Diff of the two buildlogs: -- --- b1/build.log 2025-10-18 12:23:42.381543987 +0000 +++ b2/build.log 2025-10-18 12:30:24.598038860 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Oct 18 00:18:19 -12 2025 -I: pbuilder-time-stamp: 1760789899 +I: Current time: Sat Nov 21 08:46:45 +14 2026 +I: pbuilder-time-stamp: 1795200405 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying omit_blat_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1955947/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/412032/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Nov 20 18:47 /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/412032/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/412032/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=12 ' - 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=16 ' + 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='d3b3ded5e7054d26b970e4db21446697' - 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='1955947' - PS1='# ' - PS2='> ' + INVOCATION_ID=9dcf78e963404813a4faa397b4311479 + 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=412032 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.TJW9gR24/pbuilderrc_SaIz --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.TJW9gR24/b1 --logfile b1/build.log igv_2.18.5+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TJW9gR24/pbuilderrc_kNjf --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.TJW9gR24/b2 --logfile b2/build.log igv_2.18.5+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.48+deb13-cloud-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 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1955947/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/412032/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -646,7 +678,7 @@ Get: 471 http://deb.debian.org/debian forky/main amd64 libprotobuf-java all 3.21.12-14 [1268 kB] Get: 472 http://deb.debian.org/debian forky/main amd64 libswing-layout-java all 1.0.4-5 [44.1 kB] Get: 473 http://deb.debian.org/debian forky/main amd64 openjfx amd64 11.0.11+1-7 [7036 B] -Fetched 465 MB in 11s (43.7 MB/s) +Fetched 465 MB in 9s (49.3 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.) @@ -2196,8 +2228,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Oct 18 12:22:32 UTC 2025. -Universal Time is now: Sat Oct 18 12:22:32 UTC 2025. +Local time is now: Fri Nov 20 18:51:26 UTC 2026. +Universal Time is now: Fri Nov 20 18:51:26 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2799,7 +2831,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/igv-2.18.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igv_2.18.5+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/412032/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/412032/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/igv-2.18.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../igv_2.18.5+dfsg-1_source.changes dpkg-buildpackage: info: source package igv dpkg-buildpackage: info: source version 2.18.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2815,7 +2851,7 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle Duplicate specification "unlink|u" for option "u" -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/igv-2.18.5+dfsg' if [ -e src/main/resources/log4j.xml ] ; then rm src/main/resources/log4j.xml ; fi @@ -2842,83 +2878,83 @@ mkdir ../../src/main/resources-icons && \ mv *.png ../../src/main/resources-icons/ -** (process:1993889): WARNING **: 00:23:05.386: Unable to create profile directory (Permission denied) (13) +** (process:480813): WARNING **: 08:52:32.723: Unable to create profile directory (Permission denied) (13) -** (inkscape:1993889): WARNING **: 00:23:05.392: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. -** Message: 00:23:05.392: Cannot create profile directory /nonexistent/first-build/.config/inkscape. -** Message: 00:23:05.392: Inkscape will run with default settings, and new settings will not be saved. +** (inkscape:480813): WARNING **: 08:52:32.731: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. +** Message: 08:52:32.735: Cannot create profile directory /nonexistent/second-build/.config/inkscape. +** Message: 08:52:32.735: Inkscape will run with default settings, and new settings will not be saved. -** (inkscape:1993889): WARNING **: 00:23:05.460: Could not create directory '/nonexistent/first-build/.config/inkscape' +** (inkscape:480813): WARNING **: 08:52:32.835: Could not create directory '/nonexistent/second-build/.config/inkscape' -** (inkscape:1993889): WARNING **: 00:23:05.460: Could not create extension error log file '/nonexistent/first-build/.config/inkscape/extension-errors.log' +** (inkscape:480813): WARNING **: 08:52:32.835: Could not create extension error log file '/nonexistent/second-build/.config/inkscape/extension-errors.log' -(inkscape:1993889): Gtk-CRITICAL **: 00:23:05.485: Unable to create user data directory '/nonexistent/first-build/.local/share' for storing the recently used files list: Permission denied +(inkscape:480813): Gtk-CRITICAL **: 08:52:32.872: Unable to create user data directory '/nonexistent/second-build/.local/share' for storing the recently used files list: Permission denied -** (inkscape:1993889): WARNING **: 00:23:05.485: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. +** (inkscape:480813): WARNING **: 08:52:32.872: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. -** (process:1993896): WARNING **: 00:23:05.555: Unable to create profile directory (Permission denied) (13) +** (process:480820): WARNING **: 08:52:32.961: Unable to create profile directory (Permission denied) (13) -** (inkscape:1993896): WARNING **: 00:23:05.561: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. -** Message: 00:23:05.561: Cannot create profile directory /nonexistent/first-build/.config/inkscape. -** Message: 00:23:05.561: Inkscape will run with default settings, and new settings will not be saved. +** (inkscape:480820): WARNING **: 08:52:32.968: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. +** Message: 08:52:32.969: Cannot create profile directory /nonexistent/second-build/.config/inkscape. +** Message: 08:52:32.969: Inkscape will run with default settings, and new settings will not be saved. -** (inkscape:1993896): WARNING **: 00:23:05.630: Could not create directory '/nonexistent/first-build/.config/inkscape' +** (inkscape:480820): WARNING **: 08:52:33.061: Could not create directory '/nonexistent/second-build/.config/inkscape' -** (inkscape:1993896): WARNING **: 00:23:05.630: Could not create extension error log file '/nonexistent/first-build/.config/inkscape/extension-errors.log' +** (inkscape:480820): WARNING **: 08:52:33.061: Could not create extension error log file '/nonexistent/second-build/.config/inkscape/extension-errors.log' -(inkscape:1993896): Gtk-CRITICAL **: 00:23:05.656: Unable to create user data directory '/nonexistent/first-build/.local/share' for storing the recently used files list: Permission denied +(inkscape:480820): Gtk-CRITICAL **: 08:52:33.093: Unable to create user data directory '/nonexistent/second-build/.local/share' for storing the recently used files list: Permission denied -** (inkscape:1993896): WARNING **: 00:23:05.656: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. +** (inkscape:480820): WARNING **: 08:52:33.093: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. -** (process:1993903): WARNING **: 00:23:05.739: Unable to create profile directory (Permission denied) (13) +** (process:480827): WARNING **: 08:52:33.178: Unable to create profile directory (Permission denied) (13) -** (inkscape:1993903): WARNING **: 00:23:05.745: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. -** Message: 00:23:05.745: Cannot create profile directory /nonexistent/first-build/.config/inkscape. -** Message: 00:23:05.745: Inkscape will run with default settings, and new settings will not be saved. +** (inkscape:480827): WARNING **: 08:52:33.185: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. +** Message: 08:52:33.187: Cannot create profile directory /nonexistent/second-build/.config/inkscape. +** Message: 08:52:33.187: Inkscape will run with default settings, and new settings will not be saved. -** (inkscape:1993903): WARNING **: 00:23:05.812: Could not create directory '/nonexistent/first-build/.config/inkscape' +** (inkscape:480827): WARNING **: 08:52:33.278: Could not create directory '/nonexistent/second-build/.config/inkscape' -** (inkscape:1993903): WARNING **: 00:23:05.812: Could not create extension error log file '/nonexistent/first-build/.config/inkscape/extension-errors.log' +** (inkscape:480827): WARNING **: 08:52:33.278: Could not create extension error log file '/nonexistent/second-build/.config/inkscape/extension-errors.log' -(inkscape:1993903): Gtk-CRITICAL **: 00:23:05.837: Unable to create user data directory '/nonexistent/first-build/.local/share' for storing the recently used files list: Permission denied +(inkscape:480827): Gtk-CRITICAL **: 08:52:33.310: Unable to create user data directory '/nonexistent/second-build/.local/share' for storing the recently used files list: Permission denied -** (inkscape:1993903): WARNING **: 00:23:05.837: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. +** (inkscape:480827): WARNING **: 08:52:33.310: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. -** (process:1993910): WARNING **: 00:23:05.906: Unable to create profile directory (Permission denied) (13) +** (process:480834): WARNING **: 08:52:33.397: Unable to create profile directory (Permission denied) (13) -** (inkscape:1993910): WARNING **: 00:23:05.912: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. -** Message: 00:23:05.913: Cannot create profile directory /nonexistent/first-build/.config/inkscape. -** Message: 00:23:05.913: Inkscape will run with default settings, and new settings will not be saved. +** (inkscape:480834): WARNING **: 08:52:33.404: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. +** Message: 08:52:33.404: Cannot create profile directory /nonexistent/second-build/.config/inkscape. +** Message: 08:52:33.404: Inkscape will run with default settings, and new settings will not be saved. -** (inkscape:1993910): WARNING **: 00:23:05.982: Could not create directory '/nonexistent/first-build/.config/inkscape' +** (inkscape:480834): WARNING **: 08:52:33.504: Could not create directory '/nonexistent/second-build/.config/inkscape' -** (inkscape:1993910): WARNING **: 00:23:05.982: Could not create extension error log file '/nonexistent/first-build/.config/inkscape/extension-errors.log' +** (inkscape:480834): WARNING **: 08:52:33.505: Could not create extension error log file '/nonexistent/second-build/.config/inkscape/extension-errors.log' -(inkscape:1993910): Gtk-CRITICAL **: 00:23:06.008: Unable to create user data directory '/nonexistent/first-build/.local/share' for storing the recently used files list: Permission denied +(inkscape:480834): Gtk-CRITICAL **: 08:52:33.539: Unable to create user data directory '/nonexistent/second-build/.local/share' for storing the recently used files list: Permission denied -** (inkscape:1993910): WARNING **: 00:23:06.008: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. +** (inkscape:480834): WARNING **: 08:52:33.539: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. -** (process:1993917): WARNING **: 00:23:06.079: Unable to create profile directory (Permission denied) (13) +** (process:480841): WARNING **: 08:52:33.637: Unable to create profile directory (Permission denied) (13) -** (inkscape:1993917): WARNING **: 00:23:06.085: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. -** Message: 00:23:06.085: Cannot create profile directory /nonexistent/first-build/.config/inkscape. -** Message: 00:23:06.085: Inkscape will run with default settings, and new settings will not be saved. +** (inkscape:480841): WARNING **: 08:52:33.644: Failed to wrap object of type 'PangoFT2FontMap'. Hint: this error is commonly caused by failing to call a library init() function. +** Message: 08:52:33.645: Cannot create profile directory /nonexistent/second-build/.config/inkscape. +** Message: 08:52:33.645: Inkscape will run with default settings, and new settings will not be saved. -** (inkscape:1993917): WARNING **: 00:23:06.157: Could not create directory '/nonexistent/first-build/.config/inkscape' +** (inkscape:480841): WARNING **: 08:52:33.745: Could not create directory '/nonexistent/second-build/.config/inkscape' -** (inkscape:1993917): WARNING **: 00:23:06.157: Could not create extension error log file '/nonexistent/first-build/.config/inkscape/extension-errors.log' +** (inkscape:480841): WARNING **: 08:52:33.745: Could not create extension error log file '/nonexistent/second-build/.config/inkscape/extension-errors.log' -(inkscape:1993917): Gtk-CRITICAL **: 00:23:06.184: Unable to create user data directory '/nonexistent/first-build/.local/share' for storing the recently used files list: Permission denied +(inkscape:480841): Gtk-CRITICAL **: 08:52:33.778: Unable to create user data directory '/nonexistent/second-build/.local/share' for storing the recently used files list: Permission denied -** (inkscape:1993917): WARNING **: 00:23:06.184: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. +** (inkscape:480841): WARNING **: 08:52:33.779: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function. make[1]: Leaving directory '/build/reproducible-path/igv-2.18.5+dfsg' jh_linkjars -O--buildsystem=gradle -Duplicate specification "u=s" for option "u" Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" dh_auto_build -O--buildsystem=gradle 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=igv -Dfile.encoding=UTF-8 --parallel --max-workers=12 jar + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=16 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) @@ -2926,18 +2962,18 @@ 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/igv-2.18.5+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=US -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 0.648 secs. -The client will now receive all logging from the daemon (pid: 1994038). The daemon log file: /build/reproducible-path/igv-2.18.5+dfsg/.gradle/daemon/4.4.1/daemon-1994038.out.log +An attempt to start the daemon took 1.023 secs. +The client will now receive all logging from the daemon (pid: 480958). The daemon log file: /build/reproducible-path/igv-2.18.5+dfsg/.gradle/daemon/4.4.1/daemon-480958.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6021d7d4 -Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6021d7d4 -Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@16aeb4ea +Using 16 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@56af64a8 +Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@56af64a8 +Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@25c6f494 Starting Build Compiling initialization script '/build/reproducible-path/igv-2.18.5+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@10411316 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3ab664a4 Compiling initialization script '/build/reproducible-path/igv-2.18.5+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/igv-2.18.5+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/igv-2.18.5+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2954,15 +2990,15 @@ 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/igv-2.18.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@356b6b5e +Creating new cache for annotation-processors, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1a4b0d3c Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@16aeb4ea -Creating new cache for taskHistory, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@253768f6 -Creating new cache for outputFiles, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4063d91f -:compileJava (Thread[#51,Task worker for ':' Thread 2,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@25c6f494 +Creating new cache for taskHistory, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@634d7ab9 +Creating new cache for outputFiles, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cb04e4 +:compileJava (Thread[#61,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.002 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@c704167 +Putting task artifact state for task ':compileJava' into context took 0.003 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@45bd5a13 Loading the Maven rules... Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian @@ -3063,7 +3099,7 @@ at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found -Up-to-date check for task ':compileJava' took 1.708 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 2.587 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found @@ -3073,38 +3109,38 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileJava (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 7.727 secs. -:processResources (Thread[#51,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#61,Task worker for ':',5,main]) completed. Took 10.98 secs. +:processResources (Thread[#61,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.036 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.095 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.119 secs. -:classes (Thread[#51,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#61,Task worker for ':',5,main]) completed. Took 0.225 secs. +:classes (Thread[#61,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[#51,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#61,Task worker for ':',5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[#61,Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/igv-2.18.5+dfsg/build/debian/igv.pom -:debianMavenPom (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.049 secs. -:jar (Thread[#51,Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[#61,Task worker for ':',5,main]) completed. Took 0.069 secs. +:jar (Thread[#61,Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.018 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.024 secs. It is not up-to-date because: No history is available. -:jar (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.377 secs. +:jar (Thread[#61,Task worker for ':',5,main]) completed. Took 0.525 secs. -BUILD SUCCESSFUL in 11s +BUILD SUCCESSFUL in 17s 4 actionable tasks: 4 executed jh_build -O--buildsystem=gradle dh_auto_test -O--buildsystem=gradle 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=igv -Dfile.encoding=UTF-8 --parallel --max-workers=12 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=igv -Dfile.encoding=UTF-8 --parallel --max-workers=16 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) @@ -3112,17 +3148,17 @@ 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/igv-2.18.5+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=US -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 0.625 secs. -The client will now receive all logging from the daemon (pid: 1994351). The daemon log file: /build/reproducible-path/igv-2.18.5+dfsg/.gradle/daemon/4.4.1/daemon-1994351.out.log +An attempt to start the daemon took 0.856 secs. +The client will now receive all logging from the daemon (pid: 481635). The daemon log file: /build/reproducible-path/igv-2.18.5+dfsg/.gradle/daemon/4.4.1/daemon-481635.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. -Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e6ac485 -Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e6ac485 -Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@35231a39 +Using 16 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1e075fc0 +Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1e075fc0 +Creating new cache for fileHashes, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7ea240f Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@176ce180 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@41b742c8 Settings evaluated using settings file '/build/reproducible-path/igv-2.18.5+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/igv-2.18.5+dfsg/build.gradle'. Included projects: [root project 'igv'] @@ -3134,15 +3170,15 @@ 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/igv-2.18.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2b01c1ee +Creating new cache for annotation-processors, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a4ab267 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@35231a39 -Creating new cache for taskHistory, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@718b3999 -Creating new cache for outputFiles, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4d1d340b -:compileJava (Thread[#50,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7ea240f +Creating new cache for taskHistory, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@6704b5f8 +Creating new cache for outputFiles, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e4c801d +:compileJava (Thread[#61,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.002 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@29da7d45 +Putting task artifact state for task ':compileJava' into context took 0.004 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/igv-2.18.5+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3578a528 Loading the Maven rules... Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian @@ -3195,24 +3231,24 @@ Passing through xml-apis:xml-apis-1.4:jar:debian file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found -Skipping task ':compileJava' as it is up-to-date (took 0.534 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.77 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 0.553 secs. -:processResources (Thread[#50,Task worker for ':',5,main]) started. +:compileJava (Thread[#61,Task worker for ':',5,main]) completed. Took 0.8 secs. +:processResources (Thread[#61,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Skipping task ':processResources' as it is up-to-date (took 0.026 secs). +Skipping task ':processResources' as it is up-to-date (took 0.06 secs). :processResources UP-TO-DATE -:processResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.029 secs. -:classes (Thread[#50,Task worker for ':',5,main]) started. +:processResources (Thread[#61,Task worker for ':',5,main]) completed. Took 0.065 secs. +:classes (Thread[#61,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. -:compileTestJava (Thread[#50,Task worker for ':',5,main]) started. +:classes (Thread[#61,Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[#63,Task worker for ':' Thread 3,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. -Malformed class file [SortOption.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [FrameManager$ChangeEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3261,7 +3297,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [SupplementaryAlignment$SupplementaryNeighbors.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [OAuthProvider$AuthStateEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3310,7 +3346,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [InsertionSelectionEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SortOption.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3359,7 +3395,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [FrameManager$ChangeEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SupplementaryAlignment$SupplementaryNeighbors.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3408,7 +3444,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [AlignmentTrackEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [InsertionSelectionEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3555,7 +3591,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [OAuthProvider$AuthStateEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [AlignmentTrackEvent.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3609,7 +3645,7 @@ Ignoring org.glassfish.jersey.core:jersey-common:jar:2.34 file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found -Up-to-date check for task ':compileTestJava' took 0.429 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 0.813 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found @@ -3619,19 +3655,19 @@ 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[#50,Task worker for ':',5,main]) completed. Took 2.566 secs. -:processTestResources (Thread[#50,Task worker for ':',5,main]) started. +:compileTestJava (Thread[#63,Task worker for ':' Thread 3,5,main]) completed. Took 4.737 secs. +:processTestResources (Thread[#63,Task worker for ':' Thread 3,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. file or directory '/build/reproducible-path/igv-2.18.5+dfsg/src/test/resources', not found Skipping task ':processTestResources' as it has no source files and no previous output files. :processTestResources NO-SOURCE -:processTestResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.002 secs. -:testClasses (Thread[#50,Task worker for ':',5,main]) started. +:processTestResources (Thread[#63,Task worker for ':' Thread 3,5,main]) completed. Took 0.003 secs. +:testClasses (Thread[#63,Task worker for ':' Thread 3,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. -:test (Thread[#50,Task worker for ':',5,main]) started. +:testClasses (Thread[#63,Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. +:test (Thread[#63,Task worker for ':' Thread 3,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Replacing org.junit.vintage:junit-vintage-engine:jar:5.8.2 -> org.junit.vintage:junit-vintage-engine:jar:debian @@ -3641,55 +3677,100 @@ Passing through org.opentest4j:opentest4j:jar:debian Passing through org.junit.platform:junit-platform-commons:jar:debian file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found -Up-to-date check for task ':test' took 0.527 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.72 secs. It is not up-to-date because: No history is available. file or directory '/build/reproducible-path/igv-2.18.5+dfsg/lib', not found -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath7340874083819133814txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' -Successfully started process 'Gradle Test Executor 1' Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath17205676043627361834txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath9326460676394132168txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' +Starting process 'Gradle Test Executor 7'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath9411274535172765681txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 7' Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath2049136209864652290txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath4866244007669950865txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' +Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath5472457231622943262txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Starting process 'Gradle Test Executor 4'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath7153240553567876210txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 4' -Starting process 'Gradle Test Executor 5'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath12216875602306745179txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 5' -Successfully started process 'Gradle Test Executor 2' -Starting process 'Gradle Test Executor 6'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= - -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-cloud-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT-12:00 @/tmp/gradle-worker-classpath400154596103006190txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 6' + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath8874788224710262152txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 4' +Successfully started process 'Gradle Test Executor 7' Successfully started process 'Gradle Test Executor 3' +Successfully started process 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 4' +Successfully started process 'Gradle Test Executor 2' +Starting process 'Gradle Test Executor 8'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath14930349009376760692txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 8' +Starting process 'Gradle Test Executor 5'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath1825198016403291467txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 5' +Starting process 'Gradle Test Executor 6'. Working directory: /build/reproducible-path/igv-2.18.5+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Ddebian.package=igv -Dfile.separator=/ -Dignore.ioexceptions=false -Dinclude.longrunning=false -Djava.awt.headless=true -Djava.class.path=/usr/share/gradle/lib/gradle-launcher-4.4.1.jar -Djava.class.version=65.0 -Djava.home=/usr/lib/jvm/java-21-openjdk-amd64 -Djava.library.path=/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib -Djava.runtime.name=OpenJDK Runtime Environment -Djava.runtime.version=21.0.9-ea+8-Debian-1 -Djava.specification.name=Java Platform API Specification -Djava.specification.vendor=Oracle Corporation -Djava.specification.version=21 -Djava.vendor=Debian -Djava.vendor.url=https://tracker.debian.org/openjdk-21 -Djava.vendor.url.bug=https://bugs.debian.org/openjdk-21 -Djava.version=21.0.9-ea -Djava.version.date=2025-10-21 -Djava.vm.compressedOopsMode=Zero based -Djava.vm.info=mixed mode, sharing -Djava.vm.name=OpenJDK 64-Bit Server VM -Djava.vm.specification.name=Java Virtual Machine Specification -Djava.vm.specification.vendor=Oracle Corporation -Djava.vm.specification.version=21 -Djava.vm.vendor=Debian -Djava.vm.version=21.0.9-ea+8-Debian-1 -Djdk.debug=release -Dlibrary.jansi.path=/build/reproducible-path/igv-2.18.5+dfsg/.gradle/native/jansi/null/linux64 -Dline.separator= + -Dmake.fail=false -Dnative.encoding=ANSI_X3.4-1968 -Dorg.gradle.appname=gradle -Dorg.gradle.jvmargs=-Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dorg.gradle.native=false -Dos.arch=amd64 -Dos.name=Linux -Dos.version=6.12.48+deb13-amd64 -Dpath.separator=: -Dsamjdk.snappy.disable=true -Dstderr.encoding=ANSI_X3.4-1968 -Dstdout.encoding=ANSI_X3.4-1968 -Dsun.arch.data.model=64 -Dsun.boot.library.path=/usr/lib/jvm/java-21-openjdk-amd64/lib -Dsun.cpu.endian=little -Dsun.io.unicode.encoding=UnicodeLittle -Dsun.java.command=org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 -Dsun.java.launcher=SUN_STANDARD -Dsun.jnu.encoding=ANSI_X3.4-1968 -Dsun.management.compiler=HotSpot 64-Bit Tiered Compilers -Duser.dir=/build/reproducible-path/igv-2.18.5+dfsg -Duser.home=. -Duser.name=debian -Duser.timezone=GMT+14:00 @/tmp/gradle-worker-classpath10594494990928178952txt -Xmx2g -Dfile.encoding=UTF-8 -Djava.io.tmpdir=/tmp -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 6' +Successfully started process 'Gradle Test Executor 8' Successfully started process 'Gradle Test Executor 6' Successfully started process 'Gradle Test Executor 5' -Gradle Test Executor 1 started executing tests. -Gradle Test Executor 6 started executing tests. +Gradle Test Executor 4 started executing tests. Gradle Test Executor 3 started executing tests. Gradle Test Executor 2 started executing tests. -Gradle Test Executor 4 started executing tests. +Gradle Test Executor 7 started executing tests. +Gradle Test Executor 1 started executing tests. + +org.broad.tribble.TribbleFeatureReaderTest > testQuery SKIPPED + +org.broad.tribble.TribbleFeatureReaderTest > testGetSequenceNames SKIPPED + +org.broad.igv.htsget.HtsgetVariantSourceTest > testReadFeatures SKIPPED +org.broad.igv.htsget.HtsgetVariantSourceTest > testGetHeader SKIPPED + +org.broad.igv.tdf.TDFReaderTest > testReader SKIPPED Gradle Test Executor 5 started executing tests. -org.broad.igv.sam.mods.BaseModificationsTest > testOrientBotFwd STANDARD_OUT - 115 -org.broad.igv.sam.cram.CRAMReaderTest > testQueryLocalBaiCram SKIPPED +org.broad.igv.feature.ProbeToGeneMapTest > testAgilent SKIPPED -org.broad.igv.sam.cram.CRAMReaderTest > testRemoteCraiCram SKIPPED +org.broad.igv.feature.ProbeToGeneMapTest > testAffy SKIPPED -org.broad.igv.sam.cram.CRAMReaderTest > testIterateLocalCraiCram SKIPPED +org.broad.igv.feature.ProbeToGeneMapTest > testIllumina SKIPPED +Gradle Test Executor 6 started executing tests. -org.broad.igv.sam.cram.CRAMReaderTest > testQueryLocalCraiCram SKIPPED +org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigInteract SKIPPED -org.broad.igv.sam.cram.CRAMReaderTest > testRemoteBaiCram SKIPPED +org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigRmsk SKIPPED -org.broad.igv.sam.mods.BaseModificationsTest > testOrientBotFwd STANDARD_OUT - -115 - -90 - -64 +org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigNarrowpeak SKIPPED +Gradle Test Executor 8 started executing tests. -org.broad.tribble.TribbleFeatureReaderTest > testQuery SKIPPED +org.broad.igv.htsget.HtsgetBAMReaderTest > testQueryAlignments SKIPPED -org.broad.tribble.TribbleFeatureReaderTest > testGetSequenceNames SKIPPED +org.broad.igv.htsget.HtsgetReaderTest > testReadHeader SKIPPED + +org.broad.igv.htsget.HtsgetReaderTest > testReadData SKIPPED + +org.broad.igv.batch.CommandExecutorTest STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test + +org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigGenePred SKIPPED + +org.broad.igv.tools.motiffinder.MotifFinderPluginHeadedTest STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test + +org.broad.igv.tools.converters.GFFtoBedTest > testConvert STANDARD_ERROR + Nov 21, 2026 8:53:04 AM java.util.prefs.FileSystemPreferences$1 run + INFO: Created user preferences directory. + +org.broad.igv.ui.panel.ReferenceFrameTestHeaded STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test + +org.broad.igv.util.blat.BlatClientTest > blatPOST SKIPPED + +org.broad.igv.util.blat.BlatClientTest > blatGET SKIPPED + +org.broad.igv.util.blat.BlatClientTest > blatTooShort SKIPPED + +org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > compareSequences SKIPPED + +org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > findBlockContaining SKIPPED + +org.broad.igv.ucsc.bb.BBDataSourceTest > testBigWigZoom SKIPPED + +org.broad.igv.ucsc.bb.BBDataSourceTest > testBigWigWig SKIPPED + +org.broad.igv.ucsc.bb.BBDataSourceTest > testUncompressedBigwig SKIPPED org.broad.igv.sam.SamQueryTextReaderTest > testMoran SKIPPED @@ -3699,17 +3780,98 @@ org.broad.igv.sam.SamQueryTextReaderTest > testQuery3 SKIPPED -org.broad.igv.sam.SamIndexTest > testGetIndexedChromosomes SKIPPED +org.broad.igv.util.ResourceLocatorTest > testGetFormat STANDARD_OUT + bam + +org.broad.igv.track.TrackLoaderTestHeaded STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test +Gradle Test Executor 1 finished executing tests. + +org.broad.igv.util.collections.DoubleArrayListTest > test STANDARD_OUT + IntArrayList time: 3 + +org.broad.igv.batch.CommandListenerTest STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test + +org.broad.igv.tools.motiffinder.MotifFinderDialogHeadedTest STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test + +org.broad.igv.data.cufflinks.ExpDiffCodecTest > testsamplegene_expdiff STANDARD_ERROR + SEVERE [Nov 21,2026 08:53] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be parsed as a float + SEVERE [Nov 21,2026 08:53] [ExpDiffCodec] LogRatio 1.79769e+308 cannot be parsed as a float + SEVERE [Nov 21,2026 08:53] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be parsed as a float + +org.broad.igv.util.ArrayMemoryTest > compareMemory SKIPPED + +org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesCompressed SKIPPED + +org.broad.igv.AbstractHeadlessTest > initializationError SKIPPED + +org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesByRegionCompressed SKIPPED + +org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesByRegion SKIPPED org.broad.igv.sam.mods.BaseModificationCountsTest > incrementCounts2 SKIPPED +Gradle Test Executor 4 finished executing tests. + +org.broad.igv.ucsc.bb.BBFileTest > testChromTree SKIPPED + +org.broad.igv.tools.parsers.TestBEDCodecs > testGffTags SKIPPED + +org.broad.igv.tools.parsers.TestBEDCodecs > testLength1Feature SKIPPED + +org.broad.igv.sam.BAMFileReaderTest > testClose SKIPPED + +org.broad.igv.sam.BAMFileReaderTest > testQueryAgainstSam SKIPPED +Gradle Test Executor 3 finished executing tests. org.broad.igv.feature.genome.load.JsonGenomeLoaderTest > loadGenome SKIPPED -org.broad.igv.sam.mods.BaseModificationsTest > testOrientBotFwd STANDARD_ERROR - Oct 18, 2025 12:23:26 AM java.util.prefs.FileSystemPreferences$1 run - INFO: Created user preferences directory. +org.broad.igv.ucsc.twobit.TwoBitSequenceTest > readSequenceRemote SKIPPED -org.broad.igv.sam.AsciiLineReaderTest > testSpeed SKIPPED +org.broad.igv.tools.motiffinder.MotifFinderPluginHeadlessTest STANDARD_OUT + You are trying to start a GUI in a headless environment. Aborting test +Gradle Test Executor 5 finished executing tests. + +org.broad.igv.prefs.PreferencesManagerTest > getPreferences SKIPPED + +org.broad.igv.sam.SamIndexTest > testGetIndexedChromosomes SKIPPED + +org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT + Random sort: 234 +Gradle Test Executor 6 finished executing tests. + +org.broad.igv.util.collections.IntArrayListTest > test STANDARD_OUT + IntArrayList time: 136 + +org.broad.igv.util.blat.LegacyBlatClientTest > fixWebBlat SKIPPED + +org.broad.igv.util.blat.LegacyBlatClientTest > parseUCSCResult SKIPPED + +org.broad.igv.util.blat.LegacyBlatClientTest > parseCustomResult SKIPPED + +org.broad.igv.sam.cram.CRAMReaderTest > testQueryLocalBaiCram SKIPPED + +org.broad.igv.sam.cram.CRAMReaderTest > testRemoteCraiCram SKIPPED + +org.broad.igv.sam.cram.CRAMReaderTest > testIterateLocalCraiCram SKIPPED + +org.broad.igv.sam.cram.CRAMReaderTest > testQueryLocalCraiCram SKIPPED + +org.broad.igv.sam.cram.CRAMReaderTest > testRemoteBaiCram SKIPPED +Gradle Test Executor 7 finished executing tests. + +org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT + Random sort (reversed): 198 + +org.broad.igv.util.FileUtilsTest > testFindRelativeHttpPath STANDARD_OUT + dir/test.txt + +org.broad.igv.sam.mods.BaseModificationsTest > testOrientBotFwd STANDARD_OUT + 115 + -115 + -90 + -64 org.broad.igv.sam.mods.BaseModificationsTest > testHiFINegativeAlignment STANDARD_OUT 0 0 0 @@ -3968,148 +4130,28 @@ 253 -3 253 254 -2 254 255 -1 255 - -org.broad.igv.htsget.HtsgetReaderTest > testReadHeader SKIPPED - -org.broad.igv.htsget.HtsgetReaderTest > testReadData SKIPPED - -org.broad.igv.ucsc.bb.BBFileTest > testChromTree SKIPPED - -org.broad.igv.tools.motiffinder.MotifFinderPluginHeadedTest STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test - -org.broad.igv.sam.BAMFileReaderTest > testClose SKIPPED - -org.broad.igv.sam.BAMFileReaderTest > testQueryAgainstSam SKIPPED - -org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > compareSequences SKIPPED - -org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequenceTest > findBlockContaining SKIPPED - -org.broad.igv.feature.ProbeToGeneMapTest > testAgilent SKIPPED - -org.broad.igv.feature.ProbeToGeneMapTest > testAffy SKIPPED - -org.broad.igv.feature.ProbeToGeneMapTest > testIllumina SKIPPED - -org.broad.igv.ucsc.bb.BBDataSourceTest > testBigWigZoom SKIPPED - -org.broad.igv.ucsc.bb.BBDataSourceTest > testBigWigWig SKIPPED - -org.broad.igv.ucsc.bb.BBDataSourceTest > testUncompressedBigwig SKIPPED - -org.broad.igv.tdf.TDFReaderTest > testReader SKIPPED - -org.broad.igv.prefs.PreferencesManagerTest > getPreferences SKIPPED - -org.broad.igv.tools.motiffinder.MotifFinderDialogHeadedTest STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test - -org.broad.igv.batch.CommandListenerTest STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test - -org.broad.igv.batch.CommandExecutorTest STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test - -org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesCompressed SKIPPED - -org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesByRegionCompressed SKIPPED - -org.broad.igv.sam.cram.IGVReferenceSourceTest > testGetReferenceBasesByRegion SKIPPED - -org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigInteract SKIPPED - -org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigRmsk SKIPPED - -org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigNarrowpeak SKIPPED - -org.broad.igv.util.blat.LegacyBlatClientTest > fixWebBlat SKIPPED - -org.broad.igv.util.blat.BlatClientTest > blatPOST SKIPPED - -org.broad.igv.util.blat.LegacyBlatClientTest > parseUCSCResult SKIPPED - -org.broad.igv.util.blat.LegacyBlatClientTest > parseCustomResult SKIPPED - -org.broad.igv.util.ResourceLocatorTest > testGetFormat STANDARD_OUT - bam - -org.broad.igv.util.blat.BlatClientTest > blatGET SKIPPED - -org.broad.igv.util.blat.BlatClientTest > blatTooShort SKIPPED - -org.broad.igv.ucsc.bb.BBFeatureSourceTest > testBigGenePred SKIPPED +Gradle Test Executor 8 finished executing tests. org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT - Random sort: 155 -Gradle Test Executor 5 finished executing tests. - -org.broad.igv.data.cufflinks.ExpDiffCodecTest > testsamplegene_expdiff STANDARD_ERROR - SEVERE [Oct 18,2025 00:23] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be parsed as a float - SEVERE [Oct 18,2025 00:23] [ExpDiffCodec] LogRatio 1.79769e+308 cannot be parsed as a float - -org.broad.igv.ucsc.twobit.TwoBitSequenceTest > readSequenceRemote SKIPPED - -org.broad.igv.data.cufflinks.ExpDiffCodecTest > testsamplegene_expdiff STANDARD_ERROR - SEVERE [Oct 18,2025 00:23] [ExpDiffCodec] LogRatio -1.79769e+308 cannot be parsed as a float -Gradle Test Executor 6 finished executing tests. - -org.broad.igv.tools.motiffinder.MotifFinderPluginHeadlessTest STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test + Random sort (Arrays): 592 + Sorted sort: 74 + Reverse sorted sort: 74 + Almost sorted sort: 77 org.broad.igv.util.LittleEndianInputStreamTest > testRead SKIPPED -org.broad.igv.util.ArrayMemoryTest > compareMemory SKIPPED - -org.broad.igv.htsget.HtsgetBAMReaderTest > testQueryAlignments SKIPPED - -org.broad.igv.util.collections.IntArrayListTest > test STANDARD_OUT - IntArrayList time: 65 - -org.broad.igv.tools.parsers.TestBEDCodecs > testGffTags SKIPPED - -org.broad.igv.tools.parsers.TestBEDCodecs > testLength1Feature SKIPPED - -org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT - Random sort (reversed): 154 - -org.broad.igv.htsget.HtsgetVariantSourceTest > testReadFeatures SKIPPED - -org.broad.igv.htsget.HtsgetVariantSourceTest > testGetHeader SKIPPED - -org.broad.igv.util.collections.DoubleArrayListTest > test STANDARD_OUT - IntArrayList time: 0 - -org.broad.igv.util.FileUtilsTest > testFindRelativeHttpPath STANDARD_OUT - dir/test.txt - org.broad.igv.util.IGVHttpClientUtilsTest > testExists SKIPPED org.broad.igv.util.IGVHttpClientUtilsTest > testGetContentLength SKIPPED -org.broad.igv.track.TrackLoaderTestHeaded STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test -Gradle Test Executor 3 finished executing tests. - -org.broad.igv.AbstractHeadlessTest > initializationError SKIPPED +org.broad.igv.sam.AsciiLineReaderTest > testSpeed SKIPPED Gradle Test Executor 2 finished executing tests. -Gradle Test Executor 4 finished executing tests. - -org.broad.igv.util.HeapSortTest > tesArraySort STANDARD_OUT - Random sort (Arrays): 485 - Sorted sort: 63 - Reverse sorted sort: 65 - Almost sorted sort: 76 - -org.broad.igv.ui.panel.ReferenceFrameTestHeaded STANDARD_OUT - You are trying to start a GUI in a headless environment. Aborting test -Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.04 secs) into: /build/reproducible-path/igv-2.18.5+dfsg/build/test-results/test +Finished generating test XML results (0.034 secs) into: /build/reproducible-path/igv-2.18.5+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.068 secs) into: /build/reproducible-path/igv-2.18.5+dfsg/build/reports/tests/test -:test (Thread[#50,Task worker for ':',5,main]) completed. Took 3.136 secs. +Finished generating test html results (0.061 secs) into: /build/reproducible-path/igv-2.18.5+dfsg/build/reports/tests/test +:test (Thread[#63,Task worker for ':' Thread 3,5,main]) completed. Took 4.567 secs. -BUILD SUCCESSFUL in 9s +BUILD SUCCESSFUL in 14s 4 actionable tasks: 2 executed, 2 up-to-date create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=gradle @@ -4135,7 +4177,7 @@ jh_installlibs -O--buildsystem=gradle jh_classpath -O--buildsystem=gradle jh_manifest -O--buildsystem=gradle -Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle @@ -4155,12 +4197,14 @@ 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/412032/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/412032/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/1955947 and its subdirectories -I: Current time: Sat Oct 18 00:23:41 -12 2025 -I: pbuilder-time-stamp: 1760790221 +I: removing directory /srv/workspace/pbuilder/412032 and its subdirectories +I: Current time: Sat Nov 21 08:53:24 +14 2026 +I: pbuilder-time-stamp: 1795200804