Diff of the two buildlogs: -- --- b1/build.log 2024-05-15 03:40:47.842873383 +0000 +++ b2/build.log 2024-05-15 03:51:38.091210834 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 16 21:54:19 -12 2025 -I: pbuilder-time-stamp: 1750154059 +I: Current time: Wed May 15 17:40:53 +14 2024 +I: pbuilder-time-stamp: 1715744453 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying lowering_heap_allocation.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2366329/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3381110/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 May 15 03:41 /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/3381110/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3381110/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=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='af1110badc6b49ca884cfd524bda883b' - 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='2366329' - PS1='# ' - PS2='> ' + INVOCATION_ID=f1b5303a97014422a1fc502b0304c4e1 + 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=3381110 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.h45W1OnI/pbuilderrc_scY2 --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.h45W1OnI/b1 --logfile b1/build.log snpeff_5.2.b+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.h45W1OnI/pbuilderrc_vgZd --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.h45W1OnI/b2 --logfile b2/build.log snpeff_5.2.b+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 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 16 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2366329/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 11:38 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3381110/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -569,7 +601,7 @@ Get: 411 http://deb.debian.org/debian trixie/main arm64 maven all 3.8.7-2 [19.3 kB] Get: 412 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 413 http://deb.debian.org/debian trixie/main arm64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 345 MB in 3s (108 MB/s) +Fetched 345 MB in 2s (166 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19744 files and directories currently installed.) @@ -1907,8 +1939,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 17 09:55:49 UTC 2025. -Universal Time is now: Tue Jun 17 09:55:49 UTC 2025. +Local time is now: Wed May 15 03:42:23 UTC 2024. +Universal Time is now: Wed May 15 03:42:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2444,7 +2476,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpeff-5.2.b+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 > ../snpeff_5.2.b+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3381110/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3381110/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpeff-5.2.b+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 > ../snpeff_5.2.b+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.b+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -5347,8 +5383,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 32.065 s -[INFO] Finished at: 2025-06-16T21:57:25-12:00 +[INFO] Total time: 29.086 s +[INFO] Finished at: 2024-05-15T17:44:45+14:00 [INFO] ------------------------------------------------------------------------ dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/snpeff-5.2.b\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian/maven-repo --batch-mode test @@ -5379,7 +5415,7 @@ [INFO] ------------------------------------------------------- [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta TestCasesFasta.test_01(23): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.124 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.769 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -5400,7 +5436,7 @@ TestCasesNextProt.test_05_nextprotFactory(98): Test TestCasesNextProt.test_02_nextprotFactory(42): Test TestCasesNextProt.test_13_nextprotFactory(277): Test -[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup TestCasesStructuralDup.test01_dupGene(157): Test TestCasesStructuralDup.test02(194): Test @@ -5413,15 +5449,15 @@ TestCasesStructuralDup.test09(324): Test TestCasesStructuralDup.test10(345): Test TestCasesStructuralDup.test01_dupTr(175): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.543 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.083 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric TestCasesHypergeometric.test_0(77): Test TestCasesHypergeometric.test_01_hyper(83): Test TestCasesHypergeometric.test_02_hyper(202): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare TestCasesChiSquare.test_1(26): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular TestCasesCircular.test_circular_01(26): Test TestCasesCircular.test_circular_02(54): Test @@ -5430,7 +5466,7 @@ [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils TestCasesMarkerUtils.test_collapseZeroGap(107): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test @@ -5445,7 +5481,7 @@ TestCasesApplyIns.test_apply_variant_11(159): Test TestCasesApplyIns.test_apply_variant_12(178): Test TestCasesApplyIns.test_apply_variant_13(192): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.965 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.173 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test TestCasesApplyMixed.test_apply_variant_06_longer(169): Test @@ -5465,21 +5501,21 @@ TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test TestCasesApplyMixed.test_apply_variant_01_longer(22): Test -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.685 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.964 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion TestCasesSpliceRegion.test_01(33): Test -..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.439 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction TestCasesProteinInteraction.test_02_split_codon_base(58): Test TestCasesProteinInteraction.test_01_split_codon_base(26): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.608 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.721 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse TestCasesEffectCollapse.test_01(68): Test TestCasesEffectCollapse.test_02(74): Test TestCasesEffectCollapse.test_03(80): Test TestCasesEffectCollapse.test_04(86): Test TestCasesEffectCollapse.test_05(92): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.667 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.633 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -5493,7 +5529,7 @@ TestCasesDnaSequence.test_01_short_getBase(218): Test TestCasesDnaSequence.test_04_Pe(287): Test TestCasesDnaSequence.test_01_short_replaceBase(238): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.718 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.649 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test @@ -5556,7 +5592,7 @@ Max words: 8 ......... Max words: 9 ......... Done. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.76 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.258 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup TestCasesHgvsDnaDup.test_01(31): Test TestCasesHgvsDnaDup.test_02(54): Test @@ -5569,7 +5605,7 @@ TestCasesHgvsDnaDup.test_09(247): Test TestCasesHgvsDnaDup.test_10(277): Test TestCasesHgvsDnaDup.test_11(308): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.461 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.299 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations TestCasesStructuralTranslocations.test02_2_nonFs(532): Test TestCasesStructuralTranslocations.test01_0_nonFs(286): Test @@ -5598,23 +5634,23 @@ TestCasesStructuralTranslocations.test04_0_nonFs(778): Test TestCasesStructuralTranslocations.test02_1_nonFs(477): Test TestCasesStructuralTranslocations.test06_no_gene(981): Test -[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.245 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.645 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector TestCasesGenotypeVector.test_01(23): Test TestCasesGenotypeVector.test_02(48): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial TestCasesBinomial.test_01(86): Test TestCasesBinomial.test_02(191): Test TestCasesBinomial.test_03(299): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest TestCasesFisherExactTest.test_05_fisher(313): Test TestCasesFisherExactTest.test_0(97): Test TestCasesFisherExactTest.test_03_fisher(103): Test TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test TestCasesFisherExactTest.test_04_fisher(208): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... @@ -5628,7 +5664,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.54 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.981 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns TestCasesIns.test_01(38): Test .................................................................................................... @@ -5642,7 +5678,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.175 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.679 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence TestCasesDnaNSequence.test_02_long_replaceBase(243): Test TestCasesDnaNSequence.test_13_reverseWc(253): Test @@ -5653,7 +5689,7 @@ TestCasesDnaNSequence.test_02_long_getBase(223): Test TestCasesDnaNSequence.test_01_short_getBase(184): Test TestCasesDnaNSequence.test_01_short_replaceBase(204): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.763 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.734 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer TestCasesSequenceIndexer.test_01(69): Test TestCasesSequenceIndexer.test_02(100): Test @@ -5665,10 +5701,10 @@ TestCasesSequenceIndexer.test_08(247): Test TestCasesSequenceIndexer.test_09(267): Test TestCasesSequenceIndexer.test_10(287): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.061 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.624 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 TestCasesEffectCollapse2.test_01(40): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.321 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.661 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test @@ -5687,7 +5723,7 @@ TestCasesIntervals.test_07_05(362): Test TestCasesIntervals.test_08_02(413): Test TestCasesIntervals.test_08_03(438): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.49 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.026 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome TestCasesReactome.test_01(32): Test TestCasesReactome.test_01(48): Out: 0.9051482536448667 @@ -5703,7 +5739,7 @@ TestCasesReactome.test_05(149): Test TestCasesReactome.test_05(165): Out: -0.9154962776570641 TestCasesReactome.test_05(170): Out: 0.34014843250566407 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron TestCasesHgvsIntron.test_01_intron(23): Test ............................................................... @@ -5720,7 +5756,7 @@ 1300 ........................................................................................................... 1500 ....................................................... 1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.335 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.997 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps TestCasesMnps.test_01(187): Test .................................................................................................... @@ -5734,7 +5770,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.339 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.417 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels TestCasesDels.test_01(138): Test .................................................................................................... @@ -5748,18 +5784,18 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.092 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.102 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte TestCasesDnaSequenceByte.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse TestCasesAnnParse.test_EffectType(29): Test TestCasesAnnParse.test_old_SO(45): Test TestCasesAnnParse.test_old_SO_vcf(53): Test TestCasesAnnParse.testCase_tfbs_ablation(71): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.252 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.225 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf TestCasesVcf.test_22_huge_headers(363): Test TestCasesVcf.test_12_readHeader_NL(257): Test @@ -5789,7 +5825,7 @@ TestCasesVcf.test_13_chrOri(268): Test TestCasesVcf.test_04_del(72): Test TestCasesVcf.test_14_VcfInfoValue(296): Test -[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.379 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.927 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel TestCasesApplyDel.test_apply_variant_01(21): Test TestCasesApplyDel.test_apply_variant_02(31): Test @@ -5804,7 +5840,7 @@ TestCasesApplyDel.test_apply_variant_11(176): Test TestCasesApplyDel.test_apply_variant_12(199): Test TestCasesApplyDel.test_apply_variant_13(223): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.982 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap TestCasesOverlap.test_binSeq_01(26): Test TestCasesOverlap.test_binSeq_02(32): Test @@ -5819,13 +5855,13 @@ TestCasesOverlap.test_binSeq_11(87): Test TestCasesOverlap.test_binSeq_12(94): Test TestCasesOverlap.test_binSeq_13(100): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader TestCasesSeekableReader.test_00(60): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf TestCasesSeekableReader.test_01(74): Test ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.696 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.71 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp TestCasesApplySnp.test_apply_variant_01(21): Test TestCasesApplySnp.test_apply_variant_02(31): Test @@ -5834,7 +5870,7 @@ TestCasesApplySnp.test_apply_variant_06(77): Test TestCasesApplySnp.test_apply_variant_08(95): Test TestCasesApplySnp.test_apply_variant_09(106): Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.15 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.11 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite TestCasesSpliceSite.test_01(34): Test .................................................................................................... @@ -5848,11 +5884,11 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.449 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesJaspar TestCasesJaspar.test_01(22): Test TestCasesJaspar.test_02(56): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.648 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.728 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel TestCasesStructuralDel.test02(249): Test TestCasesStructuralDel.test03(266): Test @@ -5865,11 +5901,11 @@ TestCasesStructuralDel.test10(398): Test TestCasesStructuralDel.test01_delTr(230): Test TestCasesStructuralDel.test01_delGene(212): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.607 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.698 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup TestCasesHgvsProtDup.test_01(31): Test TestCasesHgvsProtDup.test_02(70): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.606 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.631 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv TestCasesStructuralInv.test01_invGene(214): Test TestCasesStructuralInv.test02(249): Test @@ -5882,7 +5918,7 @@ TestCasesStructuralInv.test09(370): Test TestCasesStructuralInv.test10(387): Test TestCasesStructuralInv.test01_invTr(231): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.887 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.026 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign TestCasesAlign.test_01(23): Test TestCasesAlign.test_02(113): Test @@ -5891,7 +5927,7 @@ diff : | | | Name2 : XcgtactgatagtcagtcatgctagtcagX -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -5941,13 +5977,13 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.113 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.586 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative TestCasesHgvsDnaDupNegative.test_01(34): Test TestCasesHgvsDnaDupNegative.test_02(61): Test TestCasesHgvsDnaDupNegative.test_03(91): Test TestCasesHgvsDnaDupNegative.test_04(122): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.431 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.343 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray TestCasesIntervalTree.test_01(141): Test . @@ -5973,7 +6009,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.42 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.168 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree TestCasesIntervalTree.test_01(141): Test . @@ -5999,7 +6035,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.952 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.31 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . @@ -6025,20 +6061,20 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.73 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.49 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString TestCasesIubString.test_01(29): Test TestCasesIubString.test_02(39): Test TestCasesIubString.test_03(49): Test TestCasesIubString.test_04(68): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.587 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.686 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats TestCasesIntStats.test_01(31): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.41 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant TestCasesIntervalVariant.test_01(36): Test .................................................................................................... @@ -6051,7 +6087,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.648 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.146 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps TestCasesSnps.test_01(43): Test .................................................................................................... @@ -6065,11 +6101,11 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.835 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.134 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList TestCasesGenePvalueList.test_01(28): Test TestCasesGenePvalueList.test_02(46): Test @@ -6080,7 +6116,7 @@ TestCasesGenePvalueList.test_07(155): Test TestCasesGenePvalueList.test_08(187): Test TestCasesGenePvalueList.test_09(209): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.144 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.412 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp TestCasesApplyMnp.test_apply_variant_01(22): Test TestCasesApplyMnp.test_apply_variant_02(33): Test @@ -6095,17 +6131,17 @@ TestCasesApplyMnp.test_apply_variant_11(176): Test TestCasesApplyMnp.test_apply_variant_12(197): Test TestCasesApplyMnp.test_apply_variant_13(219): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.904 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.565 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage TestCasesCochranArmitage.test_01(18): Test TestCasesCochranArmitage.test_02(28): Test TestCasesCochranArmitage.test_03(37): Test TestCasesCochranArmitage.test_04(46): Test TestCasesCochranArmitage.test_05(57): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic TestCasesIntergenic.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.318 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds TestCasesCds.test_CdsPos(35): Test .................................................................................................... @@ -6122,15 +6158,15 @@ TestCasesCds.test_cdsStartEnd_1(73): Test TestCasesCds.test_cdsStartEnd_2(96): Test WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.96 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.178 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs TestCasesHgvs.test_01(56): Test TestCasesHgvs.test_02(69): Test TestCasesHgvs.test_03(83): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.892 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers TestCasesNmers.test_03_Nmers(33): Test -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test @@ -6142,16 +6178,16 @@ TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test TestCasesVariantRealignment.test_05_savant_opposite(174): Test TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.95 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.67 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBuild TestCasesBuild.test_01_chromoNamesDoNotMatch_Gff(18): Test TestCasesBuild.test_02_chromoNamesDoNotMatch_GffFasta(54): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.282 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.472 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable TestCasesCodonTable.test_01(28): Test TestCasesCodonTable.test_02(59): Test -00:02:43 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +00:03:00 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable [INFO] [INFO] Results: [INFO] @@ -6160,8 +6196,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:51 min -[INFO] Finished at: 2025-06-16T22:00:17-12:00 +[INFO] Total time: 03:10 min +[INFO] Finished at: 2024-05-15T17:47:57+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -6184,8 +6220,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.625 s -[INFO] Finished at: 2025-06-16T22:00:20-12:00 +[INFO] Total time: 1.004 s +[INFO] Finished at: 2024-05-15T17:48:01+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.b\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom @@ -6260,7 +6296,7 @@ [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. -Jun 16, 2025 10:00:31 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 15, 2024 5:48:15 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.b+dfsg/pom.xml: Dependency not found org.biojava:biojava-structure:jar:6.x ERROR: pom.xml: dependency is not packaged in the Maven repository for Debian: org.biojava:biojava-structure:6.x @@ -6402,9 +6438,9 @@ dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.b+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.b+dfsg-1_all.deb'. -dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.b+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.b+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6412,12 +6448,14 @@ 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/3381110/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3381110/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/2366329 and its subdirectories -I: Current time: Mon Jun 16 22:03:46 -12 2025 -I: pbuilder-time-stamp: 1750154626 +I: removing directory /srv/workspace/pbuilder/3381110 and its subdirectories +I: Current time: Wed May 15 17:51:36 +14 2024 +I: pbuilder-time-stamp: 1715745096