Diff of the two buildlogs: -- --- b1/build.log 2025-08-16 04:01:43.332560332 +0000 +++ b2/build.log 2025-08-16 04:12:57.005409991 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 15 15:51:06 -12 2025 -I: pbuilder-time-stamp: 1755316266 +I: Current time: Sat Sep 19 00:25:23 +14 2026 +I: pbuilder-time-stamp: 1789727123 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,85 @@ 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/2529029/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3200651/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Sep 18 10:25 /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/3200651/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3200651/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='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='cfef9a62b976432c8dc288a01d9e17f7' - 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='2529029' - PS1='# ' - PS2='> ' + INVOCATION_ID=5c4a16c365a74f97a0a6cfc7518f610a + 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=3200651 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.eZ8EFAE6/pbuilderrc_gBMh --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eZ8EFAE6/b1 --logfile b1/build.log snpeff_5.2.f+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - 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.eZ8EFAE6/pbuilderrc_rY4p --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eZ8EFAE6/b2 --logfile b2/build.log snpeff_5.2.f+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2529029/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3200651/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -578,7 +610,7 @@ Get: 423 http://deb.debian.org/debian forky/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 424 http://deb.debian.org/debian forky/main arm64 unzip arm64 6.0-29 [163 kB] Get: 425 http://deb.debian.org/debian forky/main arm64 maven-debian-helper all 2.6.7 [108 kB] -Fetched 340 MB in 1s (264 MB/s) +Fetched 340 MB in 3s (126 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared: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 ... 19963 files and directories currently installed.) @@ -1969,8 +2001,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Aug 16 03:52:00 UTC 2025. -Universal Time is now: Sat Aug 16 03:52:00 UTC 2025. +Local time is now: Fri Sep 18 10:26:38 UTC 2026. +Universal Time is now: Fri Sep 18 10:26:38 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2530,7 +2562,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpeff-5.2.f+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.f+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3200651/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3200651/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpeff-5.2.f+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.f+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.f+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2550,7 +2586,7 @@ fi make[1]: Leaving directory '/build/reproducible-path/snpeff-5.2.f+dfsg' jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -3278,8 +3314,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 31.532 s -[INFO] Finished at: 2025-08-15T15:53:12-12:00 +[INFO] Total time: 23.362 s +[INFO] Finished at: 2026-09-19T00:27:47+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.f\+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.f\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.f\+dfsg/debian/maven-repo --batch-mode test @@ -3314,7 +3350,7 @@ [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign TestCasesAlign.test_01(23): Test TestCasesAlign.test_02(112): Test -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps TestCasesSnps.test_01(43): Test .................................................................................................... @@ -3328,15 +3364,15 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.511 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.061 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps [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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric [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: 0.708 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.593 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel TestCasesStructuralDel.test02(249): Test TestCasesStructuralDel.test03(266): Test @@ -3349,7 +3385,7 @@ 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: 9.269 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.38 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test @@ -3400,21 +3436,21 @@ 900 ................................................................................................... Done. TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test -.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.323 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.127 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap [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: 0.007 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [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: 0.613 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.602 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... @@ -3428,19 +3464,19 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.862 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.733 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon [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: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.175 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.063 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel [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: 0.085 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [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: 1.332 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.139 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations TestCasesStructuralTranslocations.test02_2_nonFs(532): Test TestCasesStructuralTranslocations.test01_0_nonFs(286): Test @@ -3469,21 +3505,21 @@ 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: 22.366 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.012 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations [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: 3.908 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.77 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse [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: 0.007 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron TestCasesHgvsIntron.test_01_intron(23): Test ............................................................... @@ -3500,7 +3536,7 @@ 1300 ........................................................................................................... 1500 ....................................................... 1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.801 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.622 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals TestCasesIntervals.test_00(140): Test TestCasesIntervals.test_01(152): Test @@ -3519,7 +3555,7 @@ 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: 10.246 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.613 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test @@ -3531,7 +3567,7 @@ 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: 5.656 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.052 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup TestCasesStructuralDup.test01_dupGene(157): Test TestCasesStructuralDup.test02(194): Test @@ -3544,18 +3580,18 @@ 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: 6.47 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.432 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup [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: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector [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: 1.112 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.215 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup [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: 0.528 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.553 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test @@ -3570,7 +3606,7 @@ 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: 7.432 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.875 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp TestCasesApplyMnp.test_apply_variant_01(22): Test TestCasesApplyMnp.test_apply_variant_02(33): Test @@ -3585,7 +3621,7 @@ 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: 7.64 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.413 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps TestCasesMnps.test_01(187): Test .................................................................................................... @@ -3599,7 +3635,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.528 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.503 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp TestCasesApplySnp.test_apply_variant_01(21): Test TestCasesApplySnp.test_apply_variant_02(31): Test @@ -3608,7 +3644,7 @@ 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: 3.947 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.823 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test TestCasesApplyMixed.test_apply_variant_06_longer(169): Test @@ -3628,7 +3664,7 @@ 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: 10.635 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer TestCasesSequenceIndexer.test_01(69): Test TestCasesSequenceIndexer.test_02(100): Test @@ -3640,7 +3676,7 @@ 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: 6.232 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.513 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap TestCasesOverlap.test_binSeq_01(26): Test TestCasesOverlap.test_binSeq_02(32): Test @@ -3655,16 +3691,16 @@ 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: 0.013 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap [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: 2.339 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.298 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [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: 0.761 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.691 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant TestCasesIntervalVariant.test_01(36): Test .................................................................................................... @@ -3677,7 +3713,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.238 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.037 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv TestCasesStructuralInv.test01_invGene(214): Test TestCasesStructuralInv.test02(249): Test @@ -3690,7 +3726,7 @@ 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: 6.85 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.085 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -3740,7 +3776,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.035 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.11 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels TestCasesDels.test_01(138): Test .................................................................................................... @@ -3754,22 +3790,22 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.754 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.445 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels [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: 0.632 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.653 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader TestCasesSeekableReader.test_00(59): Test TestCasesSeekableReader.test_01(71): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.296 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.193 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader [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: 0.116 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable TestCasesCodonTable.test_01(28): Test TestCasesCodonTable.test_02(59): Test -00:02:52 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.64 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +00:02:37 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.543 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns TestCasesIns.test_01(38): Test .................................................................................................... @@ -3783,11 +3819,11 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.526 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.563 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns [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: 2.414 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.574 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild [INFO] Running 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.TestCasesCds @@ -3806,7 +3842,7 @@ 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: 1.789 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.973 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup TestCasesHgvsDnaDup.test_01(31): Test TestCasesHgvsDnaDup.test_02(54): Test @@ -3819,7 +3855,7 @@ 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: 6.775 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.42 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -3833,7 +3869,7 @@ 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: 8.684 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.467 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome TestCasesReactome.test_01(32): Test TestCasesReactome.test_02(56): Test @@ -3846,7 +3882,7 @@ TestCasesCircular.test_circular_02(54): Test TestCasesCircular.test_circular_03(83): Test TestCasesCircular.test_circular_04(103): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel TestCasesApplyDel.test_apply_variant_01(21): Test TestCasesApplyDel.test_apply_variant_02(31): Test @@ -3861,12 +3897,12 @@ 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: 7.253 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.676 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel [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: 1.795 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.957 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -3887,26 +3923,26 @@ 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: 0.015 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt [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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose [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: 2.277 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.431 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [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: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 26.056 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 26.399 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite TestCasesSpliceSite.test_01(34): Test .................................................................................................... @@ -3920,7 +3956,7 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.63 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.642 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence TestCasesDnaNSequence.test_02_long_replaceBase(243): Test TestCasesDnaNSequence.test_13_reverseWc(253): Test @@ -3931,7 +3967,7 @@ 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: 2.724 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.833 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList TestCasesGenePvalueList.test_01(28): Test TestCasesGenePvalueList.test_02(46): Test @@ -3942,7 +3978,7 @@ 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: 2.422 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.636 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri @@ -3970,7 +4006,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.594 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.467 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree TestCasesIntervalTree.test_01(141): Test . @@ -3996,7 +4032,7 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.5 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.779 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray TestCasesIntervalTree.test_01(141): Test . @@ -4022,11 +4058,11 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.952 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.146 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray [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: 1.131 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.166 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction [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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare @@ -4038,8 +4074,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 04:50 min -[INFO] Finished at: 2025-08-15T15:58:05-12:00 +[INFO] Total time: 04:36 min +[INFO] Finished at: 2026-09-19T00:32:26+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -4063,8 +4099,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.366 s -[INFO] Finished at: 2025-08-15T15:58:11-12:00 +[INFO] Total time: 0.640 s +[INFO] Finished at: 2026-09-19T00:32:28+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.f\+dfsg --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom @@ -4139,7 +4175,7 @@ [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. -Aug 15, 2025 3:58:24 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Sep 19, 2026 12:32:40 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.f+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 @@ -4281,9 +4317,9 @@ dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.f+dfsg-1_all.deb'. -dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. +dpkg-deb: building package 'snpeff' in '../snpeff_5.2.f+dfsg-1_all.deb'. +dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.f+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4291,12 +4327,14 @@ 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/3200651/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3200651/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/2529029 and its subdirectories -I: Current time: Fri Aug 15 16:01:42 -12 2025 -I: pbuilder-time-stamp: 1755316902 +I: removing directory /srv/workspace/pbuilder/3200651 and its subdirectories +I: Current time: Sat Sep 19 00:35:56 +14 2026 +I: pbuilder-time-stamp: 1789727756