Diff of the two buildlogs: -- --- b1/build.log 2025-09-11 11:02:21.506986351 +0000 +++ b2/build.log 2025-09-11 11:14:05.807866569 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 14 05:07:16 -12 2026 -I: pbuilder-time-stamp: 1791997636 +I: Current time: Fri Sep 12 01:02:26 +14 2025 +I: pbuilder-time-stamp: 1757588546 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/2715949/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/148367/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 11 11:03 /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/148367/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/148367/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ee2769f945d64cdcb5265050b3d8c977' - 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='2715949' - PS1='# ' - PS2='> ' + INVOCATION_ID=53cf8568d2774953b1874d3f2b54ac6a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=148367 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.0bgbTPxM/pbuilderrc_ZMoQ --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.0bgbTPxM/b1 --logfile b1/build.log snpeff_5.2.f+dfsg-1.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.0bgbTPxM/pbuilderrc_LIH5 --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.0bgbTPxM/b2 --logfile b2/build.log snpeff_5.2.f+dfsg-1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2715949/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/148367/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -579,7 +611,7 @@ Get: 424 http://deb.debian.org/debian forky/main amd64 maven-repo-helper all 1.12 [136 kB] Get: 425 http://deb.debian.org/debian forky/main amd64 unzip amd64 6.0-29 [173 kB] Get: 426 http://deb.debian.org/debian forky/main amd64 maven-debian-helper all 2.6.8 [107 kB] -Fetched 353 MB in 60s (5874 kB/s) +Fetched 353 MB in 27s (13.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21054 files and directories currently installed.) @@ -1974,8 +2006,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Oct 14 17:13:00 UTC 2026. -Universal Time is now: Wed Oct 14 17:13:00 UTC 2026. +Local time is now: Thu Sep 11 11:05:24 UTC 2025. +Universal Time is now: Thu Sep 11 11:05:24 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2534,7 +2566,11 @@ 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/148367/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/148367/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 @@ -2554,7 +2590,7 @@ fi make[1]: Leaving directory '/build/reproducible-path/snpeff-5.2.f+dfsg' jh_clean -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -3282,8 +3318,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 56.549 s -[INFO] Finished at: 2026-10-14T05:14:44-12:00 +[INFO] Total time: 22.004 s +[INFO] Finished at: 2025-09-12T01:06:19+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 @@ -3315,20 +3351,153 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- +[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: 2.454 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular +TestCasesCircular.test_circular_01(26): Test +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: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[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: 2.752 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +TestCasesStructuralInv.test01_invGene(214): Test +TestCasesStructuralInv.test02(249): Test +TestCasesStructuralInv.test03(266): Test +TestCasesStructuralInv.test04(283): Test +TestCasesStructuralInv.test05(300): Test +TestCasesStructuralInv.test06(317): Test +TestCasesStructuralInv.test07(334): Test +TestCasesStructuralInv.test08(352): Test +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: 5.574 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.046 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +TestCasesIntervalVariant.test_01(36): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.231 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +TestCasesApplyIns.test_apply_variant_01(21): Test +TestCasesApplyIns.test_apply_variant_02(32): Test +TestCasesApplyIns.test_apply_variant_03(43): Test +TestCasesApplyIns.test_apply_variant_04(54): Test +TestCasesApplyIns.test_apply_variant_05(72): Test +TestCasesApplyIns.test_apply_variant_06(90): Test +TestCasesApplyIns.test_apply_variant_07(108): Test +TestCasesApplyIns.test_apply_variant_08(126): Test +TestCasesApplyIns.test_apply_variant_09(137): Test +TestCasesApplyIns.test_apply_variant_10(148): Test +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: 6.109 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 +TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test +TestCasesApplyMixed.test_apply_variant_04_longer(98): Test +TestCasesApplyMixed.test_apply_variant_09_longer(259): Test +TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test +TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test +TestCasesApplyMixed.test_apply_variant_02_longer(42): Test +TestCasesApplyMixed.test_apply_variant_07_longer(203): Test +TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test +TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test +TestCasesApplyMixed.test_apply_variant_05_longer(134): Test +TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test +TestCasesApplyMixed.test_apply_variant_03_longer(64): Test +TestCasesApplyMixed.test_apply_variant_08_longer(237): Test +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: 8.537 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.355 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString +[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: 0.813 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[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: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[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: 1.367 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome TestCasesReactome.test_01(32): Test TestCasesReactome.test_02(56): Test TestCasesReactome.test_03(86): Test TestCasesReactome.test_04(114): Test TestCasesReactome.test_05(142): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome -[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: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +TestCasesApplyMnp.test_apply_variant_01(22): Test +TestCasesApplyMnp.test_apply_variant_02(33): Test +TestCasesApplyMnp.test_apply_variant_03(44): Test +TestCasesApplyMnp.test_apply_variant_04(61): Test +TestCasesApplyMnp.test_apply_variant_05(79): Test +TestCasesApplyMnp.test_apply_variant_06(97): Test +TestCasesApplyMnp.test_apply_variant_07(115): Test +TestCasesApplyMnp.test_apply_variant_08(133): Test +TestCasesApplyMnp.test_apply_variant_09(144): Test +TestCasesApplyMnp.test_apply_variant_10(155): Test +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: 6.082 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment TestCasesVariantRealignment.test_07_savant(203): Test TestCasesVariantRealignment.test_01(56): Test @@ -3340,91 +3509,35 @@ 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: 13.119 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.846 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[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: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[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: 0.107 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[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: 0.485 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats [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: 4.545 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild -[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: 0.207 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte -[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: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers -[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: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -[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: 1.995 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -[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: 0.195 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -TestCasesDnaOverlap.test_10_overlap(332): Test -TestCasesDnaOverlap.test_07_overlap(297): Test -TestCasesDnaOverlap.test_12_overlap(356): Test -TestCasesDnaOverlap.test_09_overlap(320): Test -TestCasesDnaOverlap.test_17_overlap_rand(459): Test - -Overlap random test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ................................................................................................... -Done. -TestCasesDnaOverlap.test_15_DnaCoder_copy_1(380): Test -.........TestCasesDnaOverlap.test_11_overlap(344): Test -TestCasesDnaOverlap.test_08_overlap(308): Test -TestCasesDnaOverlap.test_18_DnaCoder_score_rand(474): Test -DnaCoder.score test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ...................................................................................................Done. -TestCasesDnaOverlap.test_13_overlap(368): Test -TestCasesDnaOverlap.test_19_score_threshold_rand(493): Test - -Score (threshold) random test: -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 ................................................................................................... -Done. -TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test -.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.962 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -[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: 2.35 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs -[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 -[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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -TestCasesSpliceSite.test_01(34): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.838 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +TestCasesStructuralDup.test01_dupGene(157): Test +TestCasesStructuralDup.test02(194): Test +TestCasesStructuralDup.test03(212): Test +TestCasesStructuralDup.test04(229): Test +TestCasesStructuralDup.test05(247): Test +TestCasesStructuralDup.test06(265): Test +TestCasesStructuralDup.test07(286): Test +TestCasesStructuralDup.test08(303): Test +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: 5.347 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps +TestCasesMnps.test_01(187): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3436,20 +3549,22 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.104 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList -TestCasesGenePvalueList.test_01(28): Test -TestCasesGenePvalueList.test_02(46): Test -TestCasesGenePvalueList.test_03(64): Test -TestCasesGenePvalueList.test_04(82): Test -TestCasesGenePvalueList.test_05(111): Test -TestCasesGenePvalueList.test_06(129): Test -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: 3.45 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns -TestCasesIns.test_01(38): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.713 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[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.TestCasesCodonTable +TestCasesCodonTable.test_01(28): Test +TestCasesCodonTable.test_02(59): Test +00:01:28 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.51 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[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: 2.047 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds +TestCasesCds.test_CdsPos(35): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3461,37 +3576,10 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.412 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.235 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 67.424 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +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: 1.615 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -3541,39 +3629,7 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 49.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt -TestCasesNextProt.test_10_nextprotFactory(205): Test -TestCasesNextProt.test_09_nextprotFactory(182): Test -TestCasesNextProt.test_06_nextprotFactory(116): Test -TestCasesNextProt.test_14(304): Test -TestCasesNextProt.test_15(322): Test -TestCasesNextProt.test_16(340): Test -TestCasesNextProt.test_17(358): Test -TestCasesNextProt.test_18(376): Test -TestCasesNextProt.test_19(394): Test -TestCasesNextProt.test_03_nextprotFactory(60): Test -TestCasesNextProt.test_11_nextprotFactory(228): Test -TestCasesNextProt.test_07_nextprotFactory(136): Test -TestCasesNextProt.test_04_nextprotFactory(80): Test -TestCasesNextProt.test_01_nextprotFactory(24): Test -TestCasesNextProt.test_12_nextprotFactory(251): Test -TestCasesNextProt.test_08_nextprotFactory(159): Test -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: 0.016 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.487 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel -[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: 4.003 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: 0.856 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.144 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence TestCasesDnaNSequence.test_02_long_replaceBase(243): Test TestCasesDnaNSequence.test_13_reverseWc(253): Test @@ -3584,7 +3640,40 @@ 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: 4.526 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.636 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[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: 0.493 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +[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: 0.006 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +TestCasesHgvsExon.test_01_coding(27): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.374 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[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: 0.014 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[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: 0.98 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel TestCasesApplyDel.test_apply_variant_01(21): Test TestCasesApplyDel.test_apply_variant_02(31): Test @@ -3599,60 +3688,9 @@ 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: 13.362 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test -TestCasesApplyMixed.test_apply_variant_06_longer(169): Test -TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test -TestCasesApplyMixed.test_apply_variant_04_longer(98): Test -TestCasesApplyMixed.test_apply_variant_09_longer(259): Test -TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test -TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test -TestCasesApplyMixed.test_apply_variant_02_longer(42): Test -TestCasesApplyMixed.test_apply_variant_07_longer(203): Test -TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test -TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test -TestCasesApplyMixed.test_apply_variant_05_longer(134): Test -TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test -TestCasesApplyMixed.test_apply_variant_03_longer(64): Test -TestCasesApplyMixed.test_apply_variant_08_longer(237): Test -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: 12.755 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -TestCasesApplySnp.test_apply_variant_01(21): Test -TestCasesApplySnp.test_apply_variant_02(31): Test -TestCasesApplySnp.test_apply_variant_04(41): Test -TestCasesApplySnp.test_apply_variant_05(59): Test -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: 4.131 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -TestCasesCodonTable.test_01(28): Test -TestCasesCodonTable.test_02(59): Test -00:03:39 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -TestCasesHgvsIntron.test_01_intron(23): Test -............................................................... -100 ............................................................ -200 ................................................................ -300 ......................................................... -400 ......................................................................................................................... -600 ......................................................................................................... -800 ....................................................... -900 .................................................................. -1000 ............................................................. -1100 .................................................................. -1200 ......................................................... -1300 ........................................................................................................... -1500 ....................................................... -1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.351 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -TestCasesIntervalVariant.test_01(36): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.281 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps +TestCasesSnps.test_01(43): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3663,9 +3701,16 @@ 700 .................................................................................................... 800 .................................................................................................... 900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.297 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -TestCasesHgvsExon.test_01_coding(27): Test +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.113 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +TestCasesDnaOverlap.test_10_overlap(332): Test +TestCasesDnaOverlap.test_07_overlap(297): Test +TestCasesDnaOverlap.test_12_overlap(356): Test +TestCasesDnaOverlap.test_09_overlap(320): Test +TestCasesDnaOverlap.test_17_overlap_rand(459): Test + +Overlap random test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3675,29 +3720,13 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.507 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence -TestCasesDnaSequence.test_02_long_replaceBase(277): Test -TestCasesDnaSequence.test_05_fastqReader(320): Test -TestCasesDnaSequence.test_06_quality_long(349): Test -TestCasesDnaSequence.test_02_long_getBases(267): Test -TestCasesDnaSequence.test_01_short_getBases(228): Test -TestCasesDnaSequence.test_01_short(209): Test -TestCasesDnaSequence.test_02_long(248): Test -TestCasesDnaSequence.test_05_quality_short(340): Test -TestCasesDnaSequence.test_02_long_getBase(257): Test -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: 8.297 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence -[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] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds -TestCasesCds.test_CdsPos(35): Test +900 ................................................................................................... +Done. +TestCasesDnaOverlap.test_15_DnaCoder_copy_1(380): Test +.........TestCasesDnaOverlap.test_11_overlap(344): Test +TestCasesDnaOverlap.test_08_overlap(308): Test +TestCasesDnaOverlap.test_18_DnaCoder_score_rand(474): Test +DnaCoder.score test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3707,26 +3736,11 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -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: 1.889 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds -[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] 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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps -TestCasesMnps.test_01(187): Test +900 ...................................................................................................Done. +TestCasesDnaOverlap.test_13_overlap(368): Test +TestCasesDnaOverlap.test_19_score_threshold_rand(493): Test + +Score (threshold) random test: .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3736,20 +3750,59 @@ 600 .................................................................................................... 700 .................................................................................................... 800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.292 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps -[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: 1.673 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar -[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: 3.578 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +900 ................................................................................................... +Done. +TestCasesDnaOverlap.test_16_DnaCoder_copy_2(438): Test +.................................................................................[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.5 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +TestCasesHgvsIntron.test_01_intron(23): Test +............................................................... +100 ............................................................ +200 ................................................................ +300 ......................................................... +400 ......................................................................................................................... +600 ......................................................................................................... +800 ....................................................... +900 .................................................................. +1000 ............................................................. +1100 .................................................................. +1200 ......................................................... +1300 ........................................................................................................... +1500 ....................................................... +1600 ............................................................... +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.302 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +TestCasesHgvsDnaDup.test_01(31): Test +TestCasesHgvsDnaDup.test_02(54): Test +TestCasesHgvsDnaDup.test_03(81): Test +TestCasesHgvsDnaDup.test_04(111): Test +TestCasesHgvsDnaDup.test_05(141): Test +TestCasesHgvsDnaDup.test_06(167): Test +TestCasesHgvsDnaDup.test_07(195): Test +TestCasesHgvsDnaDup.test_08(221): Test +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: 5.506 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +TestCasesIntervals.test_00(140): Test +TestCasesIntervals.test_01(152): Test +TestCasesIntervals.test_02(163): Test +TestCasesIntervals.test_03(175): Test +TestCasesIntervals.test_04(187): Test +TestCasesIntervals.test_05(200): Test +TestCasesIntervals.test_06(231): Test +TestCasesIntervals.test_08(392): Test +TestCasesIntervals.test_10_chrOrder(475): Test +TestCasesIntervals.test_09_chrOrder(460): Test +TestCasesIntervals.test_07_01(271): Test +TestCasesIntervals.test_07_02(292): Test +TestCasesIntervals.test_07_03(313): Test +TestCasesIntervals.test_07_04(337): Test +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: 8.862 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap TestCasesOverlap.test_binSeq_01(26): Test TestCasesOverlap.test_binSeq_02(32): Test @@ -3765,10 +3818,15 @@ TestCasesOverlap.test_binSeq_12(94): Test TestCasesOverlap.test_binSeq_13(100): Test [INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -[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] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +TestCasesIntergenic.test_01(30): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.505 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[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: 2.016 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel TestCasesStructuralDel.test02(249): Test TestCasesStructuralDel.test03(266): Test @@ -3781,49 +3839,7 @@ 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: 7.325 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -[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: 0.721 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup -TestCasesHgvsDnaDup.test_01(31): Test -TestCasesHgvsDnaDup.test_02(54): Test -TestCasesHgvsDnaDup.test_03(81): Test -TestCasesHgvsDnaDup.test_04(111): Test -TestCasesHgvsDnaDup.test_05(141): Test -TestCasesHgvsDnaDup.test_06(167): Test -TestCasesHgvsDnaDup.test_07(195): Test -TestCasesHgvsDnaDup.test_08(221): Test -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: 7.917 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.598 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.526 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels TestCasesDels.test_01(138): Test .................................................................................................... @@ -3837,94 +3853,64 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.396 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.113 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns +TestCasesIns.test_01(38): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.376 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +TestCasesApplySnp.test_apply_variant_01(21): Test +TestCasesApplySnp.test_apply_variant_02(31): Test +TestCasesApplySnp.test_apply_variant_04(41): Test +TestCasesApplySnp.test_apply_variant_05(59): Test +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: 3.527 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[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 +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel [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: 0.562 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 -TestCasesApplyIns.test_apply_variant_03(43): Test -TestCasesApplyIns.test_apply_variant_04(54): Test -TestCasesApplyIns.test_apply_variant_05(72): Test -TestCasesApplyIns.test_apply_variant_06(90): Test -TestCasesApplyIns.test_apply_variant_07(108): Test -TestCasesApplyIns.test_apply_variant_08(126): Test -TestCasesApplyIns.test_apply_variant_09(137): Test -TestCasesApplyIns.test_apply_variant_10(148): Test -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: 8.04 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular -TestCasesCircular.test_circular_01(26): Test -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 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular -[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] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -TestCasesSpliceRegion.test_01(33): Test -..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.605 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.908 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -[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: 1.314 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -[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: 2.791 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -TestCasesStructuralDup.test01_dupGene(157): Test -TestCasesStructuralDup.test02(194): Test -TestCasesStructuralDup.test03(212): Test -TestCasesStructuralDup.test04(229): Test -TestCasesStructuralDup.test05(247): Test -TestCasesStructuralDup.test06(265): Test -TestCasesStructuralDup.test07(286): Test -TestCasesStructuralDup.test08(303): Test -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: 6.974 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -[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: 0.873 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps -TestCasesSnps.test_01(43): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.486 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[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] 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: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Running 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.TestCasesDnaSequence +TestCasesDnaSequence.test_02_long_replaceBase(277): Test +TestCasesDnaSequence.test_05_fastqReader(320): Test +TestCasesDnaSequence.test_06_quality_long(349): Test +TestCasesDnaSequence.test_02_long_getBases(267): Test +TestCasesDnaSequence.test_01_short_getBases(228): Test +TestCasesDnaSequence.test_01_short(209): Test +TestCasesDnaSequence.test_02_long(248): Test +TestCasesDnaSequence.test_05_quality_short(340): Test +TestCasesDnaSequence.test_02_long_getBase(257): Test +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: 7.199 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +TestCasesSpliceSite.test_01(34): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -3936,12 +3922,44 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.439 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps -[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.61 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[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] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +TestCasesGenePvalueList.test_01(28): Test +TestCasesGenePvalueList.test_02(46): Test +TestCasesGenePvalueList.test_03(64): Test +TestCasesGenePvalueList.test_04(82): Test +TestCasesGenePvalueList.test_05(111): Test +TestCasesGenePvalueList.test_06(129): Test +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: 2.625 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +TestCasesNextProt.test_10_nextprotFactory(205): Test +TestCasesNextProt.test_09_nextprotFactory(182): Test +TestCasesNextProt.test_06_nextprotFactory(116): Test +TestCasesNextProt.test_14(304): Test +TestCasesNextProt.test_15(322): Test +TestCasesNextProt.test_16(340): Test +TestCasesNextProt.test_17(358): Test +TestCasesNextProt.test_18(376): Test +TestCasesNextProt.test_19(394): Test +TestCasesNextProt.test_03_nextprotFactory(60): Test +TestCasesNextProt.test_11_nextprotFactory(228): Test +TestCasesNextProt.test_07_nextprotFactory(136): Test +TestCasesNextProt.test_04_nextprotFactory(80): Test +TestCasesNextProt.test_01_nextprotFactory(24): Test +TestCasesNextProt.test_12_nextprotFactory(251): Test +TestCasesNextProt.test_08_nextprotFactory(159): Test +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: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer TestCasesSequenceIndexer.test_01(69): Test TestCasesSequenceIndexer.test_02(100): Test @@ -3953,41 +3971,13 @@ 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: 7.817 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -TestCasesIntervals.test_00(140): Test -TestCasesIntervals.test_01(152): Test -TestCasesIntervals.test_02(163): Test -TestCasesIntervals.test_03(175): Test -TestCasesIntervals.test_04(187): Test -TestCasesIntervals.test_05(200): Test -TestCasesIntervals.test_06(231): Test -TestCasesIntervals.test_08(392): Test -TestCasesIntervals.test_10_chrOrder(475): Test -TestCasesIntervals.test_09_chrOrder(460): Test -TestCasesIntervals.test_07_01(271): Test -TestCasesIntervals.test_07_02(292): Test -TestCasesIntervals.test_07_03(313): Test -TestCasesIntervals.test_07_04(337): Test -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: 12.529 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -TestCasesApplyMnp.test_apply_variant_01(22): Test -TestCasesApplyMnp.test_apply_variant_02(33): Test -TestCasesApplyMnp.test_apply_variant_03(44): Test -TestCasesApplyMnp.test_apply_variant_04(61): Test -TestCasesApplyMnp.test_apply_variant_05(79): Test -TestCasesApplyMnp.test_apply_variant_06(97): Test -TestCasesApplyMnp.test_apply_variant_07(115): Test -TestCasesApplyMnp.test_apply_variant_08(133): Test -TestCasesApplyMnp.test_apply_variant_09(144): Test -TestCasesApplyMnp.test_apply_variant_10(155): Test -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: 10.184 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.188 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: 0.486 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[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: 0.086 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations TestCasesStructuralTranslocations.test02_2_nonFs(532): Test TestCasesStructuralTranslocations.test01_0_nonFs(286): Test @@ -4016,24 +4006,70 @@ 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: 17.423 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -TestCasesStructuralInv.test01_invGene(214): Test -TestCasesStructuralInv.test02(249): Test -TestCasesStructuralInv.test03(266): Test -TestCasesStructuralInv.test04(283): Test -TestCasesStructuralInv.test05(300): Test -TestCasesStructuralInv.test06(317): Test -TestCasesStructuralInv.test07(334): Test -TestCasesStructuralInv.test08(352): Test -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: 6.45 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -[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: 0.919 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.345 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.747 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[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: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.51 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[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: 0.985 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar [INFO] [INFO] Results: [INFO] @@ -4042,8 +4078,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 06:50 min -[INFO] Finished at: 2026-10-14T05:21:39-12:00 +[INFO] Total time: 04:12 min +[INFO] Finished at: 2025-09-12T01:10:33+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -4067,8 +4103,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.466 s -[INFO] Finished at: 2026-10-14T05:21:42-12:00 +[INFO] Total time: 0.503 s +[INFO] Finished at: 2025-09-12T01:10:34+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 @@ -4143,7 +4179,7 @@ [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. -Oct 14, 2026 5:21:53 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Sep 12, 2025 1:10:45 AM org.debian.maven.packager.DependenciesSolver$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 @@ -4285,9 +4321,9 @@ 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-doc' in '../libsnpeff-java-doc_5.2.f+dfsg-1_all.deb'. 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-genbuildinfo --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.f+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4295,12 +4331,14 @@ 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/148367/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/148367/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/2715949 and its subdirectories -I: Current time: Wed Oct 14 05:25:20 -12 2026 -I: pbuilder-time-stamp: 1791998720 +I: removing directory /srv/workspace/pbuilder/148367 and its subdirectories +I: Current time: Fri Sep 12 01:14:05 +14 2025 +I: pbuilder-time-stamp: 1757589245