Diff of the two buildlogs: -- --- b1/build.log 2024-05-02 06:59:02.485333421 +0000 +++ b2/build.log 2024-05-02 07:13:49.023640141 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 4 01:17:23 -12 2025 -I: pbuilder-time-stamp: 1749043043 +I: Current time: Thu May 2 20:59:05 +14 2024 +I: pbuilder-time-stamp: 1714633145 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying test_scope_for_junit.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1402880/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/343715/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 2 06:59 /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/343715/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/343715/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - 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=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='7a702385c7e3413cbeef42b66529e811' - 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='1402880' - PS1='# ' - PS2='> ' + INVOCATION_ID=7c7f46992df54cf595ca035d5b6c3a3c + 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=343715 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.DuYiYMto/pbuilderrc_eBbV --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/b1 --logfile b1/build.log snpsift_5.1+dfsg2-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/pbuilderrc_8cuR --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DuYiYMto/b2 --logfile b2/build.log snpsift_5.1+dfsg2-2.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://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1402880/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/343715/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -88,7 +120,7 @@ Depends: debhelper-compat (= 13), antlr4, antlr4-doc, javahelper, junit5, libcommons-math3-java, libcommons-math3-java-doc, libhtsjdk-java, libhtsjdk-java-doc, libmaven-assembly-plugin-java, libmaven-javadoc-plugin-java, libsnpeff-java, libsnpeff-java-doc, libtrove3-java, libtrove3-java-doc, maven-debian-helper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19699 files and directories currently installed.) +(Reading database ... 19875 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -656,31 +688,32 @@ Get: 325 http://deb.debian.org/debian trixie/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 326 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 324 MB in 17s (18.6 MB/s) +Fetched 324 MB in 13s (25.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. -(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 ... 19699 files and directories currently installed.) +(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 ... 19875 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64: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 ... 19692 files and directories currently installed.) +(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 ... 19868 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: + libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). -(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 ... 19698 files and directories currently installed.) +(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 ... 19874 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64: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 ... 19685 files and directories currently installed.) +(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 ... 19861 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... 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 ... 19700 files and directories currently installed.) +(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 ... 19876 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. @@ -699,7 +732,7 @@ Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20039 files and directories currently installed.) +(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 ... 20215 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. @@ -732,7 +765,7 @@ Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. -(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 ... 21031 files and directories currently installed.) +(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 ... 21207 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. @@ -1737,8 +1770,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jun 4 13:19:37 UTC 2025. -Universal Time is now: Wed Jun 4 13:19:37 UTC 2025. +Local time is now: Thu May 2 07:02:08 UTC 2024. +Universal Time is now: Thu May 2 07:02:08 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2194,7 +2227,11 @@ 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+dfsg2-2_source.changes +I: user script /srv/workspace/pbuilder/343715/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/343715/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+dfsg2-2_source.changes dpkg-buildpackage: info: source package snpsift dpkg-buildpackage: info: source version 5.1+dfsg2-2 dpkg-buildpackage: info: source distribution unstable @@ -2221,7 +2258,7 @@ dh_autoreconf dh_auto_configure mh_patchpoms -plibsnpsift-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/snpsift-5.1\+dfsg2/debian/maven-repo -Failed to parse /build/reproducible-path/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /build/reproducible-path/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -2237,7 +2274,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) -Failed to parse /build/reproducible-path/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /build/reproducible-path/snpsift-5.1+dfsg2/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -2298,32 +2335,32 @@ [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.lang.expression... +[WARNING] Loading source files for package org.snpsift.fileIterator... +[WARNING] Loading source files for package org.snpsift... [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.lang.expression... +[WARNING] Loading source files for package org.snpsift.antlr... [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.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.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.hwe... +[WARNING] Loading source files for package org.snpsift.util... +[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.unit... +[WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Constructing Javadoc information... -[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/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/unit/TestCasesAnnotate.java:16: 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/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/TestCasesAnnotate.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/TestCasesAnnotate.java:16: 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/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist @@ -2350,24 +2387,63 @@ [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/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/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/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: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] 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] 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] ^ +[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] 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] 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] 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] 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/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/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/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/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/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/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/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/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/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -2383,15 +2459,30 @@ [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] /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/TestCasesGt.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/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/TestCasesGt.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/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] 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] 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] import static org.junit.jupiter.api.Assertions.assertEquals; +[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] ^ @@ -2401,24 +2492,12 @@ [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/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/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/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/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/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/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/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/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/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -2434,33 +2513,24 @@ [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] /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/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/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/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/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/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/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/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/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/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/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/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/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/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/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -2470,47 +2540,20 @@ [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/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/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/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/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/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/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/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/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/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/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/TestCasesSplit.java:11: 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/TestCasesZzz.java:13: 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/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; @@ -2533,138 +2576,132 @@ [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:13: 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:143: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:111: error: cannot find symbol [WARNING] @Test [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:151: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:136: error: cannot find symbol [WARNING] @Test [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:159: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:158: error: cannot find symbol [WARNING] @Test [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:167: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:177: error: cannot find symbol [WARNING] @Test [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:179: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:198: error: cannot find symbol [WARNING] @Test [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:190: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:221: error: cannot find symbol [WARNING] @Test [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:215: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:239: error: cannot find symbol [WARNING] @Test [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:230: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:254: error: cannot find symbol [WARNING] @Test [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:243: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:270: error: cannot find symbol [WARNING] @Test [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:271: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:286: error: cannot find symbol [WARNING] @Test [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:298: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:302: error: cannot find symbol [WARNING] @Test [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:318: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[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] ^ [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:338: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [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:354: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [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:370: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [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:388: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [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:413: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [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:426: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [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:437: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [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:451: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [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:477: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [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:489: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [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:507: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [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:537: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [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:566: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [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] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test @@ -2868,145 +2905,91 @@ [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/util/package-tree.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Lt.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Neq.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Mod.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Div.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Na.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Le.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Ge.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/ExpressionBinary.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldSub.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/ExpressionUnary.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Exists.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldEff.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Times.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Match.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldIterator.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldIterator.IteratorType.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Gt.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldLof.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/NotMatch.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Field.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Expression.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Minus.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldConstant.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldConstant.FieldConstantNames.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Not.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldGenotype.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Has.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Xor.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Plus.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldGenotypeSub.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Or.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/And.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Literal.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldConstantFloat.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Eq.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldNmd.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/class-use/Value.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/class-use/LangFactory.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/CountVariant.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/IsHom.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/IsVariant.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/CountHet.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/In.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/IsHet.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/CountHom.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/CountRef.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/Function.html... -[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/function/class-use/IsRef.html... -[WARNING] Generating 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/build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Div.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Ge.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldEff.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Eq.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Xor.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldLof.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Neq.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/ExpressionUnary.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldGenotypeSub.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldConstant.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/FieldConstant.FieldConstantNames.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/lang/expression/class-use/Mod.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/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... @@ -3029,9 +3012,63 @@ [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/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/SnpSiftBaseVisitor.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/gwasCatalog/class-use/GwasCatalog.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/GwasCatalogFileIterator.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/VariantCounter.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/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/util/class-use/FastaSample.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/DbMarker.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDb.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/DbVcfSorted.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/VcfIndexDataChromo.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/DbVcfTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/VcfIndexTree.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/MarkerFile.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/AnnotateVcfDbSorted.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/VcfIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/DbVcf.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/QueryResult.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/annotate/class-use/DbVcfMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/pedigree/class-use/Individual.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/pedigree/class-use/PedigreeDraw.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesDbNsfp.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotate.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesPrivate.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesVarType.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesSplit.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesExtractFields.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesDbNsfpDeleteCache.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesConcordance.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilter.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterGt.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGt.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateCreateIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesCaseControl.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterALL.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesLd.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateUseIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesVcfCheck.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterChrPos.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesIntervals.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesSort.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGeneSets.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGwasCatalog.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesHwe.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/unit/class-use/TestCasesIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/class-use/TestCasesZzz.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/apidocs/org/snpsift/testCases/class-use/TestSuiteAll.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... @@ -3088,32 +3125,32 @@ [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.snpsift.lang.expression... +[WARNING] Loading source files for package org.snpsift.fileIterator... +[WARNING] Loading source files for package org.snpsift... [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.lang.expression... +[WARNING] Loading source files for package org.snpsift.antlr... [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.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.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.hwe... +[WARNING] Loading source files for package org.snpsift.util... +[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.unit... +[WARNING] Loading source files for package org.snpsift.testCases... [WARNING] Constructing Javadoc information... -[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/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/unit/TestCasesAnnotate.java:16: 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/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/TestCasesAnnotate.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/TestCasesAnnotate.java:16: 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/TestCasesPrivate.java:3: error: package org.junit.jupiter.api does not exist @@ -3140,24 +3177,63 @@ [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/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/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/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: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] 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] 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] ^ +[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] 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] 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] 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] 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/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/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/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/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/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/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/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/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/TestCasesCaseControl.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -3173,15 +3249,30 @@ [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] /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/TestCasesGt.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/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/TestCasesGt.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/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] 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] 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] import static org.junit.jupiter.api.Assertions.assertEquals; +[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] ^ @@ -3191,24 +3282,12 @@ [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/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/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/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/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/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/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/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/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/TestCasesSort.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -3224,33 +3303,24 @@ [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] /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/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/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/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/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/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/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/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/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/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/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/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/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/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/TestCasesHwe.java:3: error: package org.junit.jupiter.api does not exist [WARNING] import org.junit.jupiter.api.Test; [WARNING] ^ @@ -3260,47 +3330,20 @@ [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/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/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/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/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/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/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/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/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/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/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/TestCasesSplit.java:11: 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/TestCasesZzz.java:13: 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/TestSuiteAll.java:3: error: package org.junit.platform.suite.api does not exist [WARNING] import org.junit.platform.suite.api.SelectPackages; @@ -3323,138 +3366,132 @@ [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:13: 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:143: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:111: error: cannot find symbol [WARNING] @Test [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:151: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:136: error: cannot find symbol [WARNING] @Test [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:159: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:158: error: cannot find symbol [WARNING] @Test [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:167: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:177: error: cannot find symbol [WARNING] @Test [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:179: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:198: error: cannot find symbol [WARNING] @Test [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:190: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:221: error: cannot find symbol [WARNING] @Test [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:215: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:239: error: cannot find symbol [WARNING] @Test [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:230: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:254: error: cannot find symbol [WARNING] @Test [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:243: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:270: error: cannot find symbol [WARNING] @Test [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:271: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:286: error: cannot find symbol [WARNING] @Test [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:298: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesDbNsfp.java:302: error: cannot find symbol [WARNING] @Test [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:318: error: cannot find symbol +[WARNING] location: class TestCasesDbNsfp +[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] ^ [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:338: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:151: error: cannot find symbol [WARNING] @Test [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:354: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:159: error: cannot find symbol [WARNING] @Test [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:370: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:167: error: cannot find symbol [WARNING] @Test [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:388: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:179: error: cannot find symbol [WARNING] @Test [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:413: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:190: error: cannot find symbol [WARNING] @Test [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:426: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:215: error: cannot find symbol [WARNING] @Test [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:437: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:230: error: cannot find symbol [WARNING] @Test [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:451: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:243: error: cannot find symbol [WARNING] @Test [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:477: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:271: error: cannot find symbol [WARNING] @Test [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:489: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:298: error: cannot find symbol [WARNING] @Test [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:507: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:318: error: cannot find symbol [WARNING] @Test [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:537: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:338: error: cannot find symbol [WARNING] @Test [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:566: error: cannot find symbol +[WARNING] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:354: error: cannot find symbol [WARNING] @Test [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] /build/reproducible-path/snpsift-5.1+dfsg2/src/main/java/org/snpsift/testCases/unit/TestCasesAnnotate.java:370: error: cannot find symbol [WARNING] @Test [WARNING] ^ [WARNING] symbol: class Test @@ -3658,143 +3695,93 @@ [WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/util/package-tree.html... 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[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/SnpSiftListener.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... @@ -3818,10 +3805,60 @@ [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/SnpSiftListener.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/gwasCatalog/class-use/GwasCatalogEntry.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/GwasCatalogFileIterator.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/hwe/class-use/VcfHwe.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/util/class-use/FastaSample.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/MarkerFile.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/QueryResult.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/annotate/class-use/DbVcfSorted.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/VcfIndexDataChromo.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/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/AnnotateVcfDbTabix.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/DbVcfTabix.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/pedigree/class-use/Individual.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesDbNsfp.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotate.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesPrivate.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesVarType.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesSplit.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesExtractFields.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesDbNsfpDeleteCache.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesConcordance.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilter.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterGt.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGt.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateCreateIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesCaseControl.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterALL.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesLd.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateUseIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesVcfCheck.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesFilterChrPos.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateTabix.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesIntervals.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesSort.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGeneSets.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesAnnotateMem.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesGwasCatalog.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesHwe.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/unit/class-use/TestCasesIndex.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/class-use/TestCasesZzz.html... +[WARNING] Generating /build/reproducible-path/snpsift-5.1+dfsg2/target/site/apidocs/org/snpsift/testCases/class-use/TestSuiteAll.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... @@ -3850,8 +3887,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 11.279 s -[INFO] Finished at: 2025-06-04T01:20:11-12:00 +[INFO] Total time: 01:48 min +[INFO] Finished at: 2024-05-02T21:06:56+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snpsift-5.1+dfsg2' @@ -3887,25 +3924,128 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.snpsift.testCases.unit.TestCasesGt -TestCasesGt.test_01(25): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 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: 0.001 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: 0.064 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: 0.018 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: 0.073 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: 0.001 s - in org.snpsift.testCases.unit.TestCasesLd -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateUseIndex +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.543 s - in org.snpsift.testCases.unit.TestCasesFilterALL +[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: 9.915 s - in org.snpsift.testCases.unit.TestCasesIndex +[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: 52.632 s - in org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache +[INFO] Running org.snpsift.testCases.unit.TestCasesExtractFields +TestCasesExtractFields.test_31_ann(291): Test +TestCasesExtractFields.test_00(71): Test +TestCasesExtractFields.test_01(98): Test +TestCasesExtractFields.test_02(104): Test +TestCasesExtractFields.test_03(110): Test +TestCasesExtractFields.test_04(116): Test +TestCasesExtractFields.test_05(122): Test +TestCasesExtractFields.test_06(128): Test +TestCasesExtractFields.test_07(134): Test +TestCasesExtractFields.test_08(140): Test +TestCasesExtractFields.test_09(146): Test +TestCasesExtractFields.test_10(152): Test +TestCasesExtractFields.test_11(158): Test +TestCasesExtractFields.test_12(164): Test +TestCasesExtractFields.test_13(170): Test +TestCasesExtractFields.test_14(176): Test +TestCasesExtractFields.test_15(182): Test +TestCasesExtractFields.test_16(188): Test +TestCasesExtractFields.test_17(194): Test +TestCasesExtractFields.test_18(200): Test +TestCasesExtractFields.test_19(206): Test +TestCasesExtractFields.test_20(212): Test +TestCasesExtractFields.test_23(218): Test +TestCasesExtractFields.test_24(224): Test +TestCasesExtractFields.test_25(230): Test +TestCasesExtractFields.test_26(236): Test +TestCasesExtractFields.test_27(242): Test +TestCasesExtractFields.test_28(253): Test +TestCasesExtractFields.test_29(262): Test +TestCasesExtractFields.test_30(273): Test +TestCasesExtractFields.test_31(282): Test +TestCasesExtractFields.test_32(300): Test +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: 0.79 s - in org.snpsift.testCases.unit.TestCasesExtractFields +[INFO] Running org.snpsift.testCases.unit.TestCasesFilter +TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test +TestCasesFilter.test_32_ann(988): Test +TestCasesFilter.test_33_ann(1049): Test +TestCasesFilter.test_34_ann(1108): Test +TestCasesFilter.test_35_ann(1167): Test +TestCasesFilter.test_01(40): Test +TestCasesFilter.test_02(64): Test +TestCasesFilter.test_03(86): Test +TestCasesFilter.test_04(110): Test +TestCasesFilter.test_05(134): Test +TestCasesFilter.test_06(158): Test +TestCasesFilter.test_07(182): Test +TestCasesFilter.test_08(208): Test +TestCasesFilter.test_09(236): Test +TestCasesFilter.test_10(258): Test +TestCasesFilter.test_11(281): Test +TestCasesFilter.test_12(303): Test +TestCasesFilter.test_13(326): Test +TestCasesFilter.test_14(348): Test +TestCasesFilter.test_15(381): Test +TestCasesFilter.test_16(407): Test +TestCasesFilter.test_17(435): Test +TestCasesFilter.test_18(459): Test +TestCasesFilter.test_19(483): Test +TestCasesFilter.test_20(507): Test +TestCasesFilter.test_21(532): Test +TestCasesFilter.test_22(559): Test +TestCasesFilter.test_23(615): Test +TestCasesFilter.test_24(642): Test +TestCasesFilter.test_25(669): Test +TestCasesFilter.test_26(697): Test +TestCasesFilter.test_27(748): Test +TestCasesFilter.test_28(846): Test +TestCasesFilter.test_29(875): Test +TestCasesFilter.test_30(903): Test +TestCasesFilter.test_31(932): Test +TestCasesFilter.test_32(960): Test +TestCasesFilter.test_33(1021): Test +TestCasesFilter.test_34(1081): Test +TestCasesFilter.test_35(1140): Test +TestCasesFilter.test_36(1198): Test +TestCasesFilter.test_37(1222): Test +TestCasesFilter.test_38(1247): Test +TestCasesFilter.test_39(1272): Test +TestCasesFilter.test_40(1295): Test +TestCasesFilter.test_41(1320): Test +TestCasesFilter.test_42(1356): Test +TestCasesFilter.test_43(1374): Test +TestCasesFilter.test_44(1392): Test +TestCasesFilter.test_45(1410): Test +TestCasesFilter.test_46(1437): Test +TestCasesFilter.test_47(1448): Test +TestCasesFilter.test_48(1459): Test +TestCasesFilter.test_49(1475): Test +TestCasesFilter.test_50(1494): Test +TestCasesFilter.test_51(1526): Test +TestCasesFilter.test_52(1560): Test +TestCasesFilter.test_53(1583): Test +TestCasesFilter.test_54(1605): Test +TestCasesFilter.test_55(1627): Test +TestCasesFilter.test_22_3(589): Test +TestCasesFilter.test_55_2(1647): Test +TestCasesFilter.test_55_3(1667): Test +TestCasesFilter.test_56_empty_vcf(1687): Test +TestCasesFilter.test_58_rmFilter_info_field(1747): Test +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: 5.722 s - in org.snpsift.testCases.unit.TestCasesFilter +[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 @@ -3948,65 +4088,7 @@ 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: 9.65 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: 0.05 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: 0.01 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 -TestCasesExtractFields.test_01(98): Test -TestCasesExtractFields.test_02(104): Test -TestCasesExtractFields.test_03(110): Test -TestCasesExtractFields.test_04(116): Test -TestCasesExtractFields.test_05(122): Test -TestCasesExtractFields.test_06(128): Test -TestCasesExtractFields.test_07(134): Test -TestCasesExtractFields.test_08(140): Test -TestCasesExtractFields.test_09(146): Test -TestCasesExtractFields.test_10(152): Test -TestCasesExtractFields.test_11(158): Test -TestCasesExtractFields.test_12(164): Test -TestCasesExtractFields.test_13(170): Test -TestCasesExtractFields.test_14(176): Test -TestCasesExtractFields.test_15(182): Test -TestCasesExtractFields.test_16(188): Test -TestCasesExtractFields.test_17(194): Test -TestCasesExtractFields.test_18(200): Test -TestCasesExtractFields.test_19(206): Test -TestCasesExtractFields.test_20(212): Test -TestCasesExtractFields.test_23(218): Test -TestCasesExtractFields.test_24(224): Test -TestCasesExtractFields.test_25(230): Test -TestCasesExtractFields.test_26(236): Test -TestCasesExtractFields.test_27(242): Test -TestCasesExtractFields.test_28(253): Test -TestCasesExtractFields.test_29(262): Test -TestCasesExtractFields.test_30(273): Test -TestCasesExtractFields.test_31(282): Test -TestCasesExtractFields.test_32(300): Test -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: 0.06 s - in org.snpsift.testCases.unit.TestCasesExtractFields +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 66.435 s - in org.snpsift.testCases.unit.TestCasesAnnotateTabix [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4050,29 +4132,26 @@ 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: 8.538 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 -TestCasesCaseControl.test_03(83): Test -TestCasesCaseControl.test_04(107): Test -TestCasesCaseControl.test_05(119): Test -TestCasesCaseControl.test_06(125): Test -TestCasesCaseControl.test_07(131): Test -TestCasesCaseControl.test_08(137): Test -TestCasesCaseControl.test_09(146): Test -TestCasesCaseControl.test_10(222): Test -TestCasesCaseControl.test_02_Str2(77): Test -TestCasesCaseControl.test_03_Str2(95): Test -TestCasesCaseControl.test_03_Str3(101): Test -TestCasesCaseControl.test_01_Str(59): Test -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: 0.25 s - in org.snpsift.testCases.unit.TestCasesCaseControl +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 44.298 s - in org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex +[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: 0.008 s - in org.snpsift.testCases.unit.TestCasesSplit +[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: 0.018 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: 0.024 s - in org.snpsift.testCases.unit.TestCasesVcfCheck +[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: 0.023 s - in org.snpsift.testCases.unit.TestCasesIntervals [INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateMem TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test TestCasesAnnotate.test_29_repeated_IDs(618): Test @@ -4116,7 +4195,24 @@ 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: 8.388 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 41.054 s - in org.snpsift.testCases.unit.TestCasesAnnotateMem +[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: 0.25 s - in org.snpsift.testCases.unit.TestCasesConcordance +[INFO] Running org.snpsift.testCases.unit.TestCasesSort +TestCasesSort.test_01(30): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.snpsift.testCases.unit.TestCasesSort [INFO] Running org.snpsift.testCases.unit.TestCasesPrivate TestCasesPrivate.test_01(48): Test TestCasesPrivate.test_02(59): Test @@ -4126,11 +4222,7 @@ 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: 0.003 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: 0.003 s - in org.snpsift.testCases.unit.TestCasesIntervals +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.snpsift.testCases.unit.TestCasesPrivate [INFO] Running org.snpsift.testCases.unit.TestCasesDbNsfp TestCasesDbNsfp.test_01(113): Test TestCasesDbNsfp.test_02(138): Test @@ -4138,89 +4230,10 @@ 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: 2.492 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: 9.09 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 -TestCasesFilter.test_33_ann(1049): Test -TestCasesFilter.test_34_ann(1108): Test -TestCasesFilter.test_35_ann(1167): Test -TestCasesFilter.test_01(40): Test -TestCasesFilter.test_02(64): Test -TestCasesFilter.test_03(86): Test -TestCasesFilter.test_04(110): Test -TestCasesFilter.test_05(134): Test -TestCasesFilter.test_06(158): Test -TestCasesFilter.test_07(182): Test -TestCasesFilter.test_08(208): Test -TestCasesFilter.test_09(236): Test -TestCasesFilter.test_10(258): Test -TestCasesFilter.test_11(281): Test -TestCasesFilter.test_12(303): Test -TestCasesFilter.test_13(326): Test -TestCasesFilter.test_14(348): Test -TestCasesFilter.test_15(381): Test -TestCasesFilter.test_16(407): Test -TestCasesFilter.test_17(435): Test -TestCasesFilter.test_18(459): Test -TestCasesFilter.test_19(483): Test -TestCasesFilter.test_20(507): Test -TestCasesFilter.test_21(532): Test -TestCasesFilter.test_22(559): Test -TestCasesFilter.test_23(615): Test -TestCasesFilter.test_24(642): Test -TestCasesFilter.test_25(669): Test -TestCasesFilter.test_26(697): Test -TestCasesFilter.test_27(748): Test -TestCasesFilter.test_28(846): Test -TestCasesFilter.test_29(875): Test -TestCasesFilter.test_30(903): Test -TestCasesFilter.test_31(932): Test -TestCasesFilter.test_32(960): Test -TestCasesFilter.test_33(1021): Test -TestCasesFilter.test_34(1081): Test -TestCasesFilter.test_35(1140): Test -TestCasesFilter.test_36(1198): Test -TestCasesFilter.test_37(1222): Test -TestCasesFilter.test_38(1247): Test -TestCasesFilter.test_39(1272): Test -TestCasesFilter.test_40(1295): Test -TestCasesFilter.test_41(1320): Test -TestCasesFilter.test_42(1356): Test -TestCasesFilter.test_43(1374): Test -TestCasesFilter.test_44(1392): Test -TestCasesFilter.test_45(1410): Test -TestCasesFilter.test_46(1437): Test -TestCasesFilter.test_47(1448): Test -TestCasesFilter.test_48(1459): Test -TestCasesFilter.test_49(1475): Test -TestCasesFilter.test_50(1494): Test -TestCasesFilter.test_51(1526): Test -TestCasesFilter.test_52(1560): Test -TestCasesFilter.test_53(1583): Test -TestCasesFilter.test_54(1605): Test -TestCasesFilter.test_55(1627): Test -TestCasesFilter.test_22_3(589): Test -TestCasesFilter.test_55_2(1647): Test -TestCasesFilter.test_55_3(1667): Test -TestCasesFilter.test_56_empty_vcf(1687): Test -TestCasesFilter.test_58_rmFilter_info_field(1747): Test -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: 1.271 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: 0.014 s - in org.snpsift.testCases.unit.TestCasesGeneSets -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotateTabix +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.872 s - in org.snpsift.testCases.unit.TestCasesDbNsfp +[INFO] Running org.snpsift.testCases.unit.TestCasesLd +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.testCases.unit.TestCasesLd +[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 @@ -4263,19 +4276,31 @@ 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: 9.657 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: 0.004 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: 1.832 s - in org.snpsift.testCases.unit.TestCasesIndex +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 34.423 s - in org.snpsift.testCases.unit.TestCasesAnnotate +[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: 0.038 s - in org.snpsift.testCases.unit.TestCasesFilterChrPos +[INFO] Running org.snpsift.testCases.unit.TestCasesCaseControl +TestCasesCaseControl.test_01(53): Test +TestCasesCaseControl.test_02(65): Test +TestCasesCaseControl.test_03(83): Test +TestCasesCaseControl.test_04(107): Test +TestCasesCaseControl.test_05(119): Test +TestCasesCaseControl.test_06(125): Test +TestCasesCaseControl.test_07(131): Test +TestCasesCaseControl.test_08(137): Test +TestCasesCaseControl.test_09(146): Test +TestCasesCaseControl.test_10(222): Test +TestCasesCaseControl.test_02_Str2(77): Test +TestCasesCaseControl.test_03_Str2(95): Test +TestCasesCaseControl.test_03_Str3(101): Test +TestCasesCaseControl.test_01_Str(59): Test +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: 0.624 s - in org.snpsift.testCases.unit.TestCasesCaseControl [INFO] Running org.snpsift.testCases.unit.TestCasesGwasCatalog TestCasesGwasCatalog.test_01(34): Test WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists @@ -4306,8 +4331,20 @@ 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: 0.46 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog -[INFO] Running org.snpsift.testCases.unit.TestCasesAnnotate +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.775 s - in org.snpsift.testCases.unit.TestCasesGwasCatalog +[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: 0.036 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: 0.307 s - in org.snpsift.testCases.unit.TestCasesGt +[INFO] Running org.snpsift.testCases.unit.TestCasesHwe +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.snpsift.testCases.unit.TestCasesHwe +[INFO] Running org.snpsift.testCases.unit.TestCasesGeneSets +TestCasesGeneSets.test_01(25): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.snpsift.testCases.unit.TestCasesGeneSets +[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 @@ -4350,7 +4387,7 @@ 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: 8.814 s - in org.snpsift.testCases.unit.TestCasesAnnotate +[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 38.311 s - in org.snpsift.testCases.unit.TestCasesAnnotateUseIndex [INFO] [INFO] Results: [INFO] @@ -4359,8 +4396,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:11 min -[INFO] Finished at: 2025-06-04T01:21:25-12:00 +[INFO] Total time: 05:34 min +[INFO] Finished at: 2024-05-02T21:12:43+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/snpsift-5.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -4384,11 +4421,11 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.436 s -[INFO] Finished at: 2025-06-04T01:21:26-12:00 +[INFO] Total time: 1.623 s +[INFO] Finished at: 2024-05-02T21:12:50+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 +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -4404,7 +4441,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -4420,7 +4457,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -4436,7 +4473,7 @@ at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -4485,11 +4522,11 @@ dh_missing dh_installdeb dh_gencontrol +dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined -dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined -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' in '../libsnpsift-java_5.1+dfsg2-2_all.deb'. @@ -4502,12 +4539,14 @@ 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/343715/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/343715/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/1402880 and its subdirectories -I: Current time: Wed Jun 4 01:22:01 -12 2025 -I: pbuilder-time-stamp: 1749043321 +I: removing directory /srv/workspace/pbuilder/343715 and its subdirectories +I: Current time: Thu May 2 21:13:48 +14 2024 +I: pbuilder-time-stamp: 1714634028