Diff of the two buildlogs: -- --- b1/build.log 2025-10-03 04:26:48.604466854 +0000 +++ b2/build.log 2025-10-03 04:32:51.344911698 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Nov 4 22:46:08 -12 2026 -I: pbuilder-time-stamp: 1793875568 +I: Current time: Fri Oct 3 18:26:55 +14 2025 +I: pbuilder-time-stamp: 1759465615 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -39,53 +39,85 @@ dpkg-source: info: applying waiting_launcher.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3692653/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/697238/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Oct 3 04:27 /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/697238/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/697238/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='747aeddf37f543979a65a3832af80de3' - 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='3692653' - PS1='# ' - PS2='> ' + INVOCATION_ID=c915c3c18c784b6fb77546c090c64409 + 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=697238 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.0GESryqg/pbuilderrc_Afqz --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0GESryqg/b1 --logfile b1/build.log jalview_2.11.5.0+dfsg-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0GESryqg/pbuilderrc_moF4 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0GESryqg/b2 --logfile b2/build.log jalview_2.11.5.0+dfsg-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3692653/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/697238/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -98,7 +130,7 @@ Depends: debhelper-compat (= 13), po-debconf, default-jdk, javahelper, gradle-debian-helper, maven-repo-helper, groovy, javahelp2, libapache-mime4j-java, libaxis-java, libbiojava6-java, libcommons-math3-java, libguava-java, libhtsjdk-java, libhttpclient-java, libhttpcore-java, libhttpmime-java, libintervalstorej-java, libjaba-client-java, libjaxb-java, libjaxb-api-java, libjaxrs-api-java, libjersey1-client-java, libjersey1-core-java, libjetty9-java, libjfreesvg-java, libjmol-java (>= 14.30.2+dfsg-1~), libjson-simple-java, libjsoup-java, libjswingreader-java, liblog4j2-java, libmiglayout-java, libmockito-java, libslf4j-java, libvamsas-client-java, varna, libandroid-json-org-java, testng dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19898 files and directories currently installed.) +(Reading database ... 19919 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -656,15 +688,15 @@ Get: 459 http://deb.debian.org/debian forky/main amd64 libmockito-java all 3.3.0-2 [510 kB] Get: 460 http://deb.debian.org/debian forky/main amd64 libvamsas-client-java all 0.2+dfsg-2 [584 kB] Get: 461 http://deb.debian.org/debian forky/main amd64 varna all 3-93+ds-7 [801 kB] -Fetched 397 MB in 21s (19.0 MB/s) +Fetched 397 MB in 14s (27.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) +(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 ... 19919 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_258-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (258-1) ... Setting up libsystemd-shared:amd64 (258-1) ... Selecting previously unselected package systemd. -(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 ... 19906 files and directories currently installed.) +(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 ... 19927 files and directories currently installed.) Preparing to unpack .../systemd_258-1_amd64.deb ... Unpacking systemd (258-1) ... Setting up systemd (258-1) ... @@ -676,7 +708,7 @@ Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. Selecting previously unselected package systemd-sysv. -(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 ... 20904 files and directories currently installed.) +(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 ... 20925 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_258-1_amd64.deb ... Unpacking systemd-sysv (258-1) ... Selecting previously unselected package libdbus-1-3:amd64. @@ -719,7 +751,7 @@ Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. -(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 ... 21354 files and directories currently installed.) +(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 ... 21375 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -755,7 +787,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. -(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 ... 22369 files and directories currently installed.) +(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 ... 22390 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:amd64. @@ -2167,8 +2199,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Nov 5 10:48:09 UTC 2026. -Universal Time is now: Thu Nov 5 10:48:09 UTC 2026. +Local time is now: Fri Oct 3 04:30:58 UTC 2025. +Universal Time is now: Fri Oct 3 04:30:58 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2757,7 +2789,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jalview-2.11.5.0+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_2.11.5.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/697238/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/697238/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jalview-2.11.5.0+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_2.11.5.0+dfsg-1_source.changes dpkg-buildpackage: info: source package jalview dpkg-buildpackage: info: source version 2.11.5.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2771,7 +2807,7 @@ sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/reproducible-path/jalview-2.11.5.0\+dfsg/.gradle /build/reproducible-path/jalview-2.11.5.0\+dfsg/buildSrc/.gradle .m2 jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/jalview-2.11.5.0+dfsg' # Removing our handmade pom. @@ -2806,7 +2842,7 @@ 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=42 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=40 jar openjdk version "21.0.9-ea" 2025-10-21 OpenJDK Runtime Environment (build 21.0.9-ea+8-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.9-ea+8-Debian-1, mixed mode, sharing) @@ -2814,18 +2850,18 @@ 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-2.11.5.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 0.748 secs. -The client will now receive all logging from the daemon (pid: 3713417). The daemon log file: /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/daemon/4.4.1/daemon-3713417.out.log +An attempt to start the daemon took 1.029 secs. +The client will now receive all logging from the daemon (pid: 927143). The daemon log file: /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/daemon/4.4.1/daemon-927143.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 42 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@15ee9ad3 -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@15ee9ad3 -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@874fc13 +Using 40 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@358aa1cb +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@358aa1cb +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb7d5ee Starting Build Compiling initialization script '/build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@39df2422 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3e080e97 Compiling initialization script '/build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.5.0+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.5.0+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2852,78 +2888,81 @@ 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-2.11.5.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@19a9c5fa +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@628d0361 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-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@874fc13 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@644de7eb -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@16459dcd -:copyHelp (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb7d5ee +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4151194e +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7599e2c0 +:copyHelp (Thread[#95,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 0.118 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 0.159 secs. It is not up-to-date because: No history is available. -:copyHelp (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.542 secs. -:buildIndices (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyHelp (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.625 secs. +:buildIndices (Thread[#95,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 0.087 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.09 secs. It is not up-to-date because: No history is available. -Starting process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.5.0+dfsg/classes:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-jcolorbrewer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-core.jar com.sun.java.help.search.Indexer html +Starting process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.5.0+dfsg/classes:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-jcolorbrewer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/org.jfree.svg.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java'' -:buildIndices (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.807 secs. -:copyResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:buildIndices (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 1.168 secs. +:copyResources (Thread[#95,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 0.013 secs. It is not up-to-date because: +Up-to-date check for task ':copyResources' took 0.018 secs. It is not up-to-date because: No history is available. -:copyResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.042 secs. -:copyChannelResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyResources (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.06 secs. +:copyChannelResources (Thread[#95,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 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':copyChannelResources' took 0.007 secs. It is not up-to-date because: No history is available. -:copyChannelResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.02 secs. -:createBuildProperties (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyChannelResources (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.024 secs. +:createBuildProperties (Thread[#95,Task worker for ':' Thread 4,5,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 0.001 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-2.11.5.0+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.15 secs. -:buildResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:createBuildProperties (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.179 secs. +:buildResources (Thread[#95,Task worker for ':' Thread 4,5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. -:copyDocs (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:buildResources (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[#95,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 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':copyDocs' took 0.011 secs. It is not up-to-date because: No history is available. -:copyDocs (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.049 secs. -:convertMdFiles (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:copyDocs (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.451 secs. +:convertMdFiles (Thread[#95,Task worker for ':' Thread 4,5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. -:convertMdFiles (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:convertMdFiles (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[#95,Task worker for ':' Thread 4,5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. -:releasesTemplates (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:prepare (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:releasesTemplates (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:prepare (Thread[#95,Task worker for ':' Thread 4,5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:compileJava (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:prepare (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:compileJava (Thread[#95,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-2.11.5.0+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.5.0+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 1.225 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.78 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-2.11.5.0+dfsg/src/main/java', not found Compiling with JDK Java compiler API. +/build/reproducible-path/jalview-2.11.5.0+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-2.11.5.0+dfsg/src/jalview/bin/Jalview.java:163: warning: [removal] Policy in java.security has been deprecated and marked for removal Policy.setPolicy(new Policy() ^ @@ -2948,9 +2987,6 @@ /build/reproducible-path/jalview-2.11.5.0+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-2.11.5.0+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-2.11.5.0+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal InputStream is = System.getSecurityManager().getClass() ^ @@ -2971,32 +3007,32 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 11.445 secs. -:processResources (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 16.982 secs. +:processResources (Thread[#95,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 0.031 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.036 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.159 secs. -:classes (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.184 secs. +:classes (Thread[#95,Task worker for ':' Thread 4,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[#95,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 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/jalview-2.11.5.0+dfsg/build/debian/jalview.pom -:debianMavenPom (Thread[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.056 secs. -:jar (Thread[#94,Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.058 secs. +:jar (Thread[#95,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 0.054 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[#94,Task worker for ':' Thread 2,5,main]) completed. Took 0.904 secs. +:jar (Thread[#95,Task worker for ':' Thread 4,5,main]) completed. Took 0.839 secs. -BUILD SUCCESSFUL in 20s +BUILD SUCCESSFUL in 28s 10 actionable tasks: 10 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jalview-2.11.5.0+dfsg' @@ -3010,7 +3046,7 @@ 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=42 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=40 test openjdk version "21.0.9-ea" 2025-10-21 OpenJDK Runtime Environment (build 21.0.9-ea+8-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.9-ea+8-Debian-1, mixed mode, sharing) @@ -3018,17 +3054,17 @@ 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-2.11.5.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -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 0.751 secs. -The client will now receive all logging from the daemon (pid: 3714792). The daemon log file: /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/daemon/4.4.1/daemon-3714792.out.log +An attempt to start the daemon took 0.835 secs. +The client will now receive all logging from the daemon (pid: 929790). The daemon log file: /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/daemon/4.4.1/daemon-929790.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 42 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a933b1e -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a933b1e -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@27b61478 +Using 40 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@358aa1cb +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@358aa1cb +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb7d5ee Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7bbd99f7 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@2152654 Settings evaluated using settings file '/build/reproducible-path/jalview-2.11.5.0+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/jalview-2.11.5.0+dfsg/build.gradle'. Included projects: [root project 'jalview'] @@ -3048,83 +3084,86 @@ 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-2.11.5.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4dce906b +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@9d1789a 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-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@27b61478 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@b70b04a -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@11e70e4e -:copyHelp (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb7d5ee +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@753a1160 +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.5.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@55661808 +:copyHelp (Thread[#93,Task worker for ':',5,main]) started. :copyHelp Putting task artifact state for task ':copyHelp' into context took 0.0 secs. -Skipping task ':copyHelp' as it is up-to-date (took 0.126 secs). +Skipping task ':copyHelp' as it is up-to-date (took 0.099 secs). :copyHelp UP-TO-DATE -:copyHelp (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.136 secs. -:buildIndices (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyHelp (Thread[#93,Task worker for ':',5,main]) completed. Took 0.109 secs. +:buildIndices (Thread[#93,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 0.234 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/Jmol.jar has been removed. Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/apache-mime4j-core.jar has been removed. -Starting process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.5.0+dfsg/classes:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-jcolorbrewer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-core.jar com.sun.java.help.search.Indexer html +Starting process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java''. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/resources/help_build/help Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /build/reproducible-path/jalview-2.11.5.0+dfsg/classes:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/biojava6-jcolorbrewer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.5.0+dfsg/cpJars/junit4.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java'' -:buildIndices (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.97 secs. -:copyResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:buildIndices (Thread[#93,Task worker for ':',5,main]) completed. Took 0.947 secs. +:copyResources (Thread[#93,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 0.019 secs). +Skipping task ':copyResources' as it is up-to-date (took 0.032 secs). :copyResources UP-TO-DATE -:copyResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.022 secs. -:copyChannelResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.036 secs. +:copyChannelResources (Thread[#93,Task worker for ':',5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. -Skipping task ':copyChannelResources' as it is up-to-date (took 0.004 secs). +Skipping task ':copyChannelResources' as it is up-to-date (took 0.006 secs). :copyChannelResources UP-TO-DATE -:copyChannelResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.006 secs. -:createBuildProperties (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyChannelResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.008 secs. +:createBuildProperties (Thread[#93,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-2.11.5.0+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.145 secs. -:buildResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:createBuildProperties (Thread[#93,Task worker for ':',5,main]) completed. Took 0.153 secs. +:buildResources (Thread[#93,Task worker for ':',5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. -:copyDocs (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:buildResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[#93,Task worker for ':',5,main]) started. :copyDocs Putting task artifact state for task ':copyDocs' into context took 0.0 secs. -Skipping task ':copyDocs' as it is up-to-date (took 0.008 secs). +Skipping task ':copyDocs' as it is up-to-date (took 0.007 secs). :copyDocs UP-TO-DATE -:copyDocs (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.01 secs. -:convertMdFiles (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:copyDocs (Thread[#93,Task worker for ':',5,main]) completed. Took 0.008 secs. +:convertMdFiles (Thread[#93,Task worker for ':',5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. :convertMdFiles UP-TO-DATE -:convertMdFiles (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.001 secs. -:releasesTemplates (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:convertMdFiles (Thread[#93,Task worker for ':',5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[#93,Task worker for ':',5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. :releasesTemplates UP-TO-DATE -:releasesTemplates (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. -:prepare (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:releasesTemplates (Thread[#93,Task worker for ':',5,main]) completed. Took 0.0 secs. +:prepare (Thread[#93,Task worker for ':',5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. -:compileJava (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:prepare (Thread[#93,Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileJava (Thread[#93,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-2.11.5.0+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.5.0+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 1.081 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.031 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/classes/com/stevesoft/pat/AmpersandRule.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.5.0+dfsg/classes/com/stevesoft/pat/Any.class has been added. Setting target compatibility to 11 file or directory '/build/reproducible-path/jalview-2.11.5.0+dfsg/src/main/java', not found Compiling with JDK Java compiler API. +/build/reproducible-path/jalview-2.11.5.0+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-2.11.5.0+dfsg/src/jalview/bin/Jalview.java:163: warning: [removal] Policy in java.security has been deprecated and marked for removal Policy.setPolicy(new Policy() ^ @@ -3149,9 +3188,6 @@ /build/reproducible-path/jalview-2.11.5.0+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-2.11.5.0+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-2.11.5.0+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal InputStream is = System.getSecurityManager().getClass() ^ @@ -3172,13 +3208,13 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 11.445 secs. -:compileTestJava (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:compileJava (Thread[#93,Task worker for ':',5,main]) completed. Took 10.749 secs. +:compileTestJava (Thread[#93,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-2.11.5.0+dfsg/src/test/java', not found file or directory '/build/reproducible-path/jalview-2.11.5.0+dfsg/src/test/java', not found -Up-to-date check for task ':compileTestJava' took 0.085 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.074 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'. @@ -3188,95 +3224,95 @@ 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[#96,Task worker for ':' Thread 4,5,main]) completed. Took 3.381 secs. -:processTestResources (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:compileTestJava (Thread[#93,Task worker for ':',5,main]) completed. Took 2.722 secs. +:processTestResources (Thread[#93,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 0.03 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[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.186 secs. -:testClasses (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:processTestResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.191 secs. +:testClasses (Thread[#93,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. -:testTask0 (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:testClasses (Thread[#93,Task worker for ':',5,main]) completed. Took 0.0 secs. +:testTask0 (Thread[#93,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 0.036 secs. It is not up-to-date because: +Up-to-date check for task ':testTask0' took 0.041 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath1781489527715597680txt -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-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3618067113821708071txt -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. -Finished generating test XML results (0.051 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask0 +Finished generating test XML results (0.047 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask0 Generating HTML test report... -Finished generating test html results (0.052 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask0 -:testTask0 (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 4.09 secs. -:testTask1 (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +Finished generating test html results (0.055 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask0 +:testTask0 (Thread[#93,Task worker for ':',5,main]) completed. Took 4.137 secs. +:testTask1 (Thread[#93,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 0.008 secs. It is not up-to-date because: +Up-to-date check for task ':testTask1' took 0.007 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath12548752488351253718txt -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-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath14314692086366378871txt -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. Gradle Test Executor 2 finished executing tests. Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask1 Generating HTML test report... -Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask1 +Finished generating test html results (0.004 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask1 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask1/index.html -:testTask1 (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 1.325 secs. -:testTask2 (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:testTask1 (Thread[#93,Task worker for ':',5,main]) completed. Took 1.505 secs. +:testTask2 (Thread[#93,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 0.008 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath226697586178218304txt -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-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath2064446637930766685txt -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. Gradle Test Executor 3 finished executing tests. Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask2 Generating HTML test report... -Finished generating test html results (0.049 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask2 +Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask2 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask2/index.html -:testTask2 (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 1.544 secs. -:testTask3 (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:testTask2 (Thread[#93,Task worker for ':',5,main]) completed. Took 1.476 secs. +:testTask3 (Thread[#93,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 0.009 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 4'. Working directory: /build/reproducible-path/jalview-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath16351433406141748372txt -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-2.11.5.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4054339854064720911txt -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. Gradle Test Executor 4 finished executing tests. -Finished generating test XML results (0.0 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask3 +Finished generating test XML results (0.001 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/test-results/testTask3 Generating HTML test report... -Finished generating test html results (0.002 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask3 +Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask3 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask3/index.html -:testTask3 (Thread[#96,Task worker for ':' Thread 4,5,main]) completed. Took 1.274 secs. -:test (Thread[#96,Task worker for ':' Thread 4,5,main]) started. +:testTask3 (Thread[#93,Task worker for ':',5,main]) completed. Took 1.456 secs. +:test (Thread[#93,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[#96,Task worker for ':' Thread 4,5,main]) completed. Took 0.002 secs. +:test (Thread[#93,Task worker for ':',5,main]) completed. Took 0.002 secs. -BUILD SUCCESSFUL in 29s +BUILD SUCCESSFUL in 28s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.382 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.381 seconds│ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask0/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.272 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.454 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask1/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.449 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.428 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask2/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.227 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.408 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask3/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 6.330 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 6.671 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3377,22 +3413,22 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 29s +BUILD FAILED in 28s 13 actionable tasks: 9 executed, 4 up-to-date ┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.382 seconds│ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 2.381 seconds│ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask0/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.272 seconds │ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.454 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask1/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.449 seconds │ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.428 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask2/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.227 seconds │ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 1.408 seconds │ │Report file: /build/reproducible-path/jalview-2.11.5.0+dfsg/build/reports/tests/testTask3/index.html │ ├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 6.330 seconds │ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 6.671 seconds │ └─────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3489,8 +3525,8 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 29s -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 +BUILD FAILED in 28s +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=40 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 @@ -3542,12 +3578,14 @@ 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/697238/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/697238/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/3692653 and its subdirectories -I: Current time: Wed Nov 4 22:49:47 -12 2026 -I: pbuilder-time-stamp: 1793875787 +I: removing directory /srv/workspace/pbuilder/697238 and its subdirectories +I: Current time: Fri Oct 3 18:32:51 +14 2025 +I: pbuilder-time-stamp: 1759465971