Diff of the two buildlogs: -- --- b1/build.log 2025-02-18 00:03:06.484173350 +0000 +++ b2/build.log 2025-02-18 00:19:22.944291983 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 17 11:55:05 -12 2025 -I: pbuilder-time-stamp: 1739836505 +I: Current time: Mon Mar 23 20:26:20 +14 2026 +I: pbuilder-time-stamp: 1774247180 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -39,52 +39,84 @@ 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/529953/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1625273/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 23 06:26 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1625273/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1625273/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='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='cee15a14d1f04a66af38488cf8eebfef' - 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='529953' - PS1='# ' - PS2='> ' + INVOCATION_ID=124e7c4ca3e24cf5b7aff0cb34ddc6c6 + 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=1625273 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.oFSG4EO9/pbuilderrc_kj3G --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFSG4EO9/b1 --logfile b1/build.log jalview_2.11.4.1+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://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.oFSG4EO9/pbuilderrc_uLzT --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFSG4EO9/b2 --logfile b2/build.log jalview_2.11.4.1+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/529953/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1625273/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -97,7 +129,7 @@ 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 ... 19798 files and directories currently installed.) +(Reading database ... 19848 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: @@ -668,10 +700,10 @@ Get: 472 http://deb.debian.org/debian unstable/main amd64 libmockito-java all 3.3.0-2 [510 kB] Get: 473 http://deb.debian.org/debian unstable/main amd64 libvamsas-client-java all 0.2+dfsg-2 [584 kB] Get: 474 http://deb.debian.org/debian unstable/main amd64 varna all 3-93+ds-7 [801 kB] -Fetched 405 MB in 35s (11.5 MB/s) +Fetched 405 MB in 23s (18.0 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 ... 19798 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 ... 19848 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.3-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.3-1) ... Selecting previously unselected package libapparmor1:amd64. @@ -679,7 +711,7 @@ Unpacking libapparmor1:amd64 (3.1.7-4) ... Setting up libsystemd-shared:amd64 (257.3-1) ... 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 ... 19811 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 ... 19861 files and directories currently installed.) Preparing to unpack .../systemd_257.3-1_amd64.deb ... Unpacking systemd (257.3-1) ... Setting up libapparmor1:amd64 (3.1.7-4) ... @@ -693,7 +725,7 @@ Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 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 ... 20754 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 ... 20804 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.3-1_amd64.deb ... Unpacking systemd-sysv (257.3-1) ... Selecting previously unselected package libdbus-1-3:amd64. @@ -733,7 +765,7 @@ Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 21202 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 ... 21252 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. @@ -769,7 +801,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 22212 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 ... 22262 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package libproc2-0:amd64. @@ -2221,8 +2253,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 17 23:59:44 UTC 2025. -Universal Time is now: Mon Feb 17 23:59:44 UTC 2025. +Local time is now: Mon Mar 23 06:35:51 UTC 2026. +Universal Time is now: Mon Mar 23 06:35:51 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2823,7 +2855,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jalview-2.11.4.1+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_2.11.4.1+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1625273/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1625273/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jalview-2.11.4.1+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_2.11.4.1+dfsg-1_source.changes dpkg-buildpackage: info: source package jalview dpkg-buildpackage: info: source version 2.11.4.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2837,7 +2873,7 @@ sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/reproducible-path/jalview-2.11.4.1\+dfsg/.gradle /build/reproducible-path/jalview-2.11.4.1\+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-2.11.4.1+dfsg' # Removing our handmade pom. @@ -2872,7 +2908,7 @@ 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 "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) @@ -2880,18 +2916,18 @@ 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-2.11.4.1+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 1.232 secs. -The client will now receive all logging from the daemon (pid: 597189). The daemon log file: /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/daemon/4.4.1/daemon-597189.out.log +An attempt to start the daemon took 4.308 secs. +The client will now receive all logging from the daemon (pid: 1735764). The daemon log file: /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/daemon/4.4.1/daemon-1735764.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. -Daemon will be stopped at the end of the build stopping after processing -Using 20 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2c2f5376 -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2c2f5376 -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@3dd3182c +Using 42 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6aca3204 +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6aca3204 +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b25c345 Starting Build Compiling initialization script '/build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@7bd73ea0 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@505014bd Compiling initialization script '/build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.4.1+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/jalview-2.11.4.1+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2918,81 +2954,78 @@ 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-2.11.4.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@315f454e +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e2375e0 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-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@3dd3182c -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@123c208a -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5483e739 -:copyHelp (Thread[#76,Task worker for ':' Thread 2,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b25c345 +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@323bf433 +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@cd3c10a +:copyHelp (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :copyHelp Putting task artifact state for task ':copyHelp' into context took 0.001 secs. -Up-to-date check for task ':copyHelp' took 0.31 secs. It is not up-to-date because: +Up-to-date check for task ':copyHelp' took 0.183 secs. It is not up-to-date because: No history is available. -:copyHelp (Thread[#76,Task worker for ':' Thread 2,5,main]) completed. Took 1.173 secs. -:buildIndices (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:copyHelp (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.64 secs. +:buildIndices (Thread[#96,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 0.141 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.104 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-2.11.4.1+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-2.11.4.1+dfsg/classes:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/org.jfree.svg.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-2.11.4.1+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-2.11.4.1+dfsg/classes:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java'' -:buildIndices (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 1.575 secs. -:copyResources (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:buildIndices (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 1.136 secs. +:copyResources (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :copyResources Putting task artifact state for task ':copyResources' into context took 0.0 secs. -Up-to-date check for task ':copyResources' took 0.036 secs. It is not up-to-date because: +Up-to-date check for task ':copyResources' took 0.026 secs. It is not up-to-date because: No history is available. -:copyResources (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.087 secs. -:copyChannelResources (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:copyResources (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.061 secs. +:copyChannelResources (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :copyChannelResources Putting task artifact state for task ':copyChannelResources' into context took 0.0 secs. -Up-to-date check for task ':copyChannelResources' took 0.014 secs. It is not up-to-date because: +Up-to-date check for task ':copyChannelResources' took 0.011 secs. It is not up-to-date because: No history is available. -:copyChannelResources (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.042 secs. -:createBuildProperties (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:copyChannelResources (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.028 secs. +:createBuildProperties (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :createBuildProperties -Putting task artifact state for task ':createBuildProperties' into context took 0.002 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-2.11.4.1+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.243 secs. -:buildResources (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:createBuildProperties (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.157 secs. +:buildResources (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.001 secs. -:copyDocs (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:buildResources (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. +:copyDocs (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :copyDocs Putting task artifact state for task ':copyDocs' into context took 0.0 secs. -Up-to-date check for task ':copyDocs' took 0.016 secs. It is not up-to-date because: +Up-to-date check for task ':copyDocs' took 0.022 secs. It is not up-to-date because: No history is available. -:copyDocs (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.091 secs. -:convertMdFiles (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:copyDocs (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.077 secs. +:convertMdFiles (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. -:convertMdFiles (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:convertMdFiles (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. -:releasesTemplates (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.0 secs. -:prepare (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:releasesTemplates (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. +:prepare (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.0 secs. -:compileJava (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:prepare (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. +:compileJava (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 2.56 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 5.231 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-2.11.4.1+dfsg/src/main/java', not found Compiling with JDK Java compiler API. -/build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class - synchronized (firing) - ^ /build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/bin/Jalview.java:163: warning: [removal] Policy in java.security has been deprecated and marked for removal Policy.setPolicy(new Policy() ^ @@ -3017,6 +3050,9 @@ /build/reproducible-path/jalview-2.11.4.1+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-2.11.4.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class + synchronized (firing) + ^ /build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal InputStream is = System.getSecurityManager().getClass() ^ @@ -3037,32 +3073,32 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 31.475 secs. -:processResources (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:compileJava (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 52.546 secs. +:processResources (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.067 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.039 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.262 secs. -:classes (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:processResources (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.234 secs. +:classes (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.003 secs. -:debianMavenPom (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:classes (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[#96,Task worker for ':' Thread 2,5,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-2.11.4.1+dfsg/build/debian/jalview.pom -:debianMavenPom (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 0.086 secs. -:jar (Thread[#87,Task worker for ':' Thread 13,5,main]) started. +:debianMavenPom (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 0.077 secs. +:jar (Thread[#96,Task worker for ':' Thread 2,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.108 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.094 secs. It is not up-to-date because: No history is available. -:jar (Thread[#87,Task worker for ':' Thread 13,5,main]) completed. Took 1.704 secs. +:jar (Thread[#96,Task worker for ':' Thread 2,5,main]) completed. Took 1.143 secs. -BUILD SUCCESSFUL in 49s +BUILD SUCCESSFUL in 1m 18s 10 actionable tasks: 10 executed debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jalview-2.11.4.1+dfsg' @@ -3076,7 +3112,7 @@ 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 "21.0.6" 2025-01-21 OpenJDK Runtime Environment (build 21.0.6+7-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.6+7-Debian-1, mixed mode, sharing) @@ -3084,17 +3120,17 @@ 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-2.11.4.1+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 2.226 secs. -The client will now receive all logging from the daemon (pid: 625175). The daemon log file: /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/daemon/4.4.1/daemon-625175.out.log +An attempt to start the daemon took 1.935 secs. +The client will now receive all logging from the daemon (pid: 1778294). The daemon log file: /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/daemon/4.4.1/daemon-1778294.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. -Daemon will be stopped at the end of the build stopping after processing -Using 20 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b8ec177 -Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b8ec177 -Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@15822cb6 +Using 42 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e72c3fd +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e72c3fd +Creating new cache for fileHashes, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@340c659b Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@529836bc +Creating new cache for metadata-1.1/results, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@654ba756 Settings evaluated using settings file '/build/reproducible-path/jalview-2.11.4.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/jalview-2.11.4.1+dfsg/build.gradle'. Included projects: [root project 'jalview'] @@ -3114,86 +3150,83 @@ 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-2.11.4.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@627056ab +Creating new cache for annotation-processors, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@3ae98bd9 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-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@15822cb6 -Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@2310321b -Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@531c8118 -:copyHelp (Thread[#73,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@340c659b +Creating new cache for taskHistory, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@7380a81a +Creating new cache for outputFiles, path /build/reproducible-path/jalview-2.11.4.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4756c535 +:copyHelp (Thread[#93,Task worker for ':',5,main]) started. :copyHelp -Putting task artifact state for task ':copyHelp' into context took 0.004 secs. -Skipping task ':copyHelp' as it is up-to-date (took 0.774 secs). +Putting task artifact state for task ':copyHelp' into context took 0.001 secs. +Skipping task ':copyHelp' as it is up-to-date (took 0.144 secs). :copyHelp UP-TO-DATE -:copyHelp (Thread[#73,Task worker for ':',5,main]) completed. Took 0.824 secs. -:buildIndices (Thread[#73,Task worker for ':',5,main]) started. +:copyHelp (Thread[#93,Task worker for ':',5,main]) completed. Took 0.242 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 0.502 secs. It is not up-to-date because: +Up-to-date check for task ':buildIndices' took 0.354 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/Jmol.jar has been removed. Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+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-2.11.4.1+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-2.11.4.1+dfsg/classes:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/junit4.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-2.11.4.1+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-2.11.4.1+dfsg/classes:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/miglayout.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-server.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpcore.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/vamsas-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/biojava6-ontology.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsearch-indexer.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/mockito-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/groovy-all.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/guava.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/junit4.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jh.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/apache-mime4j-core.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/slf4j-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/intervalstorej.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jetty9-util.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis-jaxrpc.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-math3.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/testng.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jcommander.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/commons-discovery.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/Jmol.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpclient.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/axis.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/varna.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/log4j-1.2.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jsoup.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jswingreader.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/httpmime.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/json-simple.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxb-impl.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jaxrs-api.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/htsjdk.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/org.jfree.svg.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/min-jaba-client.jar:/build/reproducible-path/jalview-2.11.4.1+dfsg/cpJars/jersey1-core.jar com.sun.java.help.search.Indexer html Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/java'' -:buildIndices (Thread[#73,Task worker for ':',5,main]) completed. Took 2.146 secs. -:copyResources (Thread[#73,Task worker for ':',5,main]) started. +:buildIndices (Thread[#93,Task worker for ':',5,main]) completed. Took 2.117 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 0.039 secs). +Skipping task ':copyResources' as it is up-to-date (took 0.05 secs). :copyResources UP-TO-DATE -:copyResources (Thread[#73,Task worker for ':',5,main]) completed. Took 0.047 secs. -:copyChannelResources (Thread[#73,Task worker for ':',5,main]) started. +:copyResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.22 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 0.02 secs). +Skipping task ':copyChannelResources' as it is up-to-date (took 0.176 secs). :copyChannelResources UP-TO-DATE -:copyChannelResources (Thread[#73,Task worker for ':',5,main]) completed. Took 0.023 secs. -:createBuildProperties (Thread[#73,Task worker for ':',5,main]) started. +:copyChannelResources (Thread[#93,Task worker for ':',5,main]) completed. Took 0.179 secs. +:createBuildProperties (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :createBuildProperties -Putting task artifact state for task ':createBuildProperties' into context took 0.002 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-2.11.4.1+dfsg Command: sh debian/write_build_properties_file.sh Successfully started process 'command 'sh'' -:createBuildProperties (Thread[#73,Task worker for ':',5,main]) completed. Took 0.234 secs. -:buildResources (Thread[#73,Task worker for ':',5,main]) started. +:createBuildProperties (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 2.674 secs. +:buildResources (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :buildResources Skipping task ':buildResources' as it has no actions. -:buildResources (Thread[#73,Task worker for ':',5,main]) completed. Took 0.0 secs. -:copyDocs (Thread[#73,Task worker for ':',5,main]) started. +:buildResources (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.0 secs. +:copyDocs (Thread[#100,Task worker for ':' Thread 8,5,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 0.007 secs). :copyDocs UP-TO-DATE -:copyDocs (Thread[#73,Task worker for ':',5,main]) completed. Took 0.014 secs. -:convertMdFiles (Thread[#73,Task worker for ':',5,main]) started. +:copyDocs (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.01 secs. +:convertMdFiles (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :convertMdFiles Skipping task ':convertMdFiles' as it has no actions. :convertMdFiles UP-TO-DATE -:convertMdFiles (Thread[#73,Task worker for ':',5,main]) completed. Took 0.0 secs. -:releasesTemplates (Thread[#73,Task worker for ':',5,main]) started. +:convertMdFiles (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.0 secs. +:releasesTemplates (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :releasesTemplates Skipping task ':releasesTemplates' as it has no actions. :releasesTemplates UP-TO-DATE -:releasesTemplates (Thread[#73,Task worker for ':',5,main]) completed. Took 0.0 secs. -:prepare (Thread[#73,Task worker for ':',5,main]) started. +:releasesTemplates (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.0 secs. +:prepare (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :prepare Skipping task ':prepare' as it has no actions. -:prepare (Thread[#73,Task worker for ':',5,main]) completed. Took 0.0 secs. -:compileJava (Thread[#73,Task worker for ':',5,main]) started. +:prepare (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.0 secs. +:compileJava (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/main/java', not found file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/main/java', not found -Up-to-date check for task ':compileJava' took 2.185 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 4.059 secs. It is not up-to-date because: Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+dfsg/classes/com/github/reinert/jjschema/Attributes.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+dfsg/classes/com/stevesoft/pat/AmpersandRule.class has been added. Input property 'classpath' file /build/reproducible-path/jalview-2.11.4.1+dfsg/classes/com/stevesoft/pat/Any.class has been added. Setting target compatibility to 11 file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/main/java', not found Compiling with JDK Java compiler API. -/build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class - synchronized (firing) - ^ /build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/bin/Jalview.java:163: warning: [removal] Policy in java.security has been deprecated and marked for removal Policy.setPolicy(new Policy() ^ @@ -3218,6 +3251,9 @@ /build/reproducible-path/jalview-2.11.4.1+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-2.11.4.1+dfsg/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class + synchronized (firing) + ^ /build/reproducible-path/jalview-2.11.4.1+dfsg/src/jalview/io/AppletFormatAdapter.java:574: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal InputStream is = System.getSecurityManager().getClass() ^ @@ -3238,13 +3274,13 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings -:compileJava (Thread[#73,Task worker for ':',5,main]) completed. Took 24.656 secs. -:compileTestJava (Thread[#73,Task worker for ':',5,main]) started. +:compileJava (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 33.065 secs. +:compileTestJava (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/test/java', not found file or directory '/build/reproducible-path/jalview-2.11.4.1+dfsg/src/test/java', not found -Up-to-date check for task ':compileTestJava' took 0.134 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.502 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'. @@ -3254,96 +3290,96 @@ 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[#73,Task worker for ':',5,main]) completed. Took 6.177 secs. -:processTestResources (Thread[#73,Task worker for ':',5,main]) started. +:compileTestJava (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 15.728 secs. +:processTestResources (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.06 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.157 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#73,Task worker for ':',5,main]) completed. Took 0.35 secs. -:testClasses (Thread[#73,Task worker for ':',5,main]) started. +:processTestResources (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 1.012 secs. +:testClasses (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#73,Task worker for ':',5,main]) completed. Took 0.0 secs. -:testTask0 (Thread[#73,Task worker for ':',5,main]) started. +:testClasses (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 0.0 secs. +:testTask0 (Thread[#100,Task worker for ':' Thread 8,5,main]) started. :testTask0 Putting task artifact state for task ':testTask0' into context took 0.0 secs. -Up-to-date check for task ':testTask0' took 0.074 secs. It is not up-to-date because: +Up-to-date check for task ':testTask0' took 0.177 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/jalview-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7357961844163347721txt -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-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath205261446296773170txt -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 (0.136 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask0 +Finished generating test XML results (0.311 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask0 Generating HTML test report... -Finished generating test html results (0.106 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0 -:testTask0 (Thread[#73,Task worker for ':',5,main]) completed. Took 8.356 secs. -:testTask1 (Thread[#73,Task worker for ':',5,main]) started. +Finished generating test html results (0.191 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0 +:testTask0 (Thread[#100,Task worker for ':' Thread 8,5,main]) completed. Took 25.693 secs. +:testTask1 (Thread[#132,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 0.017 secs. It is not up-to-date because: +Up-to-date check for task ':testTask1' took 0.049 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/jalview-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath16591170753954952531txt -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-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7659609505573982391txt -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 (0.002 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask1 +Finished generating test XML results (0.021 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask1 Generating HTML test report... -Finished generating test html results (0.009 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1 +Finished generating test html results (0.052 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1/index.html -:testTask1 (Thread[#73,Task worker for ':',5,main]) completed. Took 2.574 secs. -:testTask2 (Thread[#73,Task worker for ':',5,main]) started. +:testTask1 (Thread[#132,Task worker for ':' Thread 40,5,main]) completed. Took 8.377 secs. +:testTask2 (Thread[#132,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 0.017 secs. It is not up-to-date because: +Up-to-date check for task ':testTask2' took 0.042 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/jalview-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4661962849663534566txt -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-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath11381369730265475821txt -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-2.11.4.1+dfsg/build/test-results/testTask2 +Finished generating test XML results (0.002 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask2 Generating HTML test report... -Finished generating test html results (0.003 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2 +Finished generating test html results (0.037 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2/index.html -:testTask2 (Thread[#73,Task worker for ':',5,main]) completed. Took 2.349 secs. -:testTask3 (Thread[#73,Task worker for ':',5,main]) started. +:testTask2 (Thread[#132,Task worker for ':' Thread 40,5,main]) completed. Took 7.835 secs. +:testTask3 (Thread[#132,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 0.011 secs. It is not up-to-date because: +Up-to-date check for task ':testTask3' took 0.022 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 4'. Working directory: /build/reproducible-path/jalview-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath628275176882901208txt -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-2.11.4.1+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17142049145450016023txt -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 (0.001 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask3 +Finished generating test XML results (0.01 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/test-results/testTask3 Generating HTML test report... -Finished generating test html results (0.004 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3 +Finished generating test html results (0.015 secs) into: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3 There were failing tests. See the report at: file:///build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3/index.html -:testTask3 (Thread[#73,Task worker for ':',5,main]) completed. Took 2.481 secs. -:test (Thread[#73,Task worker for ':',5,main]) started. +:testTask3 (Thread[#132,Task worker for ':' Thread 40,5,main]) completed. Took 6.653 secs. +:test (Thread[#132,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[#73,Task worker for ':',5,main]) completed. Took 0.004 secs. +:test (Thread[#132,Task worker for ':' Thread 40,5,main]) completed. Took 0.014 secs. -BUILD SUCCESSFUL in 1m 3s +BUILD SUCCESSFUL in 1m 51s 13 actionable tasks: 9 executed, 4 up-to-date -┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.367 seconds│ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.449 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.252 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.404 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 12.472 seconds │ -└─────────────────────────────────────────────────────────────────────────────────────────────────────┘ +┌──────────────────────────────────────────────────────────────────────────────────────────────────────┐ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 17.319 seconds│ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 8.089 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 7.478 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 6.403 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 39.289 seconds │ +└──────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3443,23 +3479,23 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 1m 3s +BUILD FAILED in 1m 51s 13 actionable tasks: 9 executed, 4 up-to-date -┌─────────────────────────────────────────────────────────────────────────────────────────────────────┐ -│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 5.367 seconds│ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.449 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.252 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 2.404 seconds │ -│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3/index.html │ -├─────────────────────────────────────────────────────────────────────────────────────────────────────┤ -│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 12.472 seconds │ -└─────────────────────────────────────────────────────────────────────────────────────────────────────┘ +┌──────────────────────────────────────────────────────────────────────────────────────────────────────┐ +│jalview:testTask0 results: SUCCESS (345 tests, 345 successes, 0 failures, 0 skipped) in 17.319 seconds│ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask0/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask1 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 8.089 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask1/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask2 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 7.478 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask2/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│jalview:testTask3 results: ----- (0 tests, 0 successes, 0 failures, 0 skipped) in 6.403 seconds │ +│Report file: /build/reproducible-path/jalview-2.11.4.1+dfsg/build/reports/tests/testTask3/index.html │ +├──────────────────────────────────────────────────────────────────────────────────────────────────────┤ +│OVERALL: results: FAILURE (345 tests, 345 successes, 0 failures, 0 skipped) in 39.289 seconds │ +└──────────────────────────────────────────────────────────────────────────────────────────────────────┘ FAILURE: Build failed with an exception. @@ -3555,8 +3591,8 @@ * Get more help at https://help.gradle.org -BUILD FAILED in 1m 3s -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 1m 51s +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 @@ -3608,12 +3644,14 @@ 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/1625273/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1625273/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/529953 and its subdirectories -I: Current time: Mon Feb 17 12:03:05 -12 2025 -I: pbuilder-time-stamp: 1739836985 +I: removing directory /srv/workspace/pbuilder/1625273 and its subdirectories +I: Current time: Mon Mar 23 20:42:22 +14 2026 +I: pbuilder-time-stamp: 1774248142