Up-to-date check for task ':copyDocs' took 0.009 secs. It is not up-to-date because: No history is available. -:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.765 secs. -:convertMdFiles (Thread[Task worker for ':',5,main]) started. +:copyDocs (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.05 secs. +:convertMdFiles (Thread[Task worker for ':' Thread 4,5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. -:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[Task worker for ':',5,main]) started. +:convertMdFiles (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[Task worker for ':' Thread 4,5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. -:releasesTemplates (Thread[Task worker for ':',5,main]) completed. Took 0.005 secs. -:prepare (Thread[Task worker for ':',5,main]) started. +:releasesTemplates (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:prepare (Thread[Task worker for ':' Thread 4,5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:compileJava (Thread[Task worker for ':',5,main]) started. +:prepare (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:compileJava (Thread[Task worker for ':' Thread 4,5,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 4.385 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.931 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'. file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/main/java', not found Compiling with JDK Java compiler API. -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal - Policy.setPolicy(new Policy() - ^ -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal - Policy.setPolicy(new Policy() - ^ -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:303: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal - System.setSecurityManager(null); - ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/mc_view/Atom.java:86: warning: [removal] Float(String) in Float has been deprecated and marked for removal this.x = (new Float(str.substring(30, 38).trim()).floatValue()); ^ @@ -3113,6 +3140,15 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/mc_view/Atom.java:103: warning: [removal] Float(String) in Float has been deprecated and marked for removal tfactor = (new Float(tm).floatValue()); ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal + Policy.setPolicy(new Policy() + ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal + Policy.setPolicy(new Policy() + ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:303: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal + System.setSecurityManager(null); + ^ /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) ^ @@ -3128,45 +3164,45 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/gui/FeatureEditor.java:403: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end.setValue(new Integer(firstFeature.getEnd())); ^ -/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() + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. 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 31.606 secs. -:processResources (Thread[Task worker for ':',5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 11.906 secs. +:processResources (Thread[Task worker for ':' Thread 4,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.08 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.037 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.301 secs. -:classes (Thread[Task worker for ':',5,main]) started. +:processResources (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.159 secs. +:classes (Thread[Task worker for ':' Thread 4,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 8,5,main]) started. +:classes (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[Task worker for ':' Thread 4,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.003 secs. It is not up-to-date because: +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 8,5,main]) completed. Took 0.11 secs. -:jar (Thread[Task worker for ':' Thread 8,5,main]) started. +:debianMavenPom (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.056 secs. +:jar (Thread[Task worker for ':' Thread 4,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.096 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.05 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 8,5,main]) completed. Took 1.361 secs. +:jar (Thread[Task worker for ':' Thread 4,5,main]) completed. Took 0.789 secs. -BUILD SUCCESSFUL in 48s +BUILD SUCCESSFUL in 20s 10 actionable tasks: 10 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jalview-2.11.3.1+dfsg' @@ -3180,7 +3216,7 @@ cat test.log # so that it appears in the build log mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=jalview -Dfile.encoding=UTF-8 --parallel --max-workers=20 test + 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=42 test openjdk version "17.0.11" 2024-04-16 OpenJDK Runtime Environment (build 17.0.11+9-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.11+9-Debian-1, mixed mode, sharing) @@ -3188,17 +3224,17 @@ 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-2.11.3.1+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 1.157 secs. -The client will now receive all logging from the daemon (pid: 956982). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-956982.out.log +An attempt to start the daemon took 0.669 secs. +The client will now receive all logging from the daemon (pid: 598708). The daemon log file: /build/reproducible-path/jalview-2.11.3.1+dfsg/.gradle/daemon/4.4.1/daemon-598708.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 20 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@5c57ef1a -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@5c57ef1a -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@19aac450 +Using 42 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@5c9b55d2 +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@5c9b55d2 +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@423af39f Starting Build -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@6c43d2bf +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@2c630303 Settings evaluated using settings file '/build/reproducible-path/jalview-2.11.3.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/jalview-2.11.3.1+dfsg/build.gradle'. Included projects: [root project 'jalview'] @@ -3218,92 +3254,83 @@ 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@3950ddd1 +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@6e028b19 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@19aac450 -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@4b934e5f -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@11072a54 -:copyHelp (Thread[Task worker for ':',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@423af39f +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@1ff0680a +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@44d808ad +:copyHelp (Thread[Task worker for ':' Thread 2,5,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 0.26 secs). +Skipping task ':copyHelp' as it is up-to-date (took 0.103 secs). :copyHelp UP-TO-DATE -:copyHelp (Thread[Task worker for ':',5,main]) completed. Took 0.346 secs. -:buildIndices (Thread[Task worker for ':',5,main]) started. +:copyHelp (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.114 secs. +:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) started. :buildIndices Putting task artifact state for task ':buildIndices' into context took 0.0 secs. -Up-to-date check for task ':buildIndices' took 0.417 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.239 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/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-client.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/httpcore.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-core.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/axis.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/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/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.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/jcommander.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/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/biojava6-ontology.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/htsjdk.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/varna.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/log4j-api.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/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/httpcore.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/junit4.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/mockito-core.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/guava.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/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jsearch-indexer.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/jersey1-client.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.3.1+dfsg/cpJars/vamsas-client.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 3.26 secs. -:copyResources (Thread[Task worker for ':',5,main]) started. +:buildIndices (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.967 secs. +:copyResources (Thread[Task worker for ':' Thread 2,5,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 0.045 secs). +Skipping task ':copyResources' as it is up-to-date (took 0.016 secs). :copyResources UP-TO-DATE -:copyResources (Thread[Task worker for ':',5,main]) completed. Took 0.209 secs. -:copyChannelResources (Thread[Task worker for ':',5,main]) started. +:copyResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.017 secs. +:copyChannelResources (Thread[Task worker for ':' Thread 2,5,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 0.028 secs). +Skipping task ':copyChannelResources' as it is up-to-date (took 0.003 secs). :copyChannelResources UP-TO-DATE -:copyChannelResources (Thread[Task worker for ':',5,main]) completed. Took 0.033 secs. -:createBuildProperties (Thread[Task worker for ':',5,main]) started. +:copyChannelResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.005 secs. +:createBuildProperties (Thread[Task worker for ':' Thread 2,5,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 ':',5,main]) completed. Took 0.593 secs. -:buildResources (Thread[Task worker for ':',5,main]) started. +:createBuildProperties (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.149 secs. +:buildResources (Thread[Task worker for ':' Thread 2,5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. -:copyDocs (Thread[Task worker for ':',5,main]) started. +:buildResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[Task worker for ':' Thread 33,5,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 0.011 secs). +Skipping task ':copyDocs' as it is up-to-date (took 0.006 secs). :copyDocs UP-TO-DATE -:copyDocs (Thread[Task worker for ':',5,main]) completed. Took 0.016 secs. -:convertMdFiles (Thread[Task worker for ':',5,main]) started. +:copyDocs (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.008 secs. +:convertMdFiles (Thread[Task worker for ':' Thread 33,5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. :convertMdFiles UP-TO-DATE -:convertMdFiles (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[Task worker for ':',5,main]) started. +:convertMdFiles (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[Task worker for ':' Thread 33,5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. :releasesTemplates UP-TO-DATE -:releasesTemplates (Thread[Task worker for ':',5,main]) completed. Took 0.007 secs. -:prepare (Thread[Task worker for ':',5,main]) started. +:releasesTemplates (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.0 secs. +:prepare (Thread[Task worker for ':' Thread 33,5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:compileJava (Thread[Task worker for ':',5,main]) started. +:prepare (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.0 secs. +:compileJava (Thread[Task worker for ':' Thread 33,5,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 2.476 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 0.907 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. Setting target compatibility to 11 file or directory '/build/reproducible-path/jalview-2.11.3.1+dfsg/src/main/java', not found Compiling with JDK Java compiler API. -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal - Policy.setPolicy(new Policy() - ^ -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal - Policy.setPolicy(new Policy() - ^ -/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:303: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal - System.setSecurityManager(null); - ^ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/mc_view/Atom.java:86: warning: [removal] Float(String) in Float has been deprecated and marked for removal this.x = (new Float(str.substring(30, 38).trim()).floatValue()); ^ @@ -3319,6 +3346,15 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/mc_view/Atom.java:103: warning: [removal] Float(String) in Float has been deprecated and marked for removal tfactor = (new Float(tm).floatValue()); ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal + Policy.setPolicy(new Policy() + ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:161: warning: [removal] Policy in java.security has been deprecated and marked for removal + Policy.setPolicy(new Policy() + ^ +/build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/bin/Jalview.java:303: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal + System.setSecurityManager(null); + ^ /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) ^ @@ -3334,26 +3370,26 @@ /build/reproducible-path/jalview-2.11.3.1+dfsg/src/jalview/gui/FeatureEditor.java:403: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end.setValue(new Integer(firstFeature.getEnd())); ^ -/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() + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. 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 28.566 secs. -:compileTestJava (Thread[Task worker for ':',5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 11.13 secs. +:compileTestJava (Thread[Task worker for ':' Thread 33,5,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 0.324 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.066 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'. @@ -3363,23 +3399,23 @@ 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 ':',5,main]) completed. Took 8.365 secs. -:processTestResources (Thread[Task worker for ':',5,main]) started. +:compileTestJava (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 3.08 secs. +:processTestResources (Thread[Task worker for ':' Thread 33,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.055 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.033 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.547 secs. -:testClasses (Thread[Task worker for ':',5,main]) started. +:processTestResources (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.212 secs. +:testClasses (Thread[Task worker for ':' Thread 33,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. -:testTask0 (Thread[Task worker for ':',5,main]) started. +:testClasses (Thread[Task worker for ':' Thread 33,5,main]) completed. Took 0.0 secs. +:testTask0 (Thread[Task worker for ':' Thread 40,5,main]) started. :testTask0 Putting task artifact state for task ':testTask0' into context took 0.0 secs. -Up-to-date check for task ':testTask0' took 0.084 secs. It is not up-to-date because: +Up-to-date check for task ':testTask0' took 0.045 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-classpath6946795850333282237txt -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-classpath10203361515040104258txt -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. @@ -3387,16 +3423,16 @@ 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 (0.15 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask0 +Finished generating test XML results (0.04 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask0 Generating HTML test report... -Finished generating test html results (0.119 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0 -:testTask0 (Thread[Task worker for ':',5,main]) completed. Took 7.887 secs. -:testTask1 (Thread[Task worker for ':',5,main]) started. +Finished generating test html results (0.05 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask0 +:testTask0 (Thread[Task worker for ':' Thread 40,5,main]) completed. Took 9.054 secs. +:testTask1 (Thread[Task worker for ':' Thread 40,5,main]) started. :testTask1 Putting task artifact state for task ':testTask1' into context took 0.0 secs. -Up-to-date check for task ':testTask1' took 0.014 secs. It is not up-to-date because: +Up-to-date check for task ':testTask1' took 0.012 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-classpath8152160421371233851txt -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-classpath12590405201994615222txt -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 @@ -3404,17 +3440,17 @@ 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 2 finished executing tests. -Finished generating test XML results (0.003 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask1 +Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask1 Generating HTML test report... -Finished generating test html results (0.006 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask1 +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 2.848 secs. -:testTask2 (Thread[Task worker for ':',5,main]) started. +:testTask1 (Thread[Task worker for ':' Thread 40,5,main]) completed. Took 0.881 secs. +:testTask2 (Thread[Task worker for ':' Thread 40,5,main]) started. :testTask2 Putting task artifact state for task ':testTask2' into context took 0.0 secs. -Up-to-date check for task ':testTask2' took 0.016 secs. It is not up-to-date because: +Up-to-date check for task ':testTask2' took 0.011 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-classpath9128971922497167871txt -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-classpath2477910353188542205txt -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 @@ -3422,17 +3458,17 @@ 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 (0.005 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask2 +Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/test-results/testTask2 Generating HTML test report... -Finished generating test html results (0.007 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask2 +Finished generating test html results (0.003 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 2.725 secs. -:testTask3 (Thread[Task worker for ':',5,main]) started. +:testTask2 (Thread[Task worker for ':' Thread 40,5,main]) completed. Took 0.732 secs. +:testTask3 (Thread[Task worker for ':' Thread 40,5,main]) started. :testTask3 Putting task artifact state for task ':testTask3' into context took 0.0 secs. -Up-to-date check for task ':testTask3' took 0.017 secs. It is not up-to-date because: +Up-to-date check for task ':testTask3' took 0.015 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-classpath16176606412248124736txt -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-classpath6609559454101632580txt -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 @@ -3440,34 +3476,34 @@ 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 (0.003 secs) into: /build/reproducible-path/jalview-2.11.3.1+dfsg/build/reports/tests/testTask3 +Finished generating test html results (0.002 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 2.736 secs. -:test (Thread[Task worker for ':',5,main]) started. +:testTask3 (Thread[Task worker for ':' Thread 40,5,main]) completed. Took 0.742 secs. +:test (Thread[Task worker for ':' Thread 40,5,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 ':',5,main]) completed. Took 0.002 secs. +:test (Thread[Task worker for ':' Thread 40,5,main]) completed. Took 0.003 secs. -BUILD SUCCESSFUL in 1m 6s +BUILD SUCCESSFUL in 31s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.150 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 7.452 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 2.736 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.794 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 2.579 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.678 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 2.513 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.671 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 12.978 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 9.595 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3574,22 +3610,22 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 1m 6s +BUILD FAILED in 31s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.150 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 7.452 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 2.736 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.794 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 2.579 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.678 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 2.513 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 0.671 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 12.978 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 9.595 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3692,8 +3728,8 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 1m 7s -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=20 test returned exit code 1 +BUILD FAILED in 31s +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=42 test returned exit code 1 echo "------------------------------" ------------------------------ if [ "$(perl -ne 'print if /^(?![^(]*\(0 tests).*(\d+) tests.*\1.*successes/' < test.log | wc -l)" -gt "0" ]; then echo " Tests were successful!"; echo "------------------------------"; else echo " Some tests failed!"; echo "------------------------------"; exit 1; fi @@ -3745,12 +3781,14 @@ 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/582091/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/582091/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/914194 and its subdirectories -I: Current time: Mon Apr 29 20:28:50 -12 2024 -I: pbuilder-time-stamp: 1714465730 +I: removing directory /srv/workspace/pbuilder/582091 and its subdirectories +I: Current time: Tue Jun 3 04:54:46 +14 2025 +I: pbuilder-time-stamp: 1748876086