Diff of the two buildlogs: -- --- b1/build.log 2025-01-07 22:38:36.075685386 +0000 +++ b2/build.log 2025-01-07 22:43:53.453230409 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 9 16:50:26 -12 2026 -I: pbuilder-time-stamp: 1770699026 +I: Current time: Wed Jan 8 12:38:39 +14 2025 +I: pbuilder-time-stamp: 1736289519 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying flaky_test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/126427/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/458117/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +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 Jan 7 22:38 /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/458117/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/458117/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='809322d83bf649c8897d00dceff196e8' - 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='126427' - PS1='# ' - PS2='> ' + INVOCATION_ID=4d000ff272194fa5864373e674382731 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=458117 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.0CK5FTin/pbuilderrc_FvdL --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0CK5FTin/b1 --logfile b1/build.log milib_2.2.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0CK5FTin/pbuilderrc_te3j --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0CK5FTin/b2 --logfile b2/build.log milib_2.2.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/126427/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/458117/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -524,7 +556,7 @@ Get: 377 http://deb.debian.org/debian trixie/main arm64 libmockito-java all 3.3.0-2 [510 kB] Get: 378 http://deb.debian.org/debian trixie/main arm64 libredberry-pipe-java all 1.0.0~alpha0-3 [62.7 kB] Get: 379 http://deb.debian.org/debian trixie/main arm64 libtrove3-java all 3.0.3-5 [2146 kB] -Fetched 327 MB in 3s (105 MB/s) +Fetched 327 MB in 2s (135 MB/s) Preconfiguring packages ... Selecting previously unselected package libapparmor1:arm64. (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 ... 20097 files and directories currently installed.) @@ -1778,8 +1810,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Feb 10 04:52:46 UTC 2026. -Universal Time is now: Tue Feb 10 04:52:46 UTC 2026. +Local time is now: Tue Jan 7 22:40:34 UTC 2025. +Universal Time is now: Tue Jan 7 22:40:34 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2299,7 +2331,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/milib-2.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../milib_2.2.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/458117/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/458117/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/milib-2.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../milib_2.2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package milib dpkg-buildpackage: info: source version 2.2.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2317,7 +2353,7 @@ make[1]: [debian/rules:11: override_dh_auto_clean] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/milib-2.2.0+dfsg' jh_clean -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" dh_clean debian/rules binary dh binary --with javahelper --with maven_repo_helper @@ -2342,18 +2378,18 @@ 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/milib-2.2.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-arm64/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 4.718 secs. -The client will now receive all logging from the daemon (pid: 144341). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-144341.out.log +An attempt to start the daemon took 0.982 secs. +The client will now receive all logging from the daemon (pid: 471902). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-471902.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/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5282143c -Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5282143c -Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1de65471 +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@60db9947 +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@60db9947 +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@4965d3bb Starting Build Compiling initialization script '/build/reproducible-path/milib-2.2.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@19d9883a +Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@31dc499c Compiling initialization script '/build/reproducible-path/milib-2.2.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle) @@ -2370,15 +2406,15 @@ 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/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@40589bbe +Creating new cache for annotation-processors, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@5f713c9 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1de65471 -Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@65b4dea0 -Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@57138afe -:compileJava (Thread[#50,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@4965d3bb +Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@57d42c9e +Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@3dbcff59 +:compileJava (Thread[#51,Task worker for ':' Thread 2,5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.173 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@72c10ebb +Putting task artifact state for task ':compileJava' into context took 0.009 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@248852c Loading the Maven rules... Replacing org.apache.commons:commons-math3:jar:3.6.1 -> org.apache.commons:commons-math3:jar:debian Replacing cc.redberry:pipe:jar:1.3.0 -> cc.redberry:pipe:jar:1.0.0-alpha0 @@ -2451,7 +2487,7 @@ 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) -Up-to-date check for task ':compileJava' took 10.396 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 2.208 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. @@ -2475,32 +2511,32 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 7 warnings -:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 35.795 secs. -:processResources (Thread[#50,Task worker for ':',5,main]) started. +:compileJava (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 7.719 secs. +:processResources (Thread[#51,Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.06 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.029 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.139 secs. -:classes (Thread[#50,Task worker for ':',5,main]) started. +:processResources (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.113 secs. +:classes (Thread[#51,Task worker for ':' Thread 2,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#50,Task worker for ':',5,main]) completed. Took 0.0 secs. -:debianMavenPom (Thread[#50,Task worker for ':',5,main]) started. +: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. :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: +Up-to-date check for task ':debianMavenPom' took 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/milib-2.2.0+dfsg/build/debian/milib.pom -:debianMavenPom (Thread[#50,Task worker for ':',5,main]) completed. Took 0.208 secs. -:jar (Thread[#50,Task worker for ':',5,main]) started. +:debianMavenPom (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.103 secs. +:jar (Thread[#51,Task worker for ':' Thread 2,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.065 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.042 secs. It is not up-to-date because: No history is available. -:jar (Thread[#50,Task worker for ':',5,main]) completed. Took 0.831 secs. +:jar (Thread[#51,Task worker for ':' Thread 2,5,main]) completed. Took 0.266 secs. -BUILD SUCCESSFUL in 1m 1s +BUILD SUCCESSFUL in 13s 4 actionable tasks: 4 executed dh_auto_test mkdir -p .gradle/init.d @@ -2513,17 +2549,17 @@ 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/milib-2.2.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-arm64/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 3.582 secs. -The client will now receive all logging from the daemon (pid: 147308). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-147308.out.log +An attempt to start the daemon took 1.014 secs. +The client will now receive all logging from the daemon (pid: 474857). The daemon log file: /build/reproducible-path/milib-2.2.0+dfsg/.gradle/daemon/4.4.1/daemon-474857.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/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a062323 -Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a062323 -Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2b092c4 +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1a730787 +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1a730787 +Creating new cache for fileHashes, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@287a0116 Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@47ff97bc +Creating new cache for metadata-1.1/results, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@537b4402 Settings evaluated using settings file '/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/milib-2.2.0+dfsg/settings.gradle) Root project name not defined in settings.gradle, defaulting to 'milib' instead of the name of the root directory 'milib-2.2.0+dfsg' @@ -2537,15 +2573,15 @@ 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/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e2de65 +Creating new cache for annotation-processors, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1155dce2 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/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2b092c4 -Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@101736be -Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1aa7e879 -:compileJava (Thread[#50,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@287a0116 +Creating new cache for taskHistory, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@62f15675 +Creating new cache for outputFiles, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@520a6dca +:compileJava (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.028 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3d6bc0aa +Putting task artifact state for task ':compileJava' into context took 0.012 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/milib-2.2.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@6c8a928b Loading the Maven rules... Replacing org.apache.commons:commons-math3:jar:3.6.1 -> org.apache.commons:commons-math3:jar:debian Replacing cc.redberry:pipe:jar:1.3.0 -> cc.redberry:pipe:jar:1.0.0-alpha0 @@ -2570,21 +2606,21 @@ Passing through org.jsr-305:jsr305:jar:0.x Passing through com.google.errorprone:error_prone_annotations:jar:debian Passing through com.google.errorprone:error_prone_parent:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 2.307 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.978 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#50,Task worker for ':',5,main]) completed. Took 2.454 secs. -:processResources (Thread[#50,Task worker for ':',5,main]) started. +:compileJava (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 1.045 secs. +:processResources (Thread[#52,Task worker for ':' Thread 3,5,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 0.018 secs). +Skipping task ':processResources' as it is up-to-date (took 0.013 secs). :processResources UP-TO-DATE -:processResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.033 secs. -:classes (Thread[#50,Task worker for ':',5,main]) started. +:processResources (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.02 secs. +:classes (Thread[#52,Task worker for ':' Thread 3,5,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[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. +:compileTestJava (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Replacing junit:junit:jar:4.13.2 -> junit:junit:jar:4.x @@ -2600,7 +2636,7 @@ Passing through net.bytebuddy:byte-buddy-dep:jar:debian Passing through org.ow2.asm:asm:jar:debian Passing through org.ow2.asm:asm-commons:jar:debian -Up-to-date check for task ':compileTestJava' took 6.759 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 1.927 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. @@ -2612,23 +2648,23 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileTestJava (Thread[#50,Task worker for ':',5,main]) completed. Took 29.022 secs. -:processTestResources (Thread[#50,Task worker for ':',5,main]) started. +:compileTestJava (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 6.069 secs. +:processTestResources (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.117 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.016 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#50,Task worker for ':',5,main]) completed. Took 0.23 secs. -:testClasses (Thread[#50,Task worker for ':',5,main]) started. +:processTestResources (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.065 secs. +:testClasses (Thread[#52,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[#52,Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. +:test (Thread[#52,Task worker for ':' Thread 3,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 2.365 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.653 secs. It is not up-to-date because: No history is available. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17274149600132000427txt -Xms1024m -Xmx2048m -Dfile.encoding=UTF-8 -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 1'. Working directory: /build/reproducible-path/milib-2.2.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4704472380391539925txt -Xms1024m -Xmx2048m -Dfile.encoding=UTF-8 -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' Gradle Test Executor 1 started executing tests. @@ -2644,23 +2680,23 @@ High compression: false Concurrency: 4 File size: 5608636 - Write time: 607.06ms + Write time: 244.39ms O. Stats: - Wall clock time: 615.25ms - Total CPU time: 892.72ms - User wait time: 483.29ms - Serialization time: 573.34ms (64.22%) - Checksum calculation time: 273.7ms (30.66%) - Compression time: 27.19ms (3.05%) - Total IO delay: 166.16ms - Concurrency overhead: 158.58ms + Wall clock time: 248.55ms + Total CPU time: 364.02ms + User wait time: 162.68ms + Serialization time: 200.07ms (54.96%) + Checksum calculation time: 105ms (28.85%) + Compression time: 53.53ms (14.71%) + Total IO delay: 44.7ms + Concurrency overhead: 12.54ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 5.35MiB (~617B per object; compression = 29.01%) - IO speed: 32.22MiB/s - Concurrency adjusted uncompressed speed: 43.59MiB/s - Actual uncompressed speed: 29.98MiB/s - Actual speed: 8.7MiB/s + IO speed: 121.56MiB/s + Concurrency adjusted uncompressed speed: 161.73MiB/s + Actual uncompressed speed: 74.34MiB/s + Actual speed: 21.57MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2668,18 +2704,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 1: - Wall clock time: 268.43ms - Total CPU time: 137.2ms - Serialization time: 92.21ms (67.21%) - Checksum calculation time: 5.1ms (3.71%) - Compression time: 34.91ms (25.44%) - Total IO delay: 219.55ms + Wall clock time: 124.64ms + Total CPU time: 140.49ms + Serialization time: 78.79ms (56.08%) + Checksum calculation time: 9.05ms (6.44%) + Compression time: 47.92ms (34.11%) + Total IO delay: 56.13ms Input size: 5.35MiB Decompressed size: 18.44MiB (compression = 29.01%) - IO speed: 24.42MiB/s - Concurrency adjusted uncompressed speed: 207.16MiB/s - Actual uncompressed speed: 68.79MiB/s - Actual speed: 19.96MiB/s + IO speed: 95.51MiB/s + Concurrency adjusted uncompressed speed: 376.26MiB/s + Actual uncompressed speed: 148.68MiB/s + Actual speed: 43.14MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2687,18 +2723,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 525.1ms - Total CPU time: 206.42ms - Serialization time: 121.19ms (58.71%) - Checksum calculation time: 10.11ms (4.9%) - Compression time: 65.39ms (31.68%) - Total IO delay: 373.39ms + Wall clock time: 234.18ms + Total CPU time: 233.64ms + Serialization time: 106.99ms (45.79%) + Checksum calculation time: 16.2ms (6.93%) + Compression time: 95.85ms (41.02%) + Total IO delay: 100.19ms Input size: 10.7MiB Decompressed size: 36.87MiB (compression = 29.01%) - IO speed: 28.68MiB/s - Concurrency adjusted uncompressed speed: 256.07MiB/s - Actual uncompressed speed: 70.24MiB/s - Actual speed: 20.38MiB/s + IO speed: 106.98MiB/s + Concurrency adjusted uncompressed speed: 444.26MiB/s + Actual uncompressed speed: 157.58MiB/s + Actual speed: 45.72MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2709,23 +2745,23 @@ High compression: false Concurrency: 4 File size: 5588298 - Write time: 116.41ms + Write time: 101.05ms O. Stats: - Wall clock time: 116.92ms - Total CPU time: 71.43ms - User wait time: 98.32ms - Serialization time: 32.3ms (45.22%) - Checksum calculation time: 5.04ms (7.06%) - Compression time: 31.79ms (44.5%) - Total IO delay: 83.08ms - Concurrency overhead: 12.14ms + Wall clock time: 101.83ms + Total CPU time: 114.18ms + User wait time: 83.52ms + Serialization time: 45.61ms (39.94%) + Checksum calculation time: 10.08ms (8.83%) + Compression time: 52.06ms (45.6%) + Total IO delay: 47.03ms + Concurrency overhead: 3.1ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 5.33MiB (~615B per object; compression = 28.91%) - IO speed: 64.21MiB/s - Concurrency adjusted uncompressed speed: 368.74MiB/s - Actual uncompressed speed: 158.94MiB/s - Actual speed: 45.94MiB/s + IO speed: 113.39MiB/s + Concurrency adjusted uncompressed speed: 428.77MiB/s + Actual uncompressed speed: 182.54MiB/s + Actual speed: 52.77MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 615B @@ -2733,18 +2769,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 1: - Wall clock time: 133.59ms - Total CPU time: 66.86ms - Serialization time: 25.6ms (38.29%) - Checksum calculation time: 9.49ms (14.2%) - Compression time: 30.63ms (45.81%) - Total IO delay: 107.43ms + Wall clock time: 95.13ms + Total CPU time: 126.73ms + Serialization time: 30.18ms (23.82%) + Checksum calculation time: 13.81ms (10.9%) + Compression time: 81.93ms (64.65%) + Total IO delay: 13.11ms Input size: 5.33MiB Decompressed size: 18.44MiB (compression = 28.91%) - IO speed: 49.81MiB/s - Concurrency adjusted uncompressed speed: 428.77MiB/s - Actual uncompressed speed: 138.62MiB/s - Actual speed: 40.07MiB/s + IO speed: 409.96MiB/s + Concurrency adjusted uncompressed speed: 542.26MiB/s + Actual uncompressed speed: 194.07MiB/s + Actual speed: 56.1MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 615B @@ -2752,18 +2788,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 309.37ms - Total CPU time: 140.28ms - Serialization time: 58.87ms (41.97%) - Checksum calculation time: 17.71ms (12.63%) - Compression time: 61.52ms (43.85%) - Total IO delay: 214.59ms + Wall clock time: 210.61ms + Total CPU time: 251.08ms + Serialization time: 59.33ms (23.63%) + Checksum calculation time: 27.4ms (10.91%) + Compression time: 162.7ms (64.8%) + Total IO delay: 24.56ms Input size: 10.66MiB Decompressed size: 36.87MiB (compression = 28.91%) - IO speed: 49.81MiB/s - Concurrency adjusted uncompressed speed: 419.02MiB/s - Actual uncompressed speed: 119.33MiB/s - Actual speed: 34.49MiB/s + IO speed: 444.12MiB/s + Concurrency adjusted uncompressed speed: 542.26MiB/s + Actual uncompressed speed: 175.59MiB/s + Actual speed: 50.76MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 615B @@ -2774,23 +2810,23 @@ High compression: false Concurrency: 1 File size: 5608636 - Write time: 140.68ms + Write time: 185.09ms O. Stats: - Wall clock time: 141.73ms - Total CPU time: 66.46ms - User wait time: 118.98ms - Serialization time: 24ms (36.11%) - Checksum calculation time: 5.05ms (7.6%) - Compression time: 34.91ms (52.52%) - Total IO delay: 49.2ms - Concurrency overhead: 4.04ms + Wall clock time: 188.32ms + Total CPU time: 137.75ms + User wait time: 163.28ms + Serialization time: 46.85ms (34.01%) + Checksum calculation time: 14.16ms (10.28%) + Compression time: 71.01ms (51.55%) + Total IO delay: 20.14ms + Concurrency overhead: 5.17ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 5.35MiB (~617B per object; compression = 29.01%) - IO speed: 109.16MiB/s - Concurrency adjusted uncompressed speed: 154.93MiB/s - Actual uncompressed speed: 130.76MiB/s - Actual speed: 37.93MiB/s + IO speed: 267.44MiB/s + Concurrency adjusted uncompressed speed: 113.11MiB/s + Actual uncompressed speed: 98.07MiB/s + Actual speed: 28.45MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2799,18 +2835,18 @@ Checksum ok! I. Stats 1: - Wall clock time: 168.47ms - Total CPU time: 75.74ms - Serialization time: 36.1ms (47.66%) - Checksum calculation time: 4.9ms (6.46%) - Compression time: 31.02ms (40.96%) - Total IO delay: 154.73ms + Wall clock time: 93.68ms + Total CPU time: 136.24ms + Serialization time: 36.08ms (26.48%) + Checksum calculation time: 14.02ms (10.29%) + Compression time: 84.19ms (61.79%) + Total IO delay: 15.73ms Input size: 5.35MiB Decompressed size: 18.44MiB (compression = 29.01%) - IO speed: 34.73MiB/s - Concurrency adjusted uncompressed speed: 80.16MiB/s - Actual uncompressed speed: 109.74MiB/s - Actual speed: 31.84MiB/s + IO speed: 356.59MiB/s + Concurrency adjusted uncompressed speed: 122.1MiB/s + Actual uncompressed speed: 198.25MiB/s + Actual speed: 57.51MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2818,18 +2854,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 303.04ms - Total CPU time: 131.62ms - Serialization time: 53.19ms (40.41%) - Checksum calculation time: 9.84ms (7.48%) - Compression time: 62.01ms (47.12%) - Total IO delay: 263.9ms + Wall clock time: 195.82ms + Total CPU time: 275.61ms + Serialization time: 72.25ms (26.22%) + Checksum calculation time: 28.3ms (10.27%) + Compression time: 169.88ms (61.64%) + Total IO delay: 32.81ms Input size: 10.7MiB Decompressed size: 36.87MiB (compression = 29.01%) - IO speed: 40.68MiB/s - Concurrency adjusted uncompressed speed: 93.35MiB/s - Actual uncompressed speed: 121.7MiB/s - Actual speed: 35.31MiB/s + IO speed: 334.3MiB/s + Concurrency adjusted uncompressed speed: 119.72MiB/s + Actual uncompressed speed: 189.1MiB/s + Actual speed: 54.86MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 617B @@ -2840,23 +2876,23 @@ High compression: false Concurrency: 1 File size: 5588298 - Write time: 168.7ms + Write time: 163.78ms O. Stats: - Wall clock time: 169.81ms - Total CPU time: 72.95ms - User wait time: 148.33ms - Serialization time: 22.43ms (30.75%) - Checksum calculation time: 4.95ms (6.79%) - Compression time: 43.41ms (59.51%) - Total IO delay: 65.36ms - Concurrency overhead: 1.11ms + Wall clock time: 165.85ms + Total CPU time: 133.94ms + User wait time: 147.69ms + Serialization time: 43.58ms (32.54%) + Checksum calculation time: 14.32ms (10.69%) + Compression time: 72.16ms (53.88%) + Total IO delay: 11.88ms + Concurrency overhead: 1.4ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 5.33MiB (~615B per object; compression = 28.91%) - IO speed: 81.99MiB/s - Concurrency adjusted uncompressed speed: 132.64MiB/s - Actual uncompressed speed: 109.09MiB/s - Actual speed: 31.54MiB/s + IO speed: 484.49MiB/s + Concurrency adjusted uncompressed speed: 125.42MiB/s + Actual uncompressed speed: 111.74MiB/s + Actual speed: 32.3MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 615B @@ -2865,18 +2901,18 @@ Checksum ok! I. Stats 1: - Wall clock time: 132.4ms - Total CPU time: 59.37ms - Serialization time: 14.02ms (23.61%) - Checksum calculation time: 8.95ms (15.07%) - Compression time: 35.62ms (60%) - Total IO delay: 105.06ms + Wall clock time: 92.79ms + Total CPU time: 129.72ms + Serialization time: 29.66ms (22.86%) + Checksum calculation time: 14.19ms (10.94%) + Compression time: 85.25ms (65.72%) + Total IO delay: 8.02ms Input size: 5.33MiB Decompressed size: 18.44MiB (compression = 28.91%) - IO speed: 50.76MiB/s - Concurrency adjusted uncompressed speed: 112.42MiB/s - Actual uncompressed speed: 139.67MiB/s - Actual speed: 40.37MiB/s + IO speed: 666.18MiB/s + Concurrency adjusted uncompressed speed: 134.58MiB/s + Actual uncompressed speed: 200.4MiB/s + Actual speed: 57.93MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 615B @@ -2884,46 +2920,45 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 280.52ms - Total CPU time: 121.74ms - Serialization time: 27.74ms (22.79%) - Checksum calculation time: 13.89ms (11.41%) - Compression time: 78.47ms (64.46%) - Total IO delay: 211.44ms + Wall clock time: 210.37ms + Total CPU time: 262.24ms + Serialization time: 60.57ms (23.1%) + Checksum calculation time: 28.64ms (10.92%) + Compression time: 171.81ms (65.52%) + Total IO delay: 19.24ms Input size: 10.66MiB Decompressed size: 36.87MiB (compression = 28.91%) - IO speed: 50.52MiB/s - Concurrency adjusted uncompressed speed: 110.73MiB/s - Actual uncompressed speed: 131.69MiB/s - Actual speed: 38.07MiB/s + IO speed: 560.99MiB/s + Concurrency adjusted uncompressed speed: 131.22MiB/s + Actual uncompressed speed: 175.59MiB/s + Actual speed: 50.76MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 615B Blocks: 40 (~272.87KiB each) Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 0 / 0 / 4 ================== High compression: true Concurrency: 4 File size: 4156299 - Write time: 2.4s + Write time: 1.58s O. Stats: - Wall clock time: 2.4s - Total CPU time: 6.2s - User wait time: 2.27s - Serialization time: 82.02ms (1.32%) - Checksum calculation time: 4.93ms (0.08%) - Compression time: 6.11s (98.47%) - Total IO delay: 270.22ms - Concurrency overhead: 54.7ms + Wall clock time: 1.58s + Total CPU time: 3.91s + User wait time: 1.47s + Serialization time: 39.15ms (1%) + Checksum calculation time: 10.97ms (0.28%) + Compression time: 3.85s (98.6%) + Total IO delay: 21.97ms + Concurrency overhead: 7.04ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 14.68MiB/s - Concurrency adjusted uncompressed speed: 11.03MiB/s - Actual uncompressed speed: 7.67MiB/s - Actual speed: 1.65MiB/s + IO speed: 188.75MiB/s + Concurrency adjusted uncompressed speed: 18.66MiB/s + Actual uncompressed speed: 11.68MiB/s + Actual speed: 2.51MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 457B @@ -2931,18 +2966,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 1: - Wall clock time: 102.91ms - Total CPU time: 50.67ms - Serialization time: 16.3ms (32.16%) - Checksum calculation time: 4.94ms (9.74%) - Compression time: 27.25ms (53.78%) - Total IO delay: 92.87ms + Wall clock time: 76.23ms + Total CPU time: 133.23ms + Serialization time: 29.48ms (22.12%) + Checksum calculation time: 14.37ms (10.79%) + Compression time: 87.24ms (65.48%) + Total IO delay: 12.53ms Input size: 3.96MiB Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 43.08MiB/s - Concurrency adjusted uncompressed speed: 526.77MiB/s - Actual uncompressed speed: 180.75MiB/s - Actual speed: 38.86MiB/s + IO speed: 330.31MiB/s + Concurrency adjusted uncompressed speed: 512.14MiB/s + Actual uncompressed speed: 242.59MiB/s + Actual speed: 52.15MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 457B @@ -2950,46 +2985,45 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 220.08ms - Total CPU time: 100.95ms - Serialization time: 32.46ms (32.15%) - Checksum calculation time: 9.86ms (9.76%) - Compression time: 54.48ms (53.97%) - Total IO delay: 192.38ms + Wall clock time: 167.88ms + Total CPU time: 250.65ms + Serialization time: 58.17ms (23.21%) + Checksum calculation time: 28.26ms (11.28%) + Compression time: 160.23ms (63.93%) + Total IO delay: 29.35ms Input size: 7.93MiB Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 41.29MiB/s - Concurrency adjusted uncompressed speed: 505.12MiB/s - Actual uncompressed speed: 167.61MiB/s - Actual speed: 36.03MiB/s + IO speed: 273.36MiB/s + Concurrency adjusted uncompressed speed: 526.77MiB/s + Actual uncompressed speed: 220.8MiB/s + Actual speed: 47.47MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 457B Blocks: 124 (~65.47KiB each) Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 - Pending / IO / Serde: 2 / 0 / 2 ================== High compression: true Concurrency: 4 File size: 4098671 - Write time: 3.43s + Write time: 1.83s O. Stats: - Wall clock time: 3.43s - Total CPU time: 5.87s - User wait time: 3.1s - Serialization time: 19.65ms (0.33%) - Checksum calculation time: 5.01ms (0.09%) - Compression time: 5.84s (99.47%) - Total IO delay: 132.29ms - Concurrency overhead: 26.89ms + Wall clock time: 1.83s + Total CPU time: 3.03s + User wait time: 1.62s + Serialization time: 29.06ms (0.96%) + Checksum calculation time: 10.56ms (0.35%) + Compression time: 2.99s (98.65%) + Total IO delay: 10.71ms + Concurrency overhead: 2.06ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 29.61MiB/s - Concurrency adjusted uncompressed speed: 12.07MiB/s - Actual uncompressed speed: 5.37MiB/s - Actual speed: 1.14MiB/s + IO speed: 390.88MiB/s + Concurrency adjusted uncompressed speed: 24.2MiB/s + Actual uncompressed speed: 10.1MiB/s + Actual speed: 2.14MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 451B @@ -2997,66 +3031,67 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 1: - Wall clock time: 131.39ms - Total CPU time: 48.15ms - Serialization time: 14.46ms (30.03%) - Checksum calculation time: 6.22ms (12.92%) - Compression time: 26.53ms (55.09%) - Total IO delay: 120.35ms + Wall clock time: 78.36ms + Total CPU time: 111.31ms + Serialization time: 22.97ms (20.64%) + Checksum calculation time: 14.29ms (12.84%) + Compression time: 73.7ms (66.21%) + Total IO delay: 7.04ms Input size: 3.91MiB Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 32.57MiB/s - Concurrency adjusted uncompressed speed: 438.97MiB/s - Actual uncompressed speed: 140.74MiB/s - Actual speed: 29.84MiB/s + IO speed: 558.4MiB/s + Concurrency adjusted uncompressed speed: 635.76MiB/s + Actual uncompressed speed: 236.37MiB/s + Actual speed: 50.11MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 451B Blocks: 20 (~200.13KiB each) Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 + Pending / IO / Serde: 0 / 0 / 0 I. Stats 2: - Wall clock time: 297.18ms - Total CPU time: 97.27ms - Serialization time: 31.3ms (32.18%) - Checksum calculation time: 11.25ms (11.57%) - Compression time: 53.09ms (54.58%) - Total IO delay: 241.87ms + Wall clock time: 174.32ms + Total CPU time: 222.02ms + Serialization time: 45.73ms (20.6%) + Checksum calculation time: 28.54ms (12.86%) + Compression time: 147.18ms (66.29%) + Total IO delay: 16.22ms Input size: 7.82MiB Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 32.44MiB/s - Concurrency adjusted uncompressed speed: 438.97MiB/s - Actual uncompressed speed: 124.15MiB/s - Actual speed: 26.32MiB/s + IO speed: 488.6MiB/s + Concurrency adjusted uncompressed speed: 624.98MiB/s + Actual uncompressed speed: 211.92MiB/s + Actual speed: 44.93MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 451B Blocks: 40 (~200.13KiB each) Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 1 / 0 + Pending / IO / Serde: 0 / 0 / 1 ================== High compression: true Concurrency: 1 File size: 4156299 - Write time: 4.93s + Write time: 4.79s O. Stats: - Wall clock time: 4.93s - Total CPU time: 4.74s - User wait time: 4.92s - Serialization time: 22.38ms (0.47%) - Checksum calculation time: 4.93ms (0.1%) - Compression time: 4.71s (99.38%) - Total IO delay: 80.53ms - Concurrency overhead: 47.26ms + Wall clock time: 4.79s + Total CPU time: 4.75s + User wait time: 4.77s + Serialization time: 37.86ms (0.8%) + Checksum calculation time: 13.59ms (0.29%) + Compression time: 4.69s (98.86%) + Total IO delay: 17.93ms + Concurrency overhead: 5.4ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 3.96MiB (~457B per object; compression = 21.5%) - IO speed: 49.55MiB/s - Concurrency adjusted uncompressed speed: 3.79MiB/s - Actual uncompressed speed: 3.74MiB/s - Actual speed: 822.64KiB/s + IO speed: 233.16MiB/s + Concurrency adjusted uncompressed speed: 3.87MiB/s + Actual uncompressed speed: 3.85MiB/s + Actual speed: 847.37KiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 457B @@ -3065,18 +3100,18 @@ Checksum ok! I. Stats 1: - Wall clock time: 191.03ms - Total CPU time: 50.44ms - Serialization time: 15.33ms (30.39%) - Checksum calculation time: 4.92ms (9.76%) - Compression time: 28.37ms (56.24%) - Total IO delay: 178.39ms + Wall clock time: 69.31ms + Total CPU time: 102.2ms + Serialization time: 22.67ms (22.18%) + Checksum calculation time: 12.78ms (12.5%) + Compression time: 65.92ms (64.5%) + Total IO delay: 12.92ms Input size: 3.96MiB Decompressed size: 18.44MiB (compression = 21.5%) - IO speed: 22.27MiB/s - Concurrency adjusted uncompressed speed: 80.86MiB/s - Actual uncompressed speed: 96.53MiB/s - Actual speed: 20.75MiB/s + IO speed: 330.31MiB/s + Concurrency adjusted uncompressed speed: 160.32MiB/s + Actual uncompressed speed: 267.2MiB/s + Actual speed: 57.45MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 457B @@ -3084,47 +3119,46 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 591.1ms - Total CPU time: 99.24ms - Serialization time: 29.36ms (29.58%) - Checksum calculation time: 9.82ms (9.9%) - Compression time: 55.41ms (55.83%) - Total IO delay: 507.26ms + Wall clock time: 147.44ms + Total CPU time: 208.81ms + Serialization time: 45.86ms (21.96%) + Checksum calculation time: 25.9ms (12.4%) + Compression time: 134.85ms (64.58%) + Total IO delay: 23.53ms Input size: 7.93MiB Decompressed size: 36.87MiB (compression = 21.5%) - IO speed: 15.64MiB/s - Concurrency adjusted uncompressed speed: 60.85MiB/s - Actual uncompressed speed: 62.39MiB/s - Actual speed: 13.41MiB/s + IO speed: 344.67MiB/s + Concurrency adjusted uncompressed speed: 158.94MiB/s + Actual uncompressed speed: 250.84MiB/s + Actual speed: 53.93MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 457B Blocks: 124 (~65.47KiB each) Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 Pending / IO / Serde: 0 / 0 / 1 - Pending / IO / Serde: 0 / 0 / 1 ================== High compression: true Concurrency: 1 File size: 4098671 - Write time: 5.54s + Write time: 3.4s O. Stats: - Wall clock time: 5.54s - Total CPU time: 5.38s - User wait time: 5.51s - Serialization time: 18.95ms (0.35%) - Checksum calculation time: 5.04ms (0.09%) - Compression time: 5.36s (99.53%) - Total IO delay: 62.13ms - Concurrency overhead: 20.75ms + Wall clock time: 3.4s + Total CPU time: 3.38s + User wait time: 3.39s + Serialization time: 35.95ms (1.06%) + Checksum calculation time: 13.97ms (0.41%) + Compression time: 3.33s (98.48%) + Total IO delay: 10.14ms + Concurrency overhead: 1.42ms Uncompressed size: 18.44MiB (~2.08KiB per object) Output size: 3.91MiB (~451B per object; compression = 21.2%) - IO speed: 63.05MiB/s - Concurrency adjusted uncompressed speed: 3.37MiB/s - Actual uncompressed speed: 3.33MiB/s - Actual speed: 722.88KiB/s + IO speed: 390.88MiB/s + Concurrency adjusted uncompressed speed: 5.44MiB/s + Actual uncompressed speed: 5.42MiB/s + Actual speed: 1.15MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 451B @@ -3133,18 +3167,18 @@ Checksum ok! I. Stats 1: - Wall clock time: 130.1ms - Total CPU time: 51.66ms - Serialization time: 19.66ms (38.05%) - Checksum calculation time: 4.96ms (9.6%) - Compression time: 26.58ms (51.45%) - Total IO delay: 101.81ms + Wall clock time: 78.48ms + Total CPU time: 111.27ms + Serialization time: 22.71ms (20.41%) + Checksum calculation time: 14.29ms (12.84%) + Compression time: 73.96ms (66.47%) + Total IO delay: 6.95ms Input size: 3.91MiB Decompressed size: 18.44MiB (compression = 21.2%) - IO speed: 38.7MiB/s - Concurrency adjusted uncompressed speed: 120.5MiB/s - Actual uncompressed speed: 141.82MiB/s - Actual speed: 30.07MiB/s + IO speed: 651.47MiB/s + Concurrency adjusted uncompressed speed: 156.25MiB/s + Actual uncompressed speed: 236.37MiB/s + Actual speed: 50.11MiB/s Objects: 9079 Average object size uncompressed: 2.08KiB Average object size compressed: 451B @@ -3152,18 +3186,18 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 I. Stats 2: - Wall clock time: 269.96ms - Total CPU time: 128.47ms - Serialization time: 64.34ms (50.08%) - Checksum calculation time: 9.95ms (7.75%) - Compression time: 53.12ms (41.35%) - Total IO delay: 188.84ms + Wall clock time: 171.62ms + Total CPU time: 222.2ms + Serialization time: 45.47ms (20.47%) + Checksum calculation time: 28.55ms (12.85%) + Compression time: 147.58ms (66.42%) + Total IO delay: 13.91ms Input size: 7.82MiB Decompressed size: 36.87MiB (compression = 21.2%) - IO speed: 41.58MiB/s - Concurrency adjusted uncompressed speed: 116.32MiB/s - Actual uncompressed speed: 137.08MiB/s - Actual speed: 29.06MiB/s + IO speed: 601.35MiB/s + Concurrency adjusted uncompressed speed: 156.25MiB/s + Actual uncompressed speed: 215.64MiB/s + Actual speed: 45.72MiB/s Objects: 18158 Average object size uncompressed: 2.08KiB Average object size compressed: 451B @@ -3171,23 +3205,22 @@ Ongoing and pending ops (Serde / IO / Pending): 0 / 0 / 0 com.milaboratory.primitivio.blocks.PrimitivOBlocksTest > bigBlocks STANDARD_OUT - Pending / IO / Serde / Objs: 3 / 1 / 1 / 5000 - Pending / IO / Serde / Objs: 0 / 0 / 2 / 13000 + Pending / IO / Serde / Objs: 2 / 1 / 2 / 18000 O. Stats: - Wall clock time: 5.43s - Total CPU time: 7.89s - User wait time: 67.76us - Serialization time: 3.02s (38.28%) - Checksum calculation time: 1.68s (21.27%) - Compression time: 1.49s (18.91%) - Total IO delay: 3.21s - Concurrency overhead: 36.22ms + Wall clock time: 2.23s + Total CPU time: 2.51s + User wait time: 62.28us + Serialization time: 604.61ms (24.05%) + Checksum calculation time: 1.07s (42.63%) + Compression time: 404.2ms (16.08%) + Total IO delay: 1.47s + Concurrency overhead: 5.34ms Uncompressed size: 1.86GiB (~97.66KiB per object) Output size: 1.86GiB (~97.66KiB per object; compression = 100%) - IO speed: 593.48MiB/s - Concurrency adjusted uncompressed speed: 1.31GiB/s - Actual uncompressed speed: 351.47MiB/s - Actual speed: 351.47MiB/s + IO speed: 1.27GiB/s + Concurrency adjusted uncompressed speed: 3.7GiB/s + Actual uncompressed speed: 854.21MiB/s + Actual speed: 854.21MiB/s Objects: 20000 Average object size uncompressed: 97.66KiB Average object size compressed: 97.66KiB @@ -3211,9 +3244,9 @@ 0 cAGTTccc--gaaACCtgCta--aGCTCTtaactaCTtct 35 com.milaboratory.core.alignment.AlignerTest > testCalculateScore1 STANDARD_OUT - 1.04us - 3.45us - 1.45us + 995.00ns + 975.00ns + 988.00ns com.milaboratory.core.alignment.AlignmentHelperTest > test1 STANDARD_OUT 0 GAGGTGCAGCTGGTGGAGTCTGGGGGAGGC 29 @@ -3294,10 +3327,10 @@ com.milaboratory.core.alignment.AlignmentTrimmerTest > testRandom1 STANDARD_OUT - lTrimmed = 1733 - rTrimmed = 1682 - lTrimmed = 2755 - rTrimmed = 2793 + lTrimmed = 1683 + rTrimmed = 1646 + lTrimmed = 2869 + rTrimmed = 2802 com.milaboratory.core.alignment.BandedAffineAlignerTest > test11 STANDARD_OUT 0 --------------------- -1 @@ -3485,10 +3518,10 @@ com.milaboratory.core.alignment.blast.BlastDBBuilderTest > test1 SKIPPED com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectness STANDARD_OUT - C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 350.98us - C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 256.53us - C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 180.91us - C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 177.23us + C=1182;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 86.96us + C=1642;I=1;M=0;ScE=0;R=0.0 AlignmentTime = 83.96us + C=2048;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 61.96us + C=2142;I=0;M=0;ScE=0;R=8.333333333333333E-7 AlignmentTime = 63.10us com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandom1 STANDARD_OUT ##teamcity[buildStatisticValue key='kmFound' value='0.9449'] @@ -3496,17 +3529,17 @@ ##teamcity[buildStatisticValue key='kmFalse' value='0.0058'] com.milaboratory.core.alignment.kaligner1.KAlignerTest > testRandomCorrectnessConcurrent STANDARD_OUT - C=2999;I=0;M=0;ScE=1;R=0.0 AlignmentTime = 152.78us - C=2997;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 362.06us - C=2999;I=0;M=0;ScE=1;R=0.0 AlignmentTime = 131.28us - C=2996;I=0;M=1;ScE=0;R=0.0 AlignmentTime = 171.36us + C=3000;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 128.85us + C=2999;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 126.00us + C=2999;I=0;M=0;ScE=0;R=0.0 AlignmentTime = 127.11us + C=2998;I=0;M=0;ScE=0;R=1.6666666666666667E-6 AlignmentTime = 110.28us com.milaboratory.core.alignment.kaligner1.KMapperTest > testBestOffset2 STANDARD_OUT -205 com.milaboratory.core.alignment.kaligner2.KMapper2Test > test11112 STANDARD_OUT ID: 0 - Score: 1856 + Score: 1623 Cluster 0: Q 27 -> T 15 - -12 Q 30 -> T 18 - -12 @@ -3522,27 +3555,22 @@ Q 93 -> T 59 - -34 Q 96 -> T 62 - -34 Q 99 -> T 65 - -34 - Q 111 -> T 79 - -32 Q 114 -> T 82 - -32 - Q 117 -> T 85 - -32 Cluster 2: - Q 150 -> T 92 - -58 Q 153 -> T 95 - -58 Q 156 -> T 98 - -58 Q 159 -> T 101 - -58 - Q 168 -> T 111 - -57 Cluster 3: - Q 198 -> T 120 - -78 Q 201 -> T 123 - -78 Q 204 -> T 126 - -78 Q 207 -> T 129 - -78 + Q 210 -> T 132 - -78 Q 216 -> T 139 - -77 Q 219 -> T 142 - -77 Q 222 -> T 145 - -77 Q 231 -> T 153 - -78 Q 234 -> T 156 - -78 Q 237 -> T 159 - -78 - Q 240 -> T 162 - -78 Cluster 4: Q 246 -> T 178 - -68 Q 249 -> T 181 - -68 @@ -3555,7 +3583,7 @@ com.milaboratory.core.alignment.kaligner2.KMapper2Test > test1111 STANDARD_OUT ID: 0 - Score: 1212 + Score: 1161 Cluster 0: Q 9 -> T 15 - 6 Q 12 -> T 18 - 6 @@ -3566,13 +3594,11 @@ Q 27 -> T 33 - 6 Q 30 -> T 36 - 6 Cluster 1: - Q 57 -> T 48 - -9 Q 60 -> T 51 - -9 Q 69 -> T 61 - -8 - Q 72 -> T 64 - -8 + Q 78 -> T 69 - -9 Q 81 -> T 72 - -9 Q 84 -> T 75 - -9 - Q 87 -> T 78 - -9 Cluster 2: Q 123 -> T 89 - -34 Q 126 -> T 92 - -34 @@ -3584,16 +3610,17 @@ Q 171 -> T 135 - -36 Q 174 -> T 138 - -36 Q 177 -> T 141 - -36 - Q 183 -> T 147 - -36 + Q 180 -> T 144 - -36 + Q 185 -> T 149 - -36 com.milaboratory.core.alignment.kaligner2.KMapper2Test > testRandom1 STANDARD_OUT - noHits: 281 + noHits: 262 noHits2: 0 noHits3: 0 - wrongTopHit: 45 - wrongTopHitS: 30 - noCorrectHitInList: 21 + wrongTopHit: 42 + wrongTopHitS: 33 + noCorrectHitInList: 20 @@ -3601,13 +3628,13 @@ Timings: DescriptiveStatistics: n: 100000 - min: 5360.0 - max: 4.6596584E8 - mean: 205173.73800002376 - std dev: 3691927.4270738806 - median: 61160.0 - skewness: 94.52279499550305 - kurtosis: 9997.862108549465 + min: 4280.0 + max: 1.43064629E8 + mean: 78558.7021100026 + std dev: 1382174.3640444602 + median: 59921.0 + skewness: 99.4377074114824 + kurtosis: 9928.757852517627 @@ -3615,14 +3642,14 @@ Clusters basicSize DescriptiveStatistics: - n: 99674 + n: 99696 min: 1.0 - max: 7.0 - mean: 2.8609065553705095 - std dev: 1.0986277435883456 + max: 6.0 + mean: 2.8916706788637474 + std dev: 1.1007889120149232 median: 3.0 - skewness: 0.29507202074971917 - kurtosis: -0.6692534652494913 + skewness: 0.27322452567640465 + kurtosis: -0.700049111658736 @@ -3630,20 +3657,20 @@ Top Delta DescriptiveStatistics: - n: 99698 - min: -32.0 + n: 99718 + min: -33.0 max: 0.0 - mean: -0.0012236955605935006 - std dev: 0.14725559496467125 + mean: -0.0019755711105311157 + std dev: 0.1942495616723915 median: 0.0 - skewness: -152.70570566762015 - kurtosis: 27448.10243244401 + skewness: -116.32793980411823 + kurtosis: 15207.602737480422 com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulatorTest > testScoreCorrection2 SKIPPED com.milaboratory.core.alignment.kaligner2.KAligner2Test > testBoundaries STANDARD_OUT - 4969 + 4959 com.milaboratory.core.alignment.kaligner2.KAligner2Test > caseJ1 STANDARD_OUT 52 @@ -3657,11 +3684,11 @@ com.milaboratory.core.alignment.kaligner2.KAligner2Test > testCase0 SKIPPED com.milaboratory.core.alignment.kaligner2.KAligner2Test > testSimpleRandomTest STANDARD_OUT - Time per query: 653.00us - Processed queries: 64 + Time per query: 319.35us + Processed queries: 139 Bad percent: 0.0 - False positive percent: 0.5543090933086974 - Scoring error percent: 1.5625 + False positive percent: 0.5746013299761121 + Scoring error percent: 0.7194244604316548 com.milaboratory.core.merger.MergerParametersTest > test2 STANDARD_OUT { @@ -3686,16 +3713,16 @@ S([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])|D([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E])(\d+)|I(\d+)([\Q*ACDEFGHIKLMNPQRSTVWY_XBJZ\E]) com.milaboratory.core.mutations.MutationsTest > testCanonical1 STANDARD_OUT - CATCACTTCACCTCTGCCCGGCAGAGCTCTGTTGAAATGACGCGCGTGGCTGCCAAGTGTACCTGGCCTTGATTTCGCAAACTGCGATCAACCGAGGCCCTGTCCGTCTTCCGATCATACAACGAATGGAATCCAAATCTCGGTTACTGTAGGGCCTTCCCAACTGCCAGGCTCGACATACCATCGCTGAAAAGGAGCTGATAATACTTAGTTTGTGATAGCAACTTAAGGTAGGCGTCTCCGAAATTTCGATTTTTGTTCACGGATCATGATTCGTGAACGATAGAATTACAGTTTCCTGTTAACGGTTGTGACACCACGTTCGGAAACCAGTCTATACCCACGACCCCAGGCGGCTGTCCAACGGGGACCGCCACCCATGCAGGATGTGACACCCGTAGCTACCAGTTGCGACTGGTCCACTAATTTTGGACTAGCAAAACTGACTGCCGCCACTGGTAAAA - CATCACTTCACCTCTGCCCGGCCATAGCTCTGGAAATGCGCGCAGTTGGCTGCAGGTGTACCTGGCCTTGATTTCGCAAGTGCGATCAACCGAGGCCCCTGTCCGTCTTCACGTTCATATAACGAAACGGAATCCAAATCTCGGTTCTGTGGGCCTTCCCAACTGCCAGGCTCGGACATACCTCGCTGAAAAGGAGCGATAATACTTAAGTTTGTGATAGCAACTTTAGGTAGGCGTCTCGTAAATTTCGATTTTTGTTCAGATCATGGTTCGTGAACGATAGAGCTACGTTTCCTGTTAACGGTTGTGACACACGTTCGGAACCAGTCTATACCCACGACCCCAGCGGCTGTCCAACGGGACCGCCCCCATGCAGGGATGTGACACCCGCTAGCTACCAATTGCGACTGGTCCACATAATTTTGGACTAGCAAAACTGACTGCCGCCACGGTAAAA - CATCACTTCACCTCTGCCCGGCCCAGTAGCTCTGGAAGTGCGCGCATTGGCTGCAAGGTGTACTGGCCTTGATTTCGCAAGTGCGATCCAACCGGAGGCCCCTGTCCGCTTCAGTCATTAACAAGACGGAATCCAAACTCGTTCTGTGTCCTTCCCAATGCCGGCTCGGACATACTCGCTGAAACGGAGCGATAATACTTAAGTTTGTGATACAACTTTAGGTGGCGTCTCGTAATTTCGGTTTTTGTTCAGATCATGTTCGTGAACTTATAGAGCTACGTTTCCTGTTAAGCGGTTGTGACACACGTTCGGAACCATCTATACTCACCCCAGCGGCTGTCCAACGGGACCGCCCCCACTGCAGGATGTGACACCCGCTAGCTACCAATTGCGACGTCCAGACATAAGTTTTGGACTAGCATGACGACTGCCGCCCGGTAAA - 0 CATCACTTCACCTCTGCCCGGCCCAGTAGCTCTG--GAAGTG-CGCGCATTGGCTG-CAAGGTGTA-CTGGCCTTGATTTCGC-AAGTGCGATCCAACCGGAGGCCCCTGTCCG-CTTCAG-TCATTAACAA-G-ACGGAATCCAAA-CTC-GTT-CTGT--GTCCTTCCCAA-TGCC-GGCTCGGACATA-C-TCGCTGAAACGGAGC-GATAATACTTAAGTTTGTGATA-CAACTTTAGGT-GGCGTCT-CGTAATTTCGGTTTTTGTTCA--GATCATG-TTCGTGAACTTATAGAGCTAC-GTTTCCTGTTAAGCGGTTGTGACA-CACGTTCGG-AACCA-TCTATA--CTC-ACCCCA-GCGGCTGTCCAAC-GGGACCGCC-CCCACTGCAGGATGTGACACCCGCTAGCTACCAATTGCGAC--GTCCAGACATAAGTTTTGGACTAGCATGAC-GACTGCCGCC-C-GGT-AAA 441 - ||||||||||||||||||||| ||| ||||||| ||| || ||||| |||||| ||| ||||| |||||||||||||||| || |||||| ||||| |||| ||||||||| |||| | ||| | |||| | | |||||||||| ||| ||| |||| | ||||||||| |||| ||||| |||||| | ||||||||| ||||| |||||||||| ||||||||||| |||||| |||| ||||||| || ||||||| |||||||||| ||||||| ||||||||| ||||| ||| |||||||||||| ||||||||||| ||||||||| ||||| |||||| | | |||||| ||||||||||||| ||||||||| |||| |||||||||||||||||| ||||||||| ||||||| |||| || ||| ||||||||||||| || |||||||||| | ||| ||| - 0 CATCACTTCACCTCTGCCCGG--CAG-AGCTCTGTTGAAATGACGCGC-GTGGCTGCCAA-GTGTACCTGGCCTTGATTTCGCAAACTGCGAT-CAACC-GAGG-CCCTGTCCGTCTTCCGATCA-T-ACAACGAATGGAATCCAAATCTCGGTTACTGTAGGGCCTTCCCAACTGCCAGGCTC-GACATACCATCGCTGAAAAGGAGCTGATAATACTT-AGTTTGTGATAGCAACTTAAGGTAGGCGTCTCCGAAATTTCGATTTTTGTTCACGGATCATGATTCGTGAAC-GATAGAATTACAGTTTCCTGTTAA-CGGTTGTGACACCACGTTCGGAAACCAGTCTATACCCACGACCCCAGGCGGCTGTCCAACGGGGACCGCCACCCA-TGCAGGATGTGACACCCG-TAGCTACCAGTTGCGACTGGTCC--AC-TAA-TTTTGGACTAGCAAAACTGACTGCCGCCACTGGTAAAA 463 - [I31:T,D32:T,D45:G,S46:T->G,I47:T,I52:C,S53:C->A,D55:A,I61:C,D62:C,I78:A,S80:A->C,D81:C,I113:A,S113:A->T,D114:T,D117:T,D118:A,S119:C->T,D120:A,D123:G,I125:A,I125:C,I125:G,I125:A,I141:G,D142:G,I150:A,S150:A->G,D153:G,I243:A,D244:A,I262:C,S262:C->G,D264:G,I326:A,D328:A,I339:C,I339:C,S340:C->A,I342:G,D344:G,D345:A,D349:C,I351:G,D352:G,I365:G,D366:G,I384:G,D385:G,I415:T,S415:T->G,D417:G,I460:A,D462:A] - 0 CATCACTTCACCTCTGCCCGGCAGAGCTCTG-TTGAAATGACGCGCGT-GGCTG-CCAAGTGTA-CCTGGCCTTGATTTCGC-AAACTGCGATCAACCGAGGCCCTGTCCGTCTTCCG-ATCATACAACGA----ATGGAATCCAAATCTC-GGTTACTGT-AGGGCCTTCCCAACTGCCAGGCTCGACATACCATCGCTGAAAAGGAGCTGATAATACTTAGTTTGTGATAGCAACTTAAGGTAGGCGTCTCCG-AAATTTCGATTTTTGTTCA-CGGATCATGATTCGTGAACGATAGAATTACAGTTTCCTGTTAACGGTTGTGACACCACGTTCGG-AAACCAGTCTATA--CCC-ACGACCCCA-GGCGGCTGTCCAAC-GGGGACCGCCACCCATGCA-GGATGTGACACCCGTAGCTACCAGTTGCGAC-TGGTCCACTAATTTTGGACTAGCAAAACTGACTGCCGCCACTGGT-AAAA 463 - ||||||||||||||||||||||||||||||| | |||||||||||| ||||| | | ||||| | ||||||||||||||| || ||||||||||||||||||||||||||||||| || || | |||||||||||||||| | ||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||| | | || ||| | | |||||||||||| | ||||||||||||||||| | ||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||| || | - 0 CATCACTTCACCTCTGCCCGGCAGAGCTCTGTT-GAAATGACGCGC-GTGGCTGCCAA-GTGTACC-TGGCCTTGATTTCGCAAAC-TGCGATCAACCGAGGCCCTGTCCGTCTTCCGAT-CA--T-AC-AACGAATGGAATCCAAATCTCGG-TTACTGTAGGG-CCTTCCCAACTGCCAGGCTCGACATACCATCGCTGAAAAGGAGCTGATAATACTTAGTTTGTGATAGCAACTTAAGGTAGGCGTCTCCGAA-ATTTCGATTTTTGTTCACGG-ATCATGATTCGTGAACGATAGAATTACAGTTTCCTGTTAACGGTTGTGACACCACGTTCGGAAA-CCAGTCTATACCCACGAC--CCC-AGG-CGGCTGTCCAACGG-GGACCGCCACCCATGCAGG-ATGTGACACCCGTAGCTACCAGTTGCGACTGG-TCCACTAATTTTGGACTAGCAAAACTGACTGCCGCCACTGGTAAA-A 463 + CATAGAGAACTTATAGTTCCGACGATCAGTGGGACGAAAAAAAACCCCGCTCTTCGAACATGTTCCTTCAATACCTCGGTTAGAACCGTGATTTGAGGTAACATTCTCTCACTGTCCCCTACGTCGCAACACCCACGGGCTAAATTTACCTTCAGACTCGCAGTGACCGGGCACGTAGGCCTCATAACCGGGACATGACAAAACGTATCAACTTTTTTTAGAACCGGCCCTCTAGGGACGTTATACAACCGCCTTGTATGAAAACTGCTACCATGGGATATCGGACAAACCCCGGCGGAGTTGTAGATTGCGCACGGTGACATCTACTGGAGGTCTGACCCTGGGTAGGGATTGTCAGGGCCCTATGGGAACTTGTCATTGCGTGGGGATTAGCAATAGTGAGCGTGGACAACCTGCGCCGCCACGTGCCATGTGCCCATAGTAGGCTTGTTGGCATTTTGGAAAGGGGAATACTCCGCCTACGTAGTGTGCTATCAGCTACTAGCGGGCGTTGTACCTTACTCCGGTGGGCCGGGGGAAAGATTTTAAGGGTGTAGGGATCTCACATACACAGAAGGATAGCTACGGGTCCTTCCGCCACGTCTGGTACGCTGAGTGAACTGACTATGAACGGTCACAGCTGTTACGATCCCTTGTAAATTCGCTTTGGTCTAAGGTGCGGACT + CATAGGAACCTTATAGTTCCACGATCACGTGGGACGAAAAAAAACCCCGCTCTTCGGATATGTTCCTTCGATACCTCGGTTAGAACCGTGATTTGATGTAACATTCTCTCACTGTCCCCTACGTCGCAACACCCACGGGCTAAATTTACTTCAGACCGCAGTGACCGGGCACGTATGCCTCATATACCGGTACATTACAAACGTATCAACTTTTTTAGAACCGGCCCTTAGGGGACTTTACAACGCCTGTATGAAAATGCTACATGGGTAATCGGACAAACCCTGGCGGAGTTCGAGATTGGACGGTGAATCTACTGAGAGGTCGACCCTGGGTGGGATTGTCAGGGCCCTATGGGAACTTGTCAATTGCGTGAGTGATTAGCAATAGTGAGCGTGGACACCGCGCCGCCACGTGCCATGTGCCCATAGTAGGCTTGTCGGCATTTTGGAAGGGGAATACTACCGCCTACGTAGTGTGCTATCAGCTATAGCGGGGTTGTACCTTACTCCGGTGGACCGGGGGGATGATTTTAAGGGTGTGGGATCTCAATACACAGAAGGGTAGCTATGGGTCCTTCCTCCTCGTCTGGTACGCTGAGTGACTGACTATGAACGGTCACAGCTGTTACGATCCCTTGTAAATTCGCTTTGGCTCTAAGGTGCGGACT + CATAGGAACCTTAAGTAGTTCCACGACCACGTCGGGACGAAAAAAAACCCCGCTCTCGGTATGTTCGCTGATACTCGGTTAGAACCGTGATTTGATGTAGCTTCTCTCACTGTCCCCTACGTCTACACCCGCGGGTAAATTTACTTCAACCGCTGACCGGGCACGTATGCCTCATTTACCGGTACATTACAAACGTGTCAACTTTTTTAGACCGGCCCTTATGGGATTTTACCAACGCTTGTATGAAAATGCTACTGGGTGATCGGACAACTCTGGCGGAGTTCGAGATTGGACGGTGAATCTATTAGAGGTCGACCTGGGTGGGACTTGTCAGGGCCCTATGGGACTTGTCTATTGCGTGATGATTAGCAACATTGAGCGTGGACACCGGCGCCGCACGTGCCATGTGCTCATAGAGGTTTGTCGGCATTTTGGAAGGGGAATACTACGCTACGTAGTGTGCTATCAGCTATAGCGGGGTTGTACCTTATCCGGGGATCCGGGGGGAATGATCTTATTAAGGGGTGGGATTCAATACACAGGAGGTAGCTATGGGTCCTTCCTCCTCGTTGTACGCTGAGTGACTGACTATGAACGGTCACAAGCTGTTTGGATCCCTTTGTAAATTCGCTTTGGCTCTAAGGTGCGGACT + 0 CATAG-GAACCTTAAGTAGTTCC-ACGACCACGTCGGGACGAAAAAAAACCCCGCTC-TCG-GTATGTTCGC-T-GATA-CTCGGTTAGAACCGTGATTTGATGTAGC-TTCTCTCACTGTCCCCTACGT--CTACACCCGCGGG-TAAATTTA-CTTCA-AC-CGC--TGACCGGGCACGTATGCCTCATTTACCGGTACATTAC-AAACGTGTCAAC-TTTTTTAG-ACCGGCCCT-TATGGGA--TTTTACCAA-CG-CTTGTATGAAAA-TGCTA-C-TGGG-TGATCGGAC-AACTCTGGCGGAGTTCG-AGATTG-G-ACGGTGA-ATCTATTAGAGGTC-GA-CCTGGGT-GGGACTTGTCAGGGCCCTATGGG-ACTTGTCTATTGCGTGATGATTAGCAACATTGAGCGTGGAC-ACCGGCGCCG-CACGTGCCATGTGCTCATAG-AGGTTTGTCGGCATTTTGG-AAGGGGAATACTACG-CTACGTAGTGTGCTATCAGCTA-TAGCGGG-GTTGTACCTTA-TCCGG-GGATCCGGGGGGAATGATCTTATTAAGGG-GT-GGGAT-TCA-ATACACAGGAGG-TAGCTATGGGTCCTTCCTCCTCGT-T-GTACGCTGAGTG-ACTGACTATGAACGGTCACAAGCTGTTTGGATCCCTTTGTAAATTCGCTTTGGCTCTAAGGTGCGGACT 651 + ||||| ||| ||| | ||||||| |||| || || |||||||||||||||||||||| ||| |||||| | | ||| |||||||||||||||||||||| ||| | ||||||||||||||||||||| | |||||| |||| |||||||| ||||| || ||| |||||||||||||| |||||| | ||||| |||| || |||||| ||||| |||||||| ||||||||| || |||| || || ||| || |||||||||||| ||||| | |||| | ||||||| ||| | ||||||||| | |||||| | ||||||| ||||| | |||||| || ||||||| |||| |||||||||||||||||| ||||||| |||||||| ||||||||| | ||||||||||| ||| |||||| |||||||||||||| ||||| ||| |||| |||||||||| |||||||||||| || |||||||||||||||||||||| ||||||| ||||||||||| ||||| || || ||||||| || || ||||||| || ||||| ||| |||||||| ||| |||||| |||||||||| || ||| | |||||||||||| ||||||||||||||||||| ||||||| |||||| ||||||||||||||||| ||||||||||||||| + 0 CATAGAGAA-CTT-A-TAGTTCCGACGATCA-GT-GGGACGAAAAAAAACCCCGCTCTTCGAACATGTTC-CTTCAATACCTCGGTTAGAACCGTGATTTGAGGTAACATTCTCTCACTGTCCCCTACGTCGCAACACCCACGGGCTAAATTTACCTTCAGACTCGCAGTGACCGGGCACGTAGGCCTCA-TAACCGGGACATGACAAAACGTATCAACTTTTTTTAGAACCGGCCCTCTA-GGGACGTTATA-CAACCGCCTTGTATGAAAACTGCTACCATGGGAT-ATCGGACAAACCCCGGCGGAGTT-GTAGATTGCGCACGGTGACATCTACTGGAGGTCTGACCCTGGGTAGGGA-TTGTCAGGGCCCTATGGGAACTTGTC-ATTGCGTGGGGATTAGCAATAGTGAGCGTGGACAACCTGCGCCGCCACGTGCCATGTGCCCATAGTAGGCTTGTTGGCATTTTGGAAAGGGGAATACTCCGCCTACGTAGTGTGCTATCAGCTACTAGCGGGCGTTGTACCTTACTCCGGTGG-GCC-GGGGGAAAGA--TT-TTAAGGGTGTAGGGATCTCACATACACAGAAGGATAGCTACGGGTCCTTCCGCCACGTCTGGTACGCTGAGTGAACTGACTATGAACGGTCAC-AGCTGTTACGATCCC-TTGTAAATTCGCTTTGG-TCTAAGGTGCGGACT 684 + [I52:T,D53:T,I56:A,D57:A,I68:C,S68:C->A,D69:A,I73:C,S74:C->T,D75:T,I124:C,I124:G,S125:G->A,D126:C,D128:A,I161:A,S161:A->G,D162:G,I177:G,D178:G,D184:T,S185:A->T,I186:A,I199:A,D200:A,I212:T,D213:T,I221:A,D222:A,D234:G,I236:G,I238:C,I238:G,S238:C->T,D239:G,S241:T->A,D242:A,I251:C,S252:C->T,D254:T,I277:A,S277:A->T,D278:T,I286:A,D288:A,D290:C,I293:C,I338:C,D339:C,I369:A,D370:A,D533:G,S538:A->G,I540:A,D543:T,I546:T,I618:A,D619:A,D653:T,I655:T] + 0 CATAGAGAACTTATAGTTCCGACGATCAGTGGGACGAAAAAAAACCCCGCTC-TTCG-AACATGTTCCTT-CAATA-CCTCGGTTAGAACCGTGATTTGAGGTAACATTCTCTCACTGTCCCCTACGT--CGCAACACCCACGGGCTAAATTTACCTTCAGACTCGC-AGTGACCGGGCACGTA-GGCCTCATA-ACCGGGACATGAC-AAAACGTATCAAC-TTTTTTTAG-AACCGGCCCTCTAGG-GA--CGTTATACAACCG-CCTTGTATGAAAACTGCTACCATGGG-ATATCGGAC-AAACCCC-GGCGGAGTTGTAGATTGCGCACGGTGACATCTACTGGAGGTCTGA-CCCTGGGTAGGGATTGTCAGGGCCCTATGGG-AACTTGTCATTGCGTGGGGATTAGCAATAGTGAGCGTGGACAACCTGCGCCGCCACGTGCCATGTGCCCATAGTAGGCTTGTTGGCATTTTGGAAAGGGGAATACTCCGCCTACGTAGTGTGCTATCAGCTACTAGCGGGCGTTGTACCTTACTCCGGTGGGCCGGGGGAA-AGATTT-TAAGGGTGTAGGGATCTCACATACACAGAAGGATAGCTACGGGTCCTTCCGCCACGTCTGGTACGCTGAGTG-AACTGACTATGAACGGTCACAGCTGTTACGATCCCTT-GTAAATTCGCTTTGGTCTAAGGTGCGGACT 684 + |||||||||||||||||||||||||||||||||||||||||||||||||||| | || | |||||||||| ||| | |||||||||||||||||||||||||||||||||||||||||||||||| | | |||||||||||||||||||||||||||||||| |||||||||||||| | ||||| ||||||||||||| | ||||||||||| | ||||||| | ||||||||||| | || | |||||||| | | |||||||||||||||||||||| ||||||| || | || ||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| | ||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||| + 0 CATAGAGAACTTATAGTTCCGACGATCAGTGGGACGAAAAAAAACCCCGCTCTT-CGAA-CATGTTCCTTCA-ATACCT-CGGTTAGAACCGTGATTTGAGGTAACATTCTCTCACTGTCCCCTACGTCGCA-A-CACCCACGGGCTAAATTTACCTTCAGACTCGCAG-TGACCGGGCACGTAGG-CCTCA-TAACCGGGACATGACAA-AACGTATCAACTT-TTTTTAGAA-CCGGCCCTCTA-GGGACGT-TA-TACAACCGCCTT-GTATGAAAACTGCTACCATGGGAT-ATCGGACAAA-C-CCCGGCGGAGTTGTAGATTGCGCACGGTGACATCTACTGGAGGTCTGACC-CTGGGTAGGGATTGTCAGGGCCCTATGGGAA-CTTGTCATTGCGTGGGGATTAGCAATAGTGAGCGTGGACAACCTGCGCCGCCACGTGCCATGTGCCCATAGTAGGCTTGTTGGCATTTTGGAAAGGGGAATACTCCGCCTACGTAGTGTGCTATCAGCTACTAGCGGGCGTTGTACCTTACTCCGGTGGGCC-GGGGGAAAGA-TTTTAAGGGTGTAGGGATCTCACATACACAGAAGGATAGCTACGGGTCCTTCCGCCACGTCTGGTACGCTGAGTGAA-CTGACTATGAACGGTCACAGCTGTTACGATCCC-TTGTAAATTCGCTTTGGTCTAAGGTGCGGACT 684 com.milaboratory.core.mutations.MutationsUtilTest > test1111 STANDARD_OUT S([\QAGCTNRYSWKMBDHV\E])(\d+)([\QAGCTNRYSWKMBDHV\E])|D([\QAGCTNRYSWKMBDHV\E])(\d+)|I(\d+)([\QAGCTNRYSWKMBDHV\E]) @@ -3828,16 +3855,16 @@ com.milaboratory.core.sequence.NucleotideAlphabetTest > testCalculateIntersections SKIPPED com.milaboratory.core.sequence.ShortSequenceSetTest > test1 STANDARD_OUT - 99954 elements with 366.02KiB in raw nucleotide entropy serialized into 272.83KiB + 99939 elements with 366.1KiB in raw nucleotide entropy serialized into 272.89KiB com.milaboratory.core.sequence.quality.QualityAggregatorTest > test1 STANDARD_OUT - 54 + 49 com.milaboratory.core.sequence.quality.QualityAggregatorTest > test2 STANDARD_OUT - 577 + 629 com.milaboratory.core.sequence.quality.QualityAggregatorTest > test3 STANDARD_OUT - 2534 + 2533 com.milaboratory.core.sequence.quality.QualityTrimmerTest > testParametersSerialization0 STANDARD_OUT { @@ -3902,16 +3929,16 @@ ------------------ com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1nt STANDARD_ERROR - Indexing milib_36411b79a8a285421070ddb51ae321f07e08b7069841709847026287547.fasta: 0% - Indexing milib_36411b79a8a285421070ddb51ae321f07e08b7069841709847026287547.fasta: done + Indexing milib_f33d4583a77bd8d69b2cc3ace995e6e0386164ba11354168635726125425.fasta: 0% + Indexing milib_f33d4583a77bd8d69b2cc3ace995e6e0386164ba11354168635726125425.fasta: done com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test1 STANDARD_ERROR - Indexing milib_36411b79a8a285421070ddb51ae321f07e08b7069841709847026287547.fasta: 0% - Indexing milib_36411b79a8a285421070ddb51ae321f07e08b7069841709847026287547.fasta: done + Indexing milib_f33d4583a77bd8d69b2cc3ace995e6e0386164ba11354168635726125425.fasta: 0% + Indexing milib_f33d4583a77bd8d69b2cc3ace995e6e0386164ba11354168635726125425.fasta: done com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReaderTest > test2 STANDARD_ERROR - Indexing milib_32173230c8f4ba875e7f18e621d2477c4ddfda748245369615229513941.tmp: 0% - Indexing milib_32173230c8f4ba875e7f18e621d2477c4ddfda748245369615229513941.tmp: done + Indexing milib_9dfad02cfa110a16d30a5f455470d2a71ea6b73413012143514801444340.tmp: 0% + Indexing milib_9dfad02cfa110a16d30a5f455470d2a71ea6b73413012143514801444340.tmp: done com.milaboratory.core.io.util.IOUtilTest > test111 STANDARD_OUT 3 @@ -3923,9 +3950,9 @@ {"labels":["A","B","C","null"],"hist":[1,2,0,1]} com.milaboratory.util.ByteStringTest > testSpeed1 STANDARD_OUT - Time per hash: 129ns - Addition to hash set (per operation): 565ns - Hash set removal (per operation): 295ns + Time per hash: 113ns + Addition to hash set (per operation): 368ns + Hash set removal (per operation): 218ns a com.milaboratory.util.CacheTest > test1 STANDARD_OUT @@ -3943,1199 +3970,1206 @@ com.milaboratory.util.NSequenceWithQualityPrintHelperTest > test1 SKIPPED com.milaboratory.util.RemoveActionTest > test1 STANDARD_OUT - /tmp/milib_91c5d089dbfe1312c4dc645315eab3559d1f25b37108411553737323663 + /tmp/milib_defa7d5eceafd006844ac43de98cf0d0403ee45916152265929003142054 com.milaboratory.util.RemoveActionTest > test2 STANDARD_OUT - /tmp/milib_a4fa6c7a457d6568353341f70e37a6f43419c84818033468977680404430.tmp + /tmp/milib_228b567babcaefd25fd1550da8387a10dd908e3e3165140027884898520.tmp com.milaboratory.util.sorting.HashSorterTest > testSingleton STANDARD_OUT - /tmp/milib_4ce406efe609ab6cf9c73e9721fdc3313c8081214722301104006104087 - timeInCollate: 5.73s - timeInCollatorInit: 4.02s - timeAwaitingO: 40.48ms - timeAwaitingI: 1.42s + /tmp/milib_7c422ea1f1dc2b3aad8f2756780e48dde57048105643900269200909354 + timeInCollate: 4.56s + timeInCollatorInit: 3.3s + timeAwaitingO: 15.24ms + timeAwaitingI: 988.02ms timeInFinalSorting1: 0ns - timeInFinalSorting2: 150.96ms - timeInFinalSorting3: 85.37ms - /6S (5|27|32): objs=50000 size=2.91MiB + timeInFinalSorting2: 158.03ms + timeInFinalSorting3: 36.2ms + /4S (5|27|32): objs=50000 size=2.94MiB com.milaboratory.util.sorting.HashSorterTest > test1 STANDARD_OUT - /tmp/milib_5a9a5a218b123dfa21a572be32b9d87bd0dae5b4455165745434700502 - timeInCollate: 21.75s - timeInCollatorInit: 1.23s - timeAwaitingO: 1.6s - timeAwaitingI: 5.41s - timeInFinalSorting1: 1.23s - 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+ /31/23N (2|25|36): objs=6979 size=33.42KiB + /31/24S (2|25|36): objs=131 size=112B + /31/25N (2|25|36): objs=1220 size=4.98KiB + /31/26S (2|25|36): objs=143 size=251B + /31/27S (2|25|36): objs=143 size=287B + /31/28S (2|25|36): objs=155 size=201B + /31/29N (2|25|36): objs=1278 size=5.36KiB + /31/30S (2|25|36): objs=141 size=176B + /31/31N (2|25|36): objs=746 size=3.08KiB + /31/32S (2|25|36): objs=135 size=318B + /31/33N (2|25|36): objs=3417 size=14.77KiB + /31/34S (2|25|36): objs=143 size=118B + /31/35N (2|25|36): objs=456 size=1.45KiB com.milaboratory.util.sorting.HashSorterTest > test2 SKIPPED com.milaboratory.util.sorting.SortingUtilTest > test1 STANDARD_OUT - Collation: 390.49ms - Sorting: 211.99ms + Collation: 122.23ms + Sorting: 56.93ms 1 217 - 41491 - 99524 - 99999 + 41446 + 99510 + 100000 com.milaboratory.util.VersionInfoTest > test3 SKIPPED Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.11 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test +Finished generating test XML results (0.07 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.185 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test -:test (Thread[#50,Task worker for ':',5,main]) completed. Took 4 mins 49.286 secs. +Finished generating test html results (0.105 secs) into: /build/reproducible-path/milib-2.2.0+dfsg/build/reports/tests/test +:test (Thread[#52,Task worker for ':' Thread 3,5,main]) completed. Took 2 mins 19.705 secs. -BUILD SUCCESSFUL in 5m 37s +BUILD SUCCESSFUL in 2m 32s 5 actionable tasks: 3 executed, 2 up-to-date create-stamp debian/debhelper-build-stamp dh_prep @@ -5148,7 +5182,7 @@ dh_link jh_installlibs jh_classpath -Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" jh_manifest jh_depends dh_strip_nondeterminism @@ -5167,12 +5201,14 @@ 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/458117/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/458117/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/126427 and its subdirectories -I: Current time: Mon Feb 9 17:01:34 -12 2026 -I: pbuilder-time-stamp: 1770699694 +I: removing directory /srv/workspace/pbuilder/458117 and its subdirectories +I: Current time: Wed Jan 8 12:43:52 +14 2025 +I: pbuilder-time-stamp: 1736289832