Diff of the two buildlogs: -- --- b1/build.log 2024-06-02 14:32:29.099894024 +0000 +++ b2/build.log 2024-06-02 14:37:41.246619962 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 2 02:20:10 -12 2024 -I: pbuilder-time-stamp: 1717338010 +I: Current time: Sun Jul 6 10:55:32 +14 2025 +I: pbuilder-time-stamp: 1751748932 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying test_scope_for_junit.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2879789/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/524688/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jul 5 20:55 /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/524688/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/524688/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=20 ' - DISTRIBUTION='unstable' - 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]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4fe46bac4e97446bac666061d0e040e3' - 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='2879789' - PS1='# ' - PS2='> ' + INVOCATION_ID=dcbb7119b0524a0bb08b1a40c36c7ead + 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=524688 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.MM1YxsRu/pbuilderrc_axid --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MM1YxsRu/b1 --logfile b1/build.log snpsift_5.1+dfsg2-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.MM1YxsRu/pbuilderrc_SD8f --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MM1YxsRu/b2 --logfile b2/build.log snpsift_5.1+dfsg2-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 1 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2879789/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jul 5 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/524688/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -462,7 +494,7 @@ Get: 319 http://deb.debian.org/debian unstable/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 316 MB in 16s (19.4 MB/s) +Fetched 316 MB in 20s (15.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19719 files and directories currently installed.) @@ -1510,8 +1542,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jun 2 14:24:35 UTC 2024. -Universal Time is now: Sun Jun 2 14:24:35 UTC 2024. +Local time is now: Sat Jul 5 20:57:46 UTC 2025. +Universal Time is now: Sat Jul 5 20:57:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1963,7 +1995,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpsift-5.1+dfsg2/ && 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 > ../snpsift_5.1+dfsg2-3_source.changes +I: user script /srv/workspace/pbuilder/524688/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/524688/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpsift-5.1+dfsg2/ && 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 > ../snpsift_5.1+dfsg2-3_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-3 dpkg-buildpackage: info: source distribution unstable @@ -2077,105 +2113,102 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.snpsift... -[WARNING] Loading source files for package org.snpsift.lang.function... -[WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.lang.expression... -[WARNING] Loading source files for package org.snpsift.annotate... -[WARNING] Loading source files for package org.snpsift.pedigree... -[WARNING] Loading source files for package org.snpsift.testCases... +[WARNING] Loading source files for package org.snpsift.lang... +[WARNING] Loading source files for package org.snpsift.lang.function... +[WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.testCases.unit... +[WARNING] Loading source files for package org.snpsift.testCases... +[WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.util... -[WARNING] Loading source files for package org.snpsift.antlr... +[WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... -[WARNING] Loading source files for package org.snpsift.phatsCons... +[WARNING] Loading source files for package org.snpsift.pedigree... +[WARNING] Loading source files for package org.snpsift.annotate... +[WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.caseControl... -[WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Constructing Javadoc information... -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.SelectPackages; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.Suite; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.SuiteDisplayName; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol -[WARNING] @Suite -[WARNING] ^ -[WARNING] symbol: class Suite -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol -[WARNING] @SuiteDisplayName("Unit test cases") +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] symbol: class SuiteDisplayName -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol -[WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] symbol: class SelectPackages -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.*; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; @@ -2183,146 +2216,144 @@ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.*; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol +[WARNING] @Suite [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] symbol: class Suite +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol +[WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] symbol: class SuiteDisplayName +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol +[WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) +[WARNING] ^ +[WARNING] symbol: class SelectPackages +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:143: error: cannot find symbol -[WARNING] @Test +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] symbol: class Test -[WARNING] location: class TestCasesZzz [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ @@ -2448,6 +2479,11 @@ [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:578: error: cannot find symbol +[WARNING] @Test +[WARNING] ^ +[WARNING] symbol: class Test +[WARNING] location: class TestCasesAnnotate [WARNING] Building index for all the packages and classes... 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[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseVisitor.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftListener.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftLexer.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftVisitor.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftListener.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseListener.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.LiteralIntContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionCondContext.html... @@ -2799,18 +2843,10 @@ [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionSetContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.CompilationUnitContext.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseListener.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/hwe/class-use/VcfHwe.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/hwe/class-use/SnpSiftCmdHwe.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogEntry.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalog.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/phatsCons/class-use/PhastCons.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/class-use/Summary.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/class-use/SnpSiftCmdCaseControlSummary.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/class-use/SnpSiftVisitor.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/class-use/VariantCounter.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/fileIterator/class-use/DbNsfpEntry.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/fileIterator/class-use/DbNsfp.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/class-use/SnpSiftCmdCaseControlSummary.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/caseControl/class-use/Summary.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/antlr/package-use.html... @@ -2867,105 +2903,102 @@ [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.snpsift... -[WARNING] Loading source files for package org.snpsift.lang.function... -[WARNING] Loading source files for package org.snpsift.lang... [WARNING] Loading source files for package org.snpsift.lang.expression... -[WARNING] Loading source files for package org.snpsift.annotate... -[WARNING] Loading source files for package org.snpsift.pedigree... -[WARNING] Loading source files for package org.snpsift.testCases... +[WARNING] Loading source files for package org.snpsift.lang... +[WARNING] Loading source files for package org.snpsift.lang.function... +[WARNING] Loading source files for package org.snpsift... [WARNING] Loading source files for package org.snpsift.testCases.unit... +[WARNING] Loading source files for package org.snpsift.testCases... +[WARNING] Loading source files for package org.snpsift.phatsCons... [WARNING] Loading source files for package org.snpsift.util... -[WARNING] Loading source files for package org.snpsift.antlr... +[WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Loading source files for package org.snpsift.hwe... [WARNING] Loading source files for package org.snpsift.gwasCatalog... -[WARNING] Loading source files for package org.snpsift.phatsCons... +[WARNING] Loading source files for package org.snpsift.pedigree... +[WARNING] Loading source files for package org.snpsift.annotate... +[WARNING] Loading source files for package org.snpsift.antlr... [WARNING] Loading source files for package org.snpsift.caseControl... -[WARNING] Loading source files for package org.snpsift.fileIterator... [WARNING] Constructing Javadoc information... -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.SelectPackages; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.Suite; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist -[WARNING] import org.junit.platform.suite.api.SuiteDisplayName; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol -[WARNING] @Suite -[WARNING] ^ -[WARNING] symbol: class Suite -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol -[WARNING] @SuiteDisplayName("Unit test cases") +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] symbol: class SuiteDisplayName -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol -[WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] symbol: class SelectPackages -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:16: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.*; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesPrivate.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:15: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIntervals.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; @@ -2973,146 +3006,144 @@ [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterChrPos.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:9: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGeneSets.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVarType.java:10: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:12: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertFalse; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSort.java:13: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:11: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesCaseControl.java:12: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotateTabix.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilter.java:17: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.*; -[WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterGt.java:12: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesHwe.java:7: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGwasCatalog.java:13: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:10: error: static import only from classes and interfaces +[WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; +[WARNING] ^ +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesIndex.java:15: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesFilterALL.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesLd.java:6: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesConcordance.java:9: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: package org.junit.jupiter.api does not exist [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:13: error: static import only from classes and interfaces +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesSplit.java:11: error: static import only from classes and interfaces [WARNING] import static org.junit.jupiter.api.Assertions.assertEquals; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.SelectPackages; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesExtractFields.java:14: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertNotNull; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:4: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.Suite; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:3: error: package org.junit.jupiter.api does not exist -[WARNING] import org.junit.jupiter.api.Test; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:5: error: package org.junit.platform.suite.api does not exist +[WARNING] import org.junit.platform.suite.api.SuiteDisplayName; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: package org.junit.jupiter.api does not exist -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:13: error: cannot find symbol +[WARNING] @Suite [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesGt.java:11: error: static import only from classes and interfaces -[WARNING] import static org.junit.jupiter.api.Assertions.assertTrue; +[WARNING] symbol: class Suite +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:14: error: cannot find symbol +[WARNING] @SuiteDisplayName("Unit test cases") [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesVcfCheck.java:3: error: package org.junit.jupiter.api does not exist +[WARNING] symbol: class SuiteDisplayName +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestSuiteAll.java:15: error: cannot find symbol +[WARNING] @SelectPackages({"org.snpsift.testCases.unit"}) +[WARNING] ^ +[WARNING] symbol: class SelectPackages +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ -[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:143: error: cannot find symbol -[WARNING] @Test +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/TestCasesZzz.java:13: error: package org.junit.jupiter.api does not exist +[WARNING] import static org.junit.jupiter.api.Assertions.*; [WARNING] ^ -[WARNING] symbol: class Test -[WARNING] location: class TestCasesZzz [WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:143: error: cannot find symbol [WARNING] @Test [WARNING] ^ @@ -3238,6 +3269,11 @@ [WARNING] ^ [WARNING] symbol: class Test [WARNING] location: class TestCasesAnnotate +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:578: error: cannot find symbol +[WARNING] @Test +[WARNING] ^ +[WARNING] symbol: class Test +[WARNING] location: class TestCasesAnnotate [WARNING] Building index for all the packages and classes... 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[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/util/class-use/FastaSample.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/fileIterator/class-use/DbNsfpEntry.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/fileIterator/class-use/DbNsfp.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/hwe/class-use/SnpSiftCmdHwe.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/hwe/class-use/VcfHwe.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogEntry.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalog.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/pedigree/class-use/Individual.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/pedigree/class-use/PedigreeDraw.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/DbVcfMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/VcfIndexDataChromo.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/VcfIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/VcfIndexTree.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/QueryResult.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDb.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbSorted.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/DbVcf.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/DbVcfTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/DbVcfSorted.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/MarkerFile.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/class-use/DbMarker.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseListener.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseVisitor.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftVisitor.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftLexer.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.LiteralIntContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionCondContext.html... @@ -3586,21 +3633,10 @@ [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionSetContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.ExpressionContext.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftParser.CompilationUnitContext.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftVisitor.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftListener.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftLexer.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/class-use/SnpSiftBaseListener.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/hwe/class-use/SnpSiftCmdHwe.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/hwe/class-use/VcfHwe.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalog.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/gwasCatalog/class-use/GwasCatalogEntry.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/phatsCons/class-use/PhastCons.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/caseControl/class-use/SnpSiftCmdCaseControlSummary.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/caseControl/class-use/Summary.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/caseControl/class-use/VariantCounter.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/fileIterator/class-use/DbNsfpEntry.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/fileIterator/class-use/DbNsfp.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/annotate/package-use.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/antlr/package-use.html... @@ -3629,8 +3665,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 34.213 s -[INFO] Finished at: 2024-06-02T02:27:04-12:00 +[INFO] Total time: 23.927 s +[INFO] Finished at: 2025-07-06T10:58:41+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpsift-5.1+dfsg2' @@ -3669,65 +3705,25 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.snpsift.testCases.unit.TestCasesSplit -TestCasesSplit.test_01(28): Test -TestCasesSplit.test_02(58): Test -TestCasesSplit.test_03(84): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.439 s - in org.snpsift.testCases.unit.TestCasesSplit -[INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt -TestCasesFilterGt.test_01(28): Test -TestCasesFilterGt.test_02(62): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.469 s - in org.snpsift.testCases.unit.TestCasesFilterGt +[INFO] Running org.snpsift.testCases.unit.TestCasesGt +TestCasesGt.test_01(25): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 s - in org.snpsift.testCases.unit.TestCasesGt [INFO] Running org.snpsift.testCases.unit.TestCasesFilterChrPos Annotate: ./test/filterChrPos_01.txt ./test/filterChrPos_01.vcf Annotate: ./test/filterChrPos_02.txt ./test/filterChrPos_02.vcf Annotate: ./test/filterChrPos_03.txt ./test/filterChrPos_03.vcf -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex -TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test -TestCasesAnnotate.test_29_repeated_IDs(618): Test -TestCasesAnnotate.test_01(145): Test -TestCasesAnnotate.test_02(153): Test -TestCasesAnnotate.test_03(161): Test -TestCasesAnnotate.test_04(169): Test -TestCasesAnnotate.test_05(181): Test -TestCasesAnnotate.test_06(192): Test -TestCasesAnnotate.test_07(217): Test -TestCasesAnnotate.test_08(232): Test -TestCasesAnnotate.test_09(245): Test -TestCasesAnnotate.test_11(273): Test -TestCasesAnnotate.test_12(300): Test -TestCasesAnnotate.test_13(320): Test -TestCasesAnnotate.test_14(340): Test -TestCasesAnnotate.test_15(356): Test -TestCasesAnnotate.test_16(372): Test -TestCasesAnnotate.test_17(390): Test -TestCasesAnnotate.test_18(415): Test -TestCasesAnnotate.test_19(428): Test -TestCasesAnnotate.test_20(439): Test -TestCasesAnnotate.test_21(453): Test -TestCasesAnnotate.test_22(479): Test -TestCasesAnnotate.test_24(509): Test -TestCasesAnnotate.test_25(539): Test -TestCasesAnnotate.test_35(693): Test -TestCasesAnnotate.test_36(711): Test -TestCasesAnnotate.test_38(732): Test -TestCasesAnnotate.test_39(743): Test -TestCasesAnnotate.test_40(762): Test -TestCasesAnnotate.test_41(770): Test -TestCasesAnnotate.test_42(781): Test -TestCasesAnnotate.test_43(809): Test -TestCasesAnnotate.test_44(835): Test -TestCasesAnnotate.test_45(861): Test -TestCasesAnnotate.test_33_empty_db(665): Test -TestCasesAnnotate.test_26_repeat_db_entry(568): Test -TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test -TestCasesAnnotate.test_28_exists(596): Test -TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test -TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test -TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 55.813 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos +[INFO] Running org.snpsift.testCases.unit.TestCasesFilterGt +TestCasesFilterGt.test_01(28): Test +TestCasesFilterGt.test_02(62): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.snpsift.testCases.unit.TestCasesFilterGt +[INFO] Running org.snpsift.testCases.unit.TestCasesHwe +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.snpsift.testCases.unit.TestCasesHwe +[INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 s - in org.snpsift.testCases.unit.TestCasesFilterALL +[INFO] Running org.snpsift.testCases.unit.TestCasesLd +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesLd +[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test @@ -3770,11 +3766,28 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 38.444 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem -[INFO] Running org.snpsift.testCases.unit.TestCasesLd -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.testCases.unit.TestCasesLd -[INFO] Running org.snpsift.testCases.unit.TestCasesFilterALL -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 s - in org.snpsift.testCases.unit.TestCasesFilterALL +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.028 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex +[INFO] Running org.snpsift.testCases.unit.TestCasesConcordance +TestCasesConcordance.test_01(68): Test +TestCasesConcordance.test_02(74): Test +TestCasesConcordance.test_03(80): Test +TestCasesConcordance.test_04(91): Test +TestCasesConcordance.test_05(102): Test +TestCasesConcordance.test_06(113): Test +TestCasesConcordance.test_07(125): Test +TestCasesConcordance.test_08(131): Test +TestCasesConcordance.test_09(142): Test +TestCasesConcordance.test_10(153): Test +TestCasesConcordance.test_11(164): Test +TestCasesConcordance.test_12(181): Test +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.snpsift.testCases.unit.TestCasesConcordance +[INFO] Running org.snpsift.testCases.unit.TestCasesVarType +TestCasesVarType.test_05_multiple(82): Test +TestCasesVarType.test_01_SNP(58): Test +TestCasesVarType.test_02_MNP(64): Test +TestCasesVarType.test_03_INS(70): Test +TestCasesVarType.test_04_DEL(76): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.snpsift.testCases.unit.TestCasesVarType [INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields TestCasesExtractFields.test_31_ann(291): Test TestCasesExtractFields.test_00(71): Test @@ -3811,16 +3824,8 @@ TestCasesExtractFields.test_33(312): Test TestCasesExtractFields.test_34(323): Test TestCasesExtractFields.test_35(340): Test -[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.312 s - in org.snpsift.testCases.unit.TestCasesExtractFields -[INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp -TestCasesDbNsfp.test_01(113): Test -TestCasesDbNsfp.test_02(138): Test -TestCasesDbNsfp.test_03(160): Test -TestCasesDbNsfp.test_04(179): Test -TestCasesDbNsfp.test_05(200): Test -TestCasesDbNsfp.test_06(223): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.552 s - in org.snpsift.testCases.unit.TestCasesDbNsfp -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.snpsift.testCases.unit.TestCasesExtractFields +[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test @@ -3863,62 +3868,10 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 36.29 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix -[INFO] Running org.snpsift.testCases.unit.TestCasesConcordance -TestCasesConcordance.test_01(68): Test -TestCasesConcordance.test_02(74): Test -TestCasesConcordance.test_03(80): Test -TestCasesConcordance.test_04(91): Test -TestCasesConcordance.test_05(102): Test -TestCasesConcordance.test_06(113): Test -TestCasesConcordance.test_07(125): Test -TestCasesConcordance.test_08(131): Test -TestCasesConcordance.test_09(142): Test -TestCasesConcordance.test_10(153): Test -TestCasesConcordance.test_11(164): Test -TestCasesConcordance.test_12(181): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 s - in org.snpsift.testCases.unit.TestCasesConcordance -[INFO] Running org.snpsift.testCases.unit.TestCasesVarType -TestCasesVarType.test_05_multiple(82): Test -TestCasesVarType.test_01_SNP(58): Test -TestCasesVarType.test_02_MNP(64): Test -TestCasesVarType.test_03_INS(70): Test -TestCasesVarType.test_04_DEL(76): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.snpsift.testCases.unit.TestCasesVarType -[INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck -TestCasesVcfCheck.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.snpsift.testCases.unit.TestCasesVcfCheck -[INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog -TestCasesGwasCatalog.test_01(34): Test -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs8109288' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:46172277' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11671664' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '11:116648916' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs964184' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '6:161010117' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs10455872' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '1:67705957' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11209026' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:45412078' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs7412' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '2:169763147' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs560887' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists -WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. -TestCasesGwasCatalog.test_02(50): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.627 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.747 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex +[INFO] Running org.snpsift.testCases.unit.TestCasesSort +TestCasesSort.test_01(30): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl TestCasesCaseControl.test_01(53): Test TestCasesCaseControl.test_02(65): Test @@ -3937,31 +3890,8 @@ TestCasesCaseControl.test_02_Str(71): Test TestCasesCaseControl.test_03_Str(89): Test TestCasesCaseControl.test_04_Str(113): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.772 s - in org.snpsift.testCases.unit.TestCasesCaseControl -[INFO] Running org.snpsift.testCases.unit.TestCasesGt -TestCasesGt.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 s - in org.snpsift.testCases.unit.TestCasesGt -[INFO] Running org.snpsift.testCases.unit.TestCasesPrivate -TestCasesPrivate.test_01(48): Test -TestCasesPrivate.test_02(59): Test -TestCasesPrivate.test_03(70): Test -TestCasesPrivate.test_04(81): Test -TestCasesPrivate.test_05(89): Test -TestCasesPrivate.test_06(95): Test -TestCasesPrivate.test_07(101): Test -TestCasesPrivate.test_08(107): Test -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpsift.testCases.unit.TestCasesPrivate -[INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache -TestCasesDbNsfp.test_01(113): Test -TestCasesDbNsfp.test_02(138): Test -TestCasesDbNsfp.test_03(160): Test -TestCasesDbNsfp.test_04(179): Test -TestCasesDbNsfp.test_05(200): Test -TestCasesDbNsfp.test_06(223): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.958 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache -[INFO] Running org.snpsift.testCases.unit.TestCasesHwe -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpsift.testCases.unit.TestCasesHwe -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.282 s - in org.snpsift.testCases.unit.TestCasesCaseControl +[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test TestCasesAnnotate.test_01(145): Test @@ -4004,65 +3934,37 @@ TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.204 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.574 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem +[INFO] Running org.snpsift.testCases.unit.TestCasesPrivate +TestCasesPrivate.test_01(48): Test +TestCasesPrivate.test_02(59): Test +TestCasesPrivate.test_03(70): Test +TestCasesPrivate.test_04(81): Test +TestCasesPrivate.test_05(89): Test +TestCasesPrivate.test_06(95): Test +TestCasesPrivate.test_07(101): Test +TestCasesPrivate.test_08(107): Test +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesIntervals TestCasesIntervals.test_01(25): Test TestCasesIntervals.test_02(50): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesIntervals -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate -TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test -TestCasesAnnotate.test_29_repeated_IDs(618): Test -TestCasesAnnotate.test_01(145): Test -TestCasesAnnotate.test_02(153): Test -TestCasesAnnotate.test_03(161): Test -TestCasesAnnotate.test_04(169): Test -TestCasesAnnotate.test_05(181): Test -TestCasesAnnotate.test_06(192): Test -TestCasesAnnotate.test_07(217): Test -TestCasesAnnotate.test_08(232): Test -TestCasesAnnotate.test_09(245): Test -TestCasesAnnotate.test_11(273): Test -TestCasesAnnotate.test_12(300): Test -TestCasesAnnotate.test_13(320): Test -TestCasesAnnotate.test_14(340): Test -TestCasesAnnotate.test_15(356): Test -TestCasesAnnotate.test_16(372): Test -TestCasesAnnotate.test_17(390): Test -TestCasesAnnotate.test_18(415): Test -TestCasesAnnotate.test_19(428): Test -TestCasesAnnotate.test_20(439): Test -TestCasesAnnotate.test_21(453): Test -TestCasesAnnotate.test_22(479): Test -TestCasesAnnotate.test_24(509): Test -TestCasesAnnotate.test_25(539): Test -TestCasesAnnotate.test_35(693): Test -TestCasesAnnotate.test_36(711): Test -TestCasesAnnotate.test_38(732): Test -TestCasesAnnotate.test_39(743): Test -TestCasesAnnotate.test_40(762): Test -TestCasesAnnotate.test_41(770): Test -TestCasesAnnotate.test_42(781): Test -TestCasesAnnotate.test_43(809): Test -TestCasesAnnotate.test_44(835): Test -TestCasesAnnotate.test_45(861): Test -TestCasesAnnotate.test_33_empty_db(665): Test -TestCasesAnnotate.test_26_repeat_db_entry(568): Test -TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test -TestCasesAnnotate.test_28_exists(596): Test -TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test -TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test -TestCasesAnnotate.test_27_repeat_db_entry(580): Test -[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.805 s - in org.snpsift.testCases.unit.TestCasesAnnotate -[INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets -TestCasesGeneSets.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.snpsift.testCases.unit.TestCasesGeneSets -[INFO] Running org.snpsift.testCases.unit.TestCasesIndex -TestCasesIndex.test_01(32): Test -TestCasesIndex.test_02(84): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.528 s - in org.snpsift.testCases.unit.TestCasesIndex -[INFO] Running org.snpsift.testCases.unit.TestCasesSort -TestCasesSort.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesSort +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesIntervals +[INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp +TestCasesDbNsfp.test_01(113): Test +TestCasesDbNsfp.test_02(138): Test +TestCasesDbNsfp.test_03(160): Test +TestCasesDbNsfp.test_04(179): Test +TestCasesDbNsfp.test_05(200): Test +TestCasesDbNsfp.test_06(223): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.679 s - in org.snpsift.testCases.unit.TestCasesDbNsfp +[INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache +TestCasesDbNsfp.test_01(113): Test +TestCasesDbNsfp.test_02(138): Test +TestCasesDbNsfp.test_03(160): Test +TestCasesDbNsfp.test_04(179): Test +TestCasesDbNsfp.test_05(200): Test +TestCasesDbNsfp.test_06(223): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.079 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache [INFO] Running org.snpsift.testCases.unit.TestCasesFilter TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test TestCasesFilter.test_32_ann(988): Test @@ -4132,7 +4034,141 @@ TestCasesFilter.test_27_ann2(812): Test TestCasesFilter.test_26_ann(721): Test TestCasesFilter.test_27_ann(778): Test -[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.475 s - in org.snpsift.testCases.unit.TestCasesFilter +[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.003 s - in org.snpsift.testCases.unit.TestCasesFilter +[INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets +TestCasesGeneSets.test_01(25): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.snpsift.testCases.unit.TestCasesGeneSets +[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix +TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test +TestCasesAnnotate.test_29_repeated_IDs(618): Test +TestCasesAnnotate.test_01(145): Test +TestCasesAnnotate.test_02(153): Test +TestCasesAnnotate.test_03(161): Test +TestCasesAnnotate.test_04(169): Test +TestCasesAnnotate.test_05(181): Test +TestCasesAnnotate.test_06(192): Test +TestCasesAnnotate.test_07(217): Test +TestCasesAnnotate.test_08(232): Test +TestCasesAnnotate.test_09(245): Test +TestCasesAnnotate.test_11(273): Test +TestCasesAnnotate.test_12(300): Test +TestCasesAnnotate.test_13(320): Test +TestCasesAnnotate.test_14(340): Test +TestCasesAnnotate.test_15(356): Test +TestCasesAnnotate.test_16(372): Test +TestCasesAnnotate.test_17(390): Test +TestCasesAnnotate.test_18(415): Test +TestCasesAnnotate.test_19(428): Test +TestCasesAnnotate.test_20(439): Test +TestCasesAnnotate.test_21(453): Test +TestCasesAnnotate.test_22(479): Test +TestCasesAnnotate.test_24(509): Test +TestCasesAnnotate.test_25(539): Test +TestCasesAnnotate.test_35(693): Test +TestCasesAnnotate.test_36(711): Test +TestCasesAnnotate.test_38(732): Test +TestCasesAnnotate.test_39(743): Test +TestCasesAnnotate.test_40(762): Test +TestCasesAnnotate.test_41(770): Test +TestCasesAnnotate.test_42(781): Test +TestCasesAnnotate.test_43(809): Test +TestCasesAnnotate.test_44(835): Test +TestCasesAnnotate.test_45(861): Test +TestCasesAnnotate.test_33_empty_db(665): Test +TestCasesAnnotate.test_26_repeat_db_entry(568): Test +TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test +TestCasesAnnotate.test_28_exists(596): Test +TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test +TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test +TestCasesAnnotate.test_27_repeat_db_entry(580): Test +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.695 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix +[INFO] Running org.snpsift.testCases.unit.TestCasesVcfCheck +TestCasesVcfCheck.test_01(18): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpsift.testCases.unit.TestCasesVcfCheck +[INFO] Running org.snpsift.testCases.unit.TestCasesSplit +TestCasesSplit.test_01(28): Test +TestCasesSplit.test_02(58): Test +TestCasesSplit.test_03(84): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesSplit +[INFO] Running org.snpsift.testCases.unit.TestCasesIndex +TestCasesIndex.test_01(32): Test +TestCasesIndex.test_02(84): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.692 s - in org.snpsift.testCases.unit.TestCasesIndex +[INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog +TestCasesGwasCatalog.test_01(34): Test +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs8109288' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:46172277' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11671664' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '11:116648916' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs964184' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '6:161010117' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs10455872' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '1:67705957' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs11209026' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:45412078' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs7412' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '2:169763147' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry RS number 'rs560887' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists +WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown. +TestCasesGwasCatalog.test_02(50): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.61 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog +[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate +TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test +TestCasesAnnotate.test_29_repeated_IDs(618): Test +TestCasesAnnotate.test_01(145): Test +TestCasesAnnotate.test_02(153): Test +TestCasesAnnotate.test_03(161): Test +TestCasesAnnotate.test_04(169): Test +TestCasesAnnotate.test_05(181): Test +TestCasesAnnotate.test_06(192): Test +TestCasesAnnotate.test_07(217): Test +TestCasesAnnotate.test_08(232): Test +TestCasesAnnotate.test_09(245): Test +TestCasesAnnotate.test_11(273): Test +TestCasesAnnotate.test_12(300): Test +TestCasesAnnotate.test_13(320): Test +TestCasesAnnotate.test_14(340): Test +TestCasesAnnotate.test_15(356): Test +TestCasesAnnotate.test_16(372): Test +TestCasesAnnotate.test_17(390): Test +TestCasesAnnotate.test_18(415): Test +TestCasesAnnotate.test_19(428): Test +TestCasesAnnotate.test_20(439): Test +TestCasesAnnotate.test_21(453): Test +TestCasesAnnotate.test_22(479): Test +TestCasesAnnotate.test_24(509): Test +TestCasesAnnotate.test_25(539): Test +TestCasesAnnotate.test_35(693): Test +TestCasesAnnotate.test_36(711): Test +TestCasesAnnotate.test_38(732): Test +TestCasesAnnotate.test_39(743): Test +TestCasesAnnotate.test_40(762): Test +TestCasesAnnotate.test_41(770): Test +TestCasesAnnotate.test_42(781): Test +TestCasesAnnotate.test_43(809): Test +TestCasesAnnotate.test_44(835): Test +TestCasesAnnotate.test_45(861): Test +TestCasesAnnotate.test_33_empty_db(665): Test +TestCasesAnnotate.test_26_repeat_db_entry(568): Test +TestCasesAnnotate.test_32_annotate_minimal_representation_input(654): Test +TestCasesAnnotate.test_28_exists(596): Test +TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test +TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test +TestCasesAnnotate.test_27_repeat_db_entry(580): Test +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.471 s - in org.snpsift.testCases.unit.TestCasesAnnotate [INFO] [INFO] Results: [INFO] @@ -4141,8 +4177,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 04:09 min -[INFO] Finished at: 2024-06-02T02:31:18-12:00 +[INFO] Total time: 01:21 min +[INFO] Finished at: 2025-07-06T11:00:04+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/snpsift-5.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -4166,8 +4202,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 2.599 s -[INFO] Finished at: 2024-06-02T02:31:28-12:00 +[INFO] Total time: 0.399 s +[INFO] Finished at: 2025-07-06T11:00:06+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/reproducible-path/snpsift-5.1\+dfsg2 --non-explore Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom @@ -4274,9 +4310,9 @@ dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-3_all.deb'. dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.1+dfsg2-3_all.deb'. dpkg-deb: building package 'snpsift' in '../snpsift_5.1+dfsg2-3_all.deb'. +dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.1+dfsg2-3_all.deb'. dpkg-genbuildinfo --build=binary -O../snpsift_5.1+dfsg2-3_amd64.buildinfo dpkg-genchanges --build=binary -O../snpsift_5.1+dfsg2-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4284,12 +4320,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/524688/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/524688/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/2879789 and its subdirectories -I: Current time: Sun Jun 2 02:32:28 -12 2024 -I: pbuilder-time-stamp: 1717338748 +I: removing directory /srv/workspace/pbuilder/524688 and its subdirectories +I: Current time: Sun Jul 6 11:00:40 +14 2025 +I: pbuilder-time-stamp: 1751749240