Diff of the two buildlogs: -- --- b1/build.log 2023-04-19 07:16:05.104156980 +0000 +++ b2/build.log 2023-04-19 07:34:57.241958627 +0000 @@ -1,6 +1,7 @@ +W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 18 19:05:35 -12 2023 -I: pbuilder-time-stamp: 1681887935 +I: Current time: Wed May 22 03:40:24 +14 2024 +I: pbuilder-time-stamp: 1716298824 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +17,7 @@ I: copying [./biojava4-live_4.2.12+dfsg.orig.tar.xz] I: copying [./biojava4-live_4.2.12+dfsg-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Dec 11 09:26:50 2022 -12 +gpgv: Signature made Mon Dec 12 11:26:50 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava4-live_4.2.12+dfsg-8.dsc: no acceptable signature found @@ -35,52 +36,84 @@ dpkg-source: info: applying fix_ambiguous_method_call.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/5065/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/31310/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 22 03:40 /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/31310/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/31310/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='5065' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=31310 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.x9DDLNv2/pbuilderrc_1xgZ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.x9DDLNv2/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-8.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.x9DDLNv2/pbuilderrc_frRH --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.x9DDLNv2/b2 --logfile b2/build.log --extrapackages usrmerge biojava4-live_4.2.12+dfsg-8.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 16 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/5065/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 19 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/31310/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -410,7 +443,7 @@ Get: 236 http://deb.debian.org/debian bookworm/main arm64 libnetx-java all 0.5-4 [138 kB] Get: 237 http://deb.debian.org/debian bookworm/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 238 http://deb.debian.org/debian bookworm/main arm64 libxmlunit-java all 1.6-2 [100 kB] -Fetched 363 MB in 38s (9504 kB/s) +Fetched 363 MB in 53s (6871 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -1557,8 +1590,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/31310/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/31310/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-8_source.changes dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -1570,8 +1612,8 @@ dh clean --with javahelper jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan +dpkg: waarschuwing: --compare-versions werd gebruikt met verouderde relatieoperator '>' dh_clean rm -rf build rm -rf dist @@ -1584,15 +1626,15 @@ rm -rf buildtest find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan +dpkg: waarschuwing: --compare-versions werd gebruikt met verouderde relatieoperator '>' dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml @@ -1610,11 +1652,11 @@ sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan +dpkg: waarschuwing: --compare-versions werd gebruikt met verouderde relatieoperator '>' find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ @@ -1636,13 +1678,17 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 16 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds + [javac] Warning: org/forester/application/msa_compactor.java modified in the future. + [javac] Warning: org/forester/archaeopteryx/PdfExporter.java modified in the future. + [javac] Warning: org/forester/msa_compactor/Chart.java modified in the future. + [javac] Warning: org/forester/test/Test.java modified in the future. [javac] Compiling 359 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-forester/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. @@ -1654,7 +1700,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 33 seconds +Total time: 1 minute 38 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1672,7 +1718,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 44 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1686,7 +1732,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 16 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1702,7 +1748,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 10 seconds +Total time: 23 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1720,7 +1766,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 16 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1736,7 +1782,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 11 seconds +Total time: 19 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1751,13 +1797,14 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 13 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml compile: [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds + [javac] Warning: org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java modified in the future. [javac] Compiling 483 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. @@ -1771,7 +1818,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 45 seconds +Total time: 573504 minutes 9 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1791,7 +1838,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 16 seconds +Total time: 27 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1807,7 +1854,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 14 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1825,7 +1872,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 13 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1841,7 +1888,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 11 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1855,7 +1902,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 3 seconds +Total time: 7 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1869,7 +1916,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 10 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1883,7 +1930,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 17 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -4209,12 +4256,12 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 58 seconds +Total time: 1 minute 36 seconds # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan +dpkg: waarschuwing: --compare-versions werd gebruikt met verouderde relatieoperator '>' echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -4245,198 +4292,198 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.139 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.139 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.491 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.491 sec [junit] - [junit] Testcase: testGetIndexOf took 0.06 sec + [junit] Testcase: testGetIndexOf took 0.205 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.002 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.006 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetNumGaps took 0.002 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.005 sec + [junit] Testcase: testGetNumGaps took 0.009 sec [junit] Testcase: testGetStart took 0.001 sec - [junit] Testcase: testGetSequenceIndexAt took 0.001 sec - [junit] Testcase: testGetAccession took 0 sec - [junit] Testcase: testToString took 0.003 sec + [junit] Testcase: testGetSequenceIndexAt took 0.004 sec + [junit] Testcase: testGetAccession took 0.001 sec + [junit] Testcase: testToString took 0.012 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec - [junit] Testcase: testCountCompounds took 0.001 sec + [junit] Testcase: testCountCompounds took 0.002 sec [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.005 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.017 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.004 sec + [junit] Testcase: testGetAsList took 0.046 sec [junit] Testcase: testGetOriginalSequence took 0.001 sec [junit] Testcase: testGetCompoundAt took 0.001 sec - [junit] Testcase: testGetLength took 0.001 sec - [junit] Testcase: testIsCircular took 0.001 sec + [junit] Testcase: testGetLength took 0 sec + [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetEnd took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec - [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec - [junit] Testcase: testGetOverlapCount took 0 sec + [junit] Testcase: testSimpleAlignedSequenceShort took 0.005 sec + [junit] Testcase: testGetOverlapCount took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetLocationInAlignment took 0.002 sec - [junit] Testcase: testIterator took 0.001 sec - [junit] Testcase: testGetSequenceAsString took 0.001 sec + [junit] Testcase: testGetLocationInAlignment took 0.006 sec + [junit] Testcase: testIterator took 0.005 sec + [junit] Testcase: testGetSequenceAsString took 0.004 sec [junit] Testcase: testGetLastIndexOf took 0 sec - [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.003 sec + [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.008 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.272 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.272 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.616 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.616 sec [junit] - [junit] Testcase: testGetIndexOf took 0.106 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.003 sec + [junit] Testcase: testGetIndexOf took 0.258 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.009 sec [junit] Testcase: testGetAlignedSequenceInt took 0.004 sec - [junit] Testcase: testToStringInt took 0.022 sec + [junit] Testcase: testToStringInt took 0.035 sec [junit] Testcase: testToString took 0.002 sec - [junit] Testcase: testToStringFormatted took 0.041 sec - [junit] Testcase: testSimpleProfile took 0.001 sec + [junit] Testcase: testToStringFormatted took 0.069 sec + [junit] Testcase: testSimpleProfile took 0.004 sec [junit] Testcase: testGetSize took 0.001 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec - [junit] Testcase: testGetAlignedSequences took 0.001 sec + [junit] Testcase: testGetAlignedSequences took 0.002 sec [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.001 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.002 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec [junit] Testcase: testGetIndicesAt took 0.004 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.005 sec - [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.006 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.016 sec + [junit] Testcase: testGetCompoundAtIntInt took 0.004 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetLength took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec - [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetLength took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.004 sec + [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.002 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetCompoundSet took 0.001 sec - [junit] Testcase: testGetCompoundsAt took 0.001 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundSet took 0 sec + [junit] Testcase: testGetCompoundsAt took 0 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.005 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.391 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.391 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.099 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.24 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.005 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.009 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetNumIdenticals took 0.001 sec + [junit] Testcase: testGetNumIdenticals took 0.005 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetCompoundInTargetAt took 0 sec - [junit] Testcase: testGetIndexInQueryAt took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.008 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.023 sec + [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec + [junit] Testcase: testGetIndexInQueryAt took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.002 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.29 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.29 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.116 sec - [junit] Testcase: testHashCode took 0.001 sec + [junit] Testcase: testGetAlignment took 0.226 sec + [junit] Testcase: testHashCode took 0.013 sec [junit] Testcase: testEquals took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.299 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.299 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.702 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.702 sec [junit] ------------- Standard Error ----------------- - [junit] Apr 18, 2023 7:12:21 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:49 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 18, 2023 7:12:21 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:49 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 0 sec [junit] SKIPPED: Attemps to use the network - [junit] Testcase: testConstructorWithFactoryGuess took 0.272 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.598 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastTabularParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.612 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.612 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.035 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.035 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- - [junit] Apr 18, 2023 7:12:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:51 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 18, 2023 7:12:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:51 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results - [junit] Apr 18, 2023 7:12:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:51 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 18, 2023 7:12:23 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 22, 2024 3:52:51 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testCreateObjects took 2.587 sec + [junit] Testcase: testCreateObjects took 3.987 sec [junit] Testcase: testGetFileExtensions took 0.001 sec - [junit] Testcase: testSetFile took 0 sec + [junit] Testcase: testSetFile took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastXMLParserTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.076 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.076 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.231 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.231 sec [junit] ------------- Standard Output --------------- [junit] getFileExtensions [junit] setFile @@ -4444,120 +4491,120 @@ [junit] [junit] Testcase: testCreateObjects took 0 sec [junit] SKIPPED: Attempts to use the network - [junit] Testcase: testStoreObjects took 0.006 sec + [junit] Testcase: testStoreObjects took 0.032 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED - [junit] Testcase: testGetFileExtensions took 0.037 sec + [junit] Testcase: testGetFileExtensions took 0.131 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED [junit] Testcase: testSetFile took 0 sec [junit] Running org.biojava.nbio.core.sequence.DNATest [junit] Testsuite: org.biojava.nbio.core.sequence.DNATest - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.346 sec - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.346 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.762 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.762 sec [junit] - [junit] Testcase: sequenceEquality took 0.078 sec - [junit] Testcase: subSequence took 0.015 sec - [junit] Testcase: singleCompoundSequence took 0.012 sec - [junit] Testcase: translateToRna took 0.101 sec - [junit] Testcase: kmerNonOverlap took 0.015 sec - [junit] Testcase: twoBit took 0.011 sec - [junit] Testcase: composition took 0.009 sec - [junit] Testcase: fourBit took 0.014 sec - [junit] Testcase: complement took 0.007 sec - [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.005 sec + [junit] Testcase: sequenceEquality took 0.164 sec + [junit] Testcase: subSequence took 0.025 sec + [junit] Testcase: singleCompoundSequence took 0.023 sec + [junit] Testcase: translateToRna took 0.313 sec + [junit] Testcase: kmerNonOverlap took 0.019 sec + [junit] Testcase: twoBit took 0.016 sec + [junit] Testcase: composition took 0.013 sec + [junit] Testcase: fourBit took 0.027 sec + [junit] Testcase: complement took 0.009 sec + [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.013 sec [junit] Testcase: at took 0.005 sec - [junit] Testcase: gc took 0.005 sec + [junit] Testcase: gc took 0.013 sec [junit] Testcase: basesEqual took 0.004 sec [junit] Testcase: bogusSequence took 0.004 sec - [junit] Testcase: kmerOverlap took 0.004 sec - [junit] Testcase: reverseComplement took 0.007 sec - [junit] Testcase: reverse took 0.004 sec - [junit] Testcase: respectCase took 0.004 sec + [junit] Testcase: kmerOverlap took 0.013 sec + [junit] Testcase: reverseComplement took 0.013 sec + [junit] Testcase: reverse took 0.005 sec + [junit] Testcase: respectCase took 0.013 sec [junit] Testcase: basesEquivalent took 0.005 sec - [junit] Testcase: badTwoBit took 0.004 sec + [junit] Testcase: badTwoBit took 0.009 sec [junit] Running org.biojava.nbio.core.sequence.EditSequenceTest [junit] Testsuite: org.biojava.nbio.core.sequence.EditSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec [junit] - [junit] Testcase: badSubstitute took 0.063 sec - [junit] Testcase: delete took 0.009 sec + [junit] Testcase: badSubstitute took 0.194 sec + [junit] Testcase: delete took 0.01 sec [junit] Testcase: insert took 0.002 sec [junit] Testcase: substitute took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.JoiningSequenceReaderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 sec [junit] - [junit] Testcase: empty took 0.064 sec - [junit] Testcase: canScan took 0.002 sec + [junit] Testcase: empty took 0.168 sec + [junit] Testcase: canScan took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [junit] Testsuite: org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 sec [junit] - [junit] Testcase: testGetCompoundsAt took 0.066 sec + [junit] Testcase: testGetCompoundsAt took 0.26 sec [junit] Running org.biojava.nbio.core.sequence.SequenceViewTest [junit] Testsuite: org.biojava.nbio.core.sequence.SequenceViewTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 sec [junit] - [junit] Testcase: testLastIndexOf took 0.066 sec + [junit] Testcase: testLastIndexOf took 0.18 sec [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testInverse took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.TranslationTest [junit] Testsuite: org.biojava.nbio.core.sequence.TranslationTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.975 sec - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.975 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.76 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.76 sec [junit] - [junit] Testcase: translateN took 0.103 sec - [junit] Testcase: basicTranslation took 0.005 sec - [junit] Testcase: translateBrca2 took 0.69 sec - [junit] Testcase: translateStopAtInternalStops took 0.007 sec - [junit] Testcase: getUniversal took 0.001 sec - [junit] Testcase: translateInternalStops took 0.007 sec - [junit] Testcase: multiFrameTranslation took 0.012 sec - [junit] Testcase: waitForStartCodon took 0.002 sec - [junit] Testcase: translateInitMet took 0.001 sec + [junit] Testcase: translateN took 0.214 sec + [junit] Testcase: basicTranslation took 0.007 sec + [junit] Testcase: translateBrca2 took 1.041 sec + [junit] Testcase: translateStopAtInternalStops took 0.008 sec + [junit] Testcase: getUniversal took 0.009 sec + [junit] Testcase: translateInternalStops took 0.017 sec + [junit] Testcase: multiFrameTranslation took 0.023 sec + [junit] Testcase: waitForStartCodon took 0.011 sec + [junit] Testcase: translateInitMet took 0.002 sec [junit] Testcase: lowerCases took 0.001 sec [junit] Testcase: testHashCollision took 0.002 sec [junit] Testcase: translateBrca2ExonOne took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Testsuite: org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 sec [junit] - [junit] Testcase: testAmbiguity took 0.054 sec - [junit] Testcase: testBasicAmbiguity took 0 sec + [junit] Testcase: testAmbiguity took 0.105 sec + [junit] Testcase: testBasicAmbiguity took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] - [junit] Testcase: testConstructor took 0.058 sec + [junit] Testcase: testConstructor took 0.113 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaReaderTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.443 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.443 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.FastaReaderTest - process [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testSmallFasta2 took 0.043 sec - [junit] Testcase: testProcess took 0.14 sec - [junit] Testcase: testSmallFasta took 0.002 sec + [junit] Testcase: testSmallFasta2 took 0.051 sec + [junit] Testcase: testProcess took 0.357 sec + [junit] Testcase: testSmallFasta took 0.003 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaWriterTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec [junit] - [junit] Testcase: writeBasicFasta took 0.076 sec + [junit] Testcase: writeBasicFasta took 0.262 sec [junit] Testcase: writeFastaEqualToLineLength took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankCookbookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.29 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.29 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.629 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.629 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - DNA Sequence: AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS @@ -4565,11 +4612,11 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testProcess took 0.242 sec + [junit] Testcase: testProcess took 0.512 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankReaderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.848 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.848 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process protein [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process DNA @@ -4577,57 +4624,57 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - protein sequences: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testProcess took 0.181 sec - [junit] Testcase: CDStest took 0.027 sec + [junit] Testcase: testProcess took 0.73 sec + [junit] Testcase: CDStest took 0.044 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankWriterTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.563 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.563 sec [junit] - [junit] Testcase: testProcess took 0.306 sec + [junit] Testcase: testProcess took 0.536 sec [junit] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - parseHeader [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testParseHeader took 0.032 sec + [junit] Testcase: testParseHeader took 0.074 sec [junit] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] - [junit] Testcase: testProteinSequenceFactoring[0] took 0.006 sec - [junit] Testcase: testFeatures[0] took 0 sec + [junit] Testcase: testProteinSequenceFactoring[0] took 0.017 sec + [junit] Testcase: testFeatures[0] took 0.001 sec [junit] Testcase: testProteinSequenceFactoring[1] took 0.001 sec [junit] Testcase: testFeatures[1] took 0 sec [junit] Testcase: testProteinSequenceFactoring[2] took 0 sec [junit] Testcase: testFeatures[2] took 0 sec - [junit] Testcase: testProteinSequenceFactoring[3] took 0.001 sec + [junit] Testcase: testProteinSequenceFactoring[3] took 0 sec [junit] Testcase: testFeatures[3] took 0.001 sec - [junit] Testcase: testProteinSequenceFactoring[4] took 0 sec - [junit] Testcase: testFeatures[4] took 0 sec - [junit] Testcase: testProteinSequenceFactoring[5] took 0 sec - [junit] Testcase: testFeatures[5] took 0 sec - [junit] Testcase: testProteinSequenceFactoring[6] took 0 sec - [junit] Testcase: testFeatures[6] took 0.001 sec - [junit] Testcase: testProteinSequenceFactoring[7] took 0.001 sec - [junit] Testcase: testFeatures[7] took 0.007 sec + [junit] Testcase: testProteinSequenceFactoring[4] took 0.001 sec + [junit] Testcase: testFeatures[4] took 0.002 sec + [junit] Testcase: testProteinSequenceFactoring[5] took 0.001 sec + [junit] Testcase: testFeatures[5] took 0.001 sec + [junit] Testcase: testProteinSequenceFactoring[6] took 0.001 sec + [junit] Testcase: testFeatures[6] took 0 sec + [junit] Testcase: testProteinSequenceFactoring[7] took 0 sec + [junit] Testcase: testFeatures[7] took 0.008 sec [junit] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.769 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.769 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.571 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.571 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - test wrong sequence [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testWrongSequence took 0.749 sec + [junit] Testcase: testWrongSequence took 1.519 sec [junit] Running org.biojava.nbio.core.sequence.location.InsdcParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.InsdcParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - test accession [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(CP001663.1:6463934..6465826) @@ -4635,12 +4682,12 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(NC_000932.1:69611..69724) [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: extractAccessionTest[0] took 0.064 sec + [junit] Testcase: extractAccessionTest[0] took 0.136 sec [junit] Testcase: extractAccessionTest[1] took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.location.LocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.068 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.068 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.078 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.078 sec [junit] [junit] Testcase: moreComplex took 0 sec [junit] SKIPPED @@ -4648,28 +4695,28 @@ [junit] SKIPPED [junit] Running org.biojava.nbio.core.sequence.location.LocationTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 sec [junit] - [junit] Testcase: testWithStrandSwitch took 0.065 sec - [junit] Testcase: modulateCircular took 0.002 sec + [junit] Testcase: testWithStrandSwitch took 0.192 sec + [junit] Testcase: modulateCircular took 0.003 sec [junit] Testcase: testStrandFlip took 0.002 sec - [junit] Testcase: testBasicCircularLocation took 0.003 sec - [junit] Testcase: badLocations took 0.002 sec - [junit] Testcase: completePasses took 0 sec - [junit] Testcase: testSubLocations took 0.003 sec + [junit] Testcase: testBasicCircularLocation took 0.011 sec + [junit] Testcase: badLocations took 0.01 sec + [junit] Testcase: completePasses took 0.001 sec + [junit] Testcase: testSubLocations took 0.004 sec [junit] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.TargetedLocationParserTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 sec [junit] - [junit] Testcase: locationTest[0] took 0.034 sec - [junit] Testcase: locationTest[1] took 0.001 sec + [junit] Testcase: locationTest[0] took 0.183 sec + [junit] Testcase: locationTest[1] took 0.002 sec [junit] Testcase: locationTest[2] took 0.001 sec - [junit] Testcase: locationTest[3] took 0.001 sec + [junit] Testcase: locationTest[3] took 0.002 sec BUILD SUCCESSFUL -Total time: 39 seconds +Total time: 1 minute 21 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -4684,11 +4731,11 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 sec [junit] - [junit] Testcase: testGetQuery took 0.161 sec - [junit] Testcase: testGetScore took 0.047 sec + [junit] Testcase: testGetQuery took 0.22 sec + [junit] Testcase: testGetScore took 0.068 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec @@ -4696,20 +4743,20 @@ [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec [junit] - [junit] Testcase: testGetQuery took 0.26 sec - [junit] Testcase: testGetScore took 0.06 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec - [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testGetQuery took 0.203 sec + [junit] Testcase: testGetScore took 0.065 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.003 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.005 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testGetMaxScore took 0.006 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.75 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.75 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.945 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.945 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -4721,157 +4768,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.546 sec - [junit] Testcase: testToString took 0.014 sec - [junit] Testcase: testGetScoreMatrix took 0.024 sec - [junit] Testcase: testGetRoot took 0.072 sec - [junit] Testcase: testGetSequences took 0.005 sec - [junit] Testcase: testGetDistanceMatrix took 0.01 sec - [junit] Testcase: testGetAllPairsScores took 0.01 sec - [junit] Testcase: testIterator took 0.008 sec + [junit] Testcase: testGuideTree took 0.535 sec + [junit] Testcase: testToString took 0.051 sec + [junit] Testcase: testGetScoreMatrix took 0.017 sec + [junit] Testcase: testGetRoot took 0.232 sec + [junit] Testcase: testGetSequences took 0.022 sec + [junit] Testcase: testGetDistanceMatrix took 0.012 sec + [junit] Testcase: testGetAllPairsScores took 0.022 sec + [junit] Testcase: testIterator took 0.013 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.508 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.431 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.481 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.084 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.084 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.464 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.464 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.25 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.185 sec [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.058 sec - [junit] Testcase: should_align_middle_anchor took 0.059 sec + [junit] Testcase: testGetComputationTime took 0.084 sec + [junit] Testcase: should_align_middle_anchor took 0.174 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.002 sec - [junit] Testcase: testNeedlemanWunsch took 0.002 sec + [junit] Testcase: testNeedlemanWunsch took 0.02 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec - [junit] Testcase: testGetPair took 0.001 sec - [junit] Testcase: should_align_multiple_anchors took 0.003 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.016 sec - [junit] Testcase: testGetProfile took 0.003 sec - [junit] Testcase: testGetMinScore took 0.002 sec + [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: should_align_multiple_anchors took 0.006 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.015 sec + [junit] Testcase: testGetProfile took 0.002 sec + [junit] Testcase: testGetMinScore took 0.005 sec [junit] Testcase: should_align_ending_anchor took 0.001 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.01 sec - [junit] Testcase: testComplex took 0.053 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.119 sec - [junit] Testcase: should_align_starting_anchor took 0.003 sec - [junit] Testcase: anchors_should_not_change_score took 0.003 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.011 sec + [junit] Testcase: testComplex took 0.069 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.132 sec + [junit] Testcase: should_align_starting_anchor took 0.002 sec + [junit] Testcase: anchors_should_not_change_score took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: testIntOverflowBug took 0.413 sec + [junit] Testcase: testIntOverflowBug took 0.675 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec [junit] - [junit] Testcase: testOpenPenalty took 0.019 sec + [junit] Testcase: testOpenPenalty took 0.016 sec [junit] Testcase: testType took 0.001 sec [junit] Testcase: testExtensionPenalty took 0.001 sec - [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec - [junit] Testcase: testSimpleGapPenalty took 0 sec + [junit] Testcase: testSimpleGapPenaltyShortShort took 0.009 sec + [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.523 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.523 sec [junit] - [junit] Testcase: testGetQuery took 0.256 sec + [junit] Testcase: testGetQuery took 0.425 sec [junit] Testcase: testGetTarget took 0.002 sec - [junit] Testcase: testSimpleProfilePair took 0.01 sec + [junit] Testcase: testSimpleProfilePair took 0.021 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.695 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.695 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.947 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.947 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.243 sec - [junit] Testcase: testGetGapPenalty took 0.062 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.551 sec + [junit] Testcase: testGetGapPenalty took 0.016 sec [junit] Testcase: testGetComputationTime took 0.019 sec - [junit] Testcase: testGetQuery took 0.011 sec - [junit] Testcase: testGetScore took 0.009 sec - [junit] Testcase: testGetScoreMatrix took 0.009 sec - [junit] Testcase: testGetPair took 0.094 sec - [junit] Testcase: testGetProfile took 0.029 sec - [junit] Testcase: testGetMinScore took 0.004 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.012 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.13 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.003 sec - [junit] Testcase: testGetTarget took 0.008 sec - [junit] Testcase: testGetMaxScore took 0.009 sec + [junit] Testcase: testGetQuery took 0.014 sec + [junit] Testcase: testGetScore took 0.011 sec + [junit] Testcase: testGetScoreMatrix took 0.015 sec + [junit] Testcase: testGetPair took 0.028 sec + [junit] Testcase: testGetProfile took 0.005 sec + [junit] Testcase: testGetMinScore took 0.017 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.182 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.007 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.012 sec + [junit] Testcase: testGetTarget took 0.003 sec + [junit] Testcase: testGetMaxScore took 0.012 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.459 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.459 sec [junit] [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.014 sec - [junit] Testcase: testSetDescription took 0.048 sec - [junit] Testcase: testToString took 0.08 sec - [junit] Testcase: testCaseEquivalence took 0.003 sec - [junit] Testcase: test took 0.019 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.01 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.009 sec - [junit] Testcase: testSetName took 0.01 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.005 sec + [junit] Testcase: testSetDescription took 0.071 sec + [junit] Testcase: testToString took 0.112 sec + [junit] Testcase: testCaseEquivalence took 0.011 sec + [junit] Testcase: test took 0.099 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.02 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.03 sec + [junit] Testcase: testSetName took 0.033 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.025 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.021 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.021 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.172 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.341 sec [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.035 sec - [junit] Testcase: testGetQuery took 0.002 sec - [junit] Testcase: testGetScore took 0.003 sec - [junit] Testcase: testGetScoreMatrix took 0.003 sec - [junit] Testcase: testGetPair took 0.01 sec + [junit] Testcase: testGetComputationTime took 0.254 sec + [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetScore took 0.016 sec + [junit] Testcase: testGetScoreMatrix took 0.002 sec + [junit] Testcase: testGetPair took 0.024 sec [junit] Testcase: testSmithWaterman took 0.002 sec - [junit] Testcase: testGetProfile took 0.002 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testGetProfile took 0.015 sec + [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.111 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.314 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.124 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.009 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.004 sec - [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.021 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.013 sec + [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec - [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec - [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec + [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0.001 sec + [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.001 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.001 sec - [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.001 sec + [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.247 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.247 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 sec [junit] - [junit] Testcase: testGetComputationTime took 0.166 sec + [junit] Testcase: testGetComputationTime took 0.234 sec [junit] Testcase: testGuanUberbacher took 0.002 sec [junit] Testcase: testGetScore took 0.002 sec - [junit] Testcase: testGetPair took 0.008 sec + [junit] Testcase: testGetPair took 0.013 sec [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.002 sec - [junit] Testcase: should_align_shorter_target took 0.036 sec - [junit] Testcase: should_align_multiple_cuts took 0.001 sec + [junit] Testcase: should_align_shorter_target took 0.283 sec + [junit] Testcase: should_align_multiple_cuts took 0.005 sec [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: should_align_shorter_query took 0.001 sec + [junit] Testcase: should_align_shorter_query took 0.007 sec BUILD SUCCESSFUL -Total time: 31 seconds +Total time: 46 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -4889,8 +4936,8 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.317 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.317 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.271 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.271 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -4898,41 +4945,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 1.11 sec - [junit] Testcase: testExample1 took 0.079 sec - [junit] Testcase: testExample2 took 0.016 sec - [junit] Testcase: testExample3 took 0.014 sec - [junit] Testcase: testExample1WithCSV took 0.056 sec - [junit] Testcase: testWithCases took 0.011 sec + [junit] Testcase: testAdvancedXMLExample took 1.97 sec + [junit] Testcase: testExample1 took 0.122 sec + [junit] Testcase: testExample2 took 0.03 sec + [junit] Testcase: testExample3 took 0.019 sec + [junit] Testcase: testExample1WithCSV took 0.063 sec + [junit] Testcase: testWithCases took 0.022 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.134 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.134 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.511 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.511 sec [junit] - [junit] Testcase: shortExample1 took 0.073 sec - [junit] Testcase: shortExample2 took 0.764 sec - [junit] Testcase: shortExample3 took 0.202 sec - [junit] Testcase: shortExample4 took 0.015 sec - [junit] Testcase: shortExample5 took 0.056 sec + [junit] Testcase: shortExample1 took 0.123 sec + [junit] Testcase: shortExample2 took 2.03 sec + [junit] Testcase: shortExample3 took 0.289 sec + [junit] Testcase: shortExample4 took 0.003 sec + [junit] Testcase: shortExample5 took 0.018 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.267 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.267 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.951 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.951 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 1.988 sec - [junit] Testcase: testExample1 took 0.07 sec - [junit] Testcase: testExample2 took 0.062 sec - [junit] Testcase: testExample3 took 0.045 sec - [junit] Testcase: testExample1WithCSV took 0.038 sec - [junit] Testcase: testWithCases took 0.03 sec + [junit] Testcase: testAdvancedXMLExample took 2.489 sec + [junit] Testcase: testExample1 took 0.101 sec + [junit] Testcase: testExample2 took 0.055 sec + [junit] Testcase: testExample3 took 0.108 sec + [junit] Testcase: testExample1WithCSV took 0.087 sec + [junit] Testcase: testWithCases took 0.046 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.104 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.104 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.866 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.866 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. @@ -5147,74 +5194,74 @@ [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAbsorbance took 0.129 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 1.016 sec - [junit] Testcase: testEnrichment took 0.029 sec + [junit] Testcase: testAbsorbance took 0.154 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 1.607 sec + [junit] Testcase: testEnrichment took 0.058 sec [junit] Testcase: testApliphaticIndex took 0.003 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.022 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.033 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.01 sec - [junit] Testcase: testAbsorbanceNull took 0.001 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.006 sec + [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0.001 sec - [junit] Testcase: testAverageHydropathy took 0.002 sec + [junit] Testcase: testAverageHydropathy took 0.004 sec [junit] Testcase: testExtinctionCoefficient took 0.003 sec [junit] Testcase: testAAComposition took 0.002 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.123 sec - [junit] Testcase: testMolecularWeight took 0.009 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.006 sec - [junit] Testcase: testNetChargeNull took 0.003 sec - [junit] Testcase: testExtinctionCoefficientNull took 0 sec - [junit] Testcase: testNetCharge took 0.505 sec - [junit] Testcase: testEnrichmentNull took 0.002 sec - [junit] Testcase: testInstabilityIndexNull took 0.001 sec - [junit] Testcase: testAverageHydropathyNull took 0.001 sec - [junit] Testcase: testMolecularWeightXML took 0.193 sec - [junit] Testcase: testInstabilityIndex took 0.002 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.187 sec + [junit] Testcase: testMolecularWeight took 0.003 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.01 sec + [junit] Testcase: testNetChargeNull took 0.001 sec + [junit] Testcase: testExtinctionCoefficientNull took 0.005 sec + [junit] Testcase: testNetCharge took 0.531 sec + [junit] Testcase: testEnrichmentNull took 0.001 sec + [junit] Testcase: testInstabilityIndexNull took 0 sec + [junit] Testcase: testAverageHydropathyNull took 0 sec + [junit] Testcase: testMolecularWeightXML took 0.206 sec + [junit] Testcase: testInstabilityIndex took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec [junit] - [junit] Testcase: testFake took 0.006 sec + [junit] Testcase: testFake took 0.009 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] - [junit] Testcase: testFakeTest took 0.048 sec + [junit] Testcase: testFakeTest took 0.055 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.174 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.174 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.696 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.696 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: generateSchema took 1.15 sec - [junit] Testcase: readWithIDXml took 0.396 sec - [junit] Testcase: readMinXml took 0.197 sec - [junit] Testcase: readAdvancedXml took 0.13 sec - [junit] Testcase: generateXml took 0.077 sec - [junit] Testcase: readXml took 0.19 sec + [junit] Testcase: generateSchema took 1.335 sec + [junit] Testcase: readWithIDXml took 0.501 sec + [junit] Testcase: readMinXml took 0.313 sec + [junit] Testcase: readAdvancedXml took 0.167 sec + [junit] Testcase: generateXml took 0.114 sec + [junit] Testcase: readXml took 0.222 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.254 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.254 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.611 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.611 sec [junit] - [junit] Testcase: generateSchema took 1.54 sec - [junit] Testcase: generateXml took 0.211 sec - [junit] Testcase: readXml took 0.476 sec + [junit] Testcase: generateSchema took 1.538 sec + [junit] Testcase: generateXml took 0.203 sec + [junit] Testcase: readXml took 0.819 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec [junit] - [junit] Testcase: testFake took 0.037 sec + [junit] Testcase: testFake took 0.061 sec BUILD SUCCESSFUL -Total time: 33 seconds +Total time: 49 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -5231,7 +5278,7 @@ [echo] Using java version 17.0.6 BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 9 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -5247,256 +5294,256 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 sec [junit] - [junit] Testcase: testConvert took 0.287 sec + [junit] Testcase: testConvert took 0.431 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.009 sec - [junit] Testcase: testBuildNullDescription took 0 sec - [junit] Testcase: testBuildAppendQuality took 0 sec + [junit] Testcase: testBuildAppendSequence took 0.014 sec + [junit] Testcase: testBuildNullDescription took 0.001 sec + [junit] Testcase: testBuildAppendQuality took 0.001 sec [junit] Testcase: testBuild took 0.002 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec - [junit] Testcase: testBuildDefaultVariant took 0 sec - [junit] Testcase: testBuildMissingQuality took 0 sec + [junit] Testcase: testBuildDefaultVariant took 0.008 sec + [junit] Testcase: testBuildMissingQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec - [junit] Testcase: testBuildNullAppendQuality took 0.001 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.001 sec + [junit] Testcase: testBuildNullAppendQuality took 0 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0.001 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0.001 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0.001 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec - [junit] Testcase: testBuildMissingSequence took 0 sec + [junit] Testcase: testBuildMissingSequence took 0.001 sec [junit] Testcase: testBuildNullQuality took 0 sec - [junit] Testcase: testBuildMultiple took 0.001 sec + [junit] Testcase: testBuildMultiple took 0 sec [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testImmutable took 0.003 sec - [junit] Testcase: testBuilder took 0.004 sec + [junit] Testcase: testImmutable took 0.005 sec + [junit] Testcase: testBuilder took 0.005 sec [junit] Testcase: testVariant took 0.001 sec - [junit] Testcase: testQuality took 0.006 sec - [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testQuality took 0.007 sec + [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec - [junit] Testcase: testConstructor took 0 sec - [junit] Testcase: testSequence took 0.001 sec + [junit] Testcase: testConstructor took 0.001 sec + [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.306 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.306 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.004 sec - [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.01 sec + [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.002 sec [junit] Testcase: testConvertNullVariant took 0 sec - [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.003 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.124 sec - [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec - [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec + [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.005 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.17 sec + [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec + [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec - [junit] Testcase: testQualityScoresNullIntArray took 0.001 sec - [junit] Testcase: testConvertNullFastq took 0 sec + [junit] Testcase: testQualityScoresNullIntArray took 0 sec + [junit] Testcase: testConvertNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.002 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec - [junit] Testcase: testCreateDNASequenceNullFastq took 0.001 sec + [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec - [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec - [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec + [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec - [junit] Testcase: testToListNotAList took 0.016 sec - [junit] Testcase: testConvertQualitiesNullVariant took 0 sec + [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0.001 sec + [junit] Testcase: testToListNotAList took 0.004 sec + [junit] Testcase: testConvertQualitiesNullVariant took 0.005 sec [junit] Testcase: testConvertSameVariant took 0.001 sec - [junit] Testcase: testQualityScores took 0.015 sec - [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec + [junit] Testcase: testQualityScores took 0.019 sec + [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec - [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec - [junit] Testcase: testCreateDNASequence took 0.001 sec + [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0.001 sec + [junit] Testcase: testCreateDNASequence took 0.004 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec + [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testToList took 0 sec + [junit] Testcase: testToList took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec - [junit] Testcase: testErrorProbabilities took 0.001 sec + [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.014 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec + [junit] Testcase: testParseFastqVariant took 0.011 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec - [junit] Testcase: testIsSanger took 0.015 sec - [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec + [junit] Testcase: testIsSanger took 0.009 sec + [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 sec [junit] Testcase: testIsSolexa took 0 sec - [junit] Testcase: testIsIllumina took 0.001 sec + [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.426 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.426 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.089 sec - [junit] Testcase: testWrappingAsIllumina took 0.013 sec - [junit] Testcase: testValidateDescription took 0.034 sec - [junit] Testcase: testValidateRepeatDescription took 0.012 sec + [junit] Testcase: testFullRangeAsIllumina took 0.112 sec + [junit] Testcase: testWrappingAsIllumina took 0.005 sec + [junit] Testcase: testValidateDescription took 0.028 sec + [junit] Testcase: testValidateRepeatDescription took 0.005 sec [junit] Testcase: testMiscDnaAsIllumina took 0.004 sec [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec - [junit] Testcase: testLongReadsAsIllumina took 0.014 sec + [junit] Testcase: testLongReadsAsIllumina took 0.011 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.115 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.058 sec - [junit] Testcase: testParse took 0.002 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.095 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.089 sec + [junit] Testcase: testParse took 0.001 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.002 sec - [junit] Testcase: testReadEmptyInputStream took 0.002 sec + [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testReadFile took 0.005 sec [junit] Testcase: testMultipleWrappedQuality took 0.002 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec - [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testCreateFastqWriter took 0.006 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0.002 sec + [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.014 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.007 sec - [junit] Testcase: testWriteFileIterable took 0.091 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.002 sec - [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.013 sec + [junit] Testcase: testWriteFileIterable took 0.121 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec + [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.009 sec + [junit] Testcase: testWriteFileVararg took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.114 sec - [junit] Testcase: testFullRangeAsSanger took 0.007 sec - [junit] Testcase: testWrappingOriginal took 0.004 sec - [junit] Testcase: testLongReadsOriginal took 0.013 sec - [junit] Testcase: testMiscDnaOriginal took 0.003 sec + [junit] Testcase: testMiscRnaAsSanger took 0.099 sec + [junit] Testcase: testFullRangeAsSanger took 0.011 sec + [junit] Testcase: testWrappingOriginal took 0.005 sec + [junit] Testcase: testLongReadsOriginal took 0.015 sec + [junit] Testcase: testMiscDnaOriginal took 0.004 sec [junit] Testcase: testMiscRnaOriginal took 0.003 sec - [junit] Testcase: testValidateDescription took 0.015 sec - [junit] Testcase: testValidateRepeatDescription took 0.002 sec + [junit] Testcase: testValidateDescription took 0.031 sec + [junit] Testcase: testValidateRepeatDescription took 0.003 sec [junit] Testcase: testFullRangeOriginal took 0.002 sec [junit] Testcase: testWrappingAsSanger took 0.002 sec - [junit] Testcase: testLongReadsAsSanger took 0.005 sec - [junit] Testcase: testMiscDnaAsSanger took 0.002 sec - [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.076 sec + [junit] Testcase: testLongReadsAsSanger took 0.006 sec + [junit] Testcase: testMiscDnaAsSanger took 0.007 sec + [junit] Testcase: testParseNullReadable took 0.002 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.125 sec [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.03 sec - [junit] Testcase: testParse took 0.002 sec + [junit] Testcase: testErrorExamples took 0.086 sec + [junit] Testcase: testParse took 0.012 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec - [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testMultipleWrappedQuality took 0.006 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec - [junit] Testcase: testWrappedQuality took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.01 sec + [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.014 sec + [junit] Testcase: testConvertNotSangerVariant took 0.038 sec [junit] Testcase: testAppendVararg took 0.001 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.008 sec - [junit] Testcase: testWriteFileIterable took 0.077 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.01 sec + [junit] Testcase: testWriteFileIterable took 0.122 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.371 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.371 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.414 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.414 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.101 sec - [junit] Testcase: testFullRangeAsSolexa took 0.005 sec - [junit] Testcase: testValidateDescription took 0.018 sec - [junit] Testcase: testValidateRepeatDescription took 0.005 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.121 sec + [junit] Testcase: testFullRangeAsSolexa took 0.006 sec + [junit] Testcase: testValidateDescription took 0.022 sec + [junit] Testcase: testValidateRepeatDescription took 0.009 sec [junit] Testcase: testWrappingAsSolexa took 0.004 sec [junit] Testcase: testLongReadsAsSolexa took 0.008 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.008 sec - [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.108 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec + [junit] Testcase: testParseNullReadable took 0.006 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.116 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.047 sec + [junit] Testcase: testErrorExamples took 0.058 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.003 sec - [junit] Testcase: testReadEmptyInputStream took 0.002 sec + [junit] Testcase: testReadInputStream took 0.001 sec + [junit] Testcase: testWrappedSequence took 0.002 sec + [junit] Testcase: testReadEmptyInputStream took 0.005 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.003 sec + [junit] Testcase: testMultipleWrappedQuality took 0.007 sec [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec - [junit] Testcase: testWrappedQuality took 0.001 sec + [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.028 sec - [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.017 sec + [junit] Testcase: testAppendVararg took 0.005 sec [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.009 sec - [junit] Testcase: testWriteFileIterable took 0.104 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.007 sec + [junit] Testcase: testWriteFileIterable took 0.095 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0 sec - [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testWriteFileVararg took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.01 sec - [junit] Testcase: testStreamNullListener took 0.007 sec + [junit] Testcase: testStreamNullVariant took 0.005 sec + [junit] Testcase: testStreamNullListener took 0.006 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL -Total time: 25 seconds +Total time: 36 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -5517,39 +5564,39 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec [junit] [junit] Testcase: testMe took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testSomeMethod took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec [junit] - [junit] Testcase: testGetColor took 0.009 sec + [junit] Testcase: testGetColor took 0.008 sec [junit] Testcase: testSetStructure took 0.001 sec - [junit] Testcase: testClear took 0 sec - [junit] Testcase: testGetSelection took 0.008 sec - [junit] Testcase: testRepaint took 0.001 sec + [junit] Testcase: testClear took 0.004 sec + [junit] Testcase: testGetSelection took 0.007 sec + [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec - [junit] Testcase: testSetZoom took 0.001 sec - [junit] Testcase: testSetColor took 0 sec + [junit] Testcase: testSetZoom took 0 sec + [junit] Testcase: testSetColor took 0.001 sec [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec [junit] - [junit] Testcase: testStructureLoad took 0.001 sec + [junit] Testcase: testStructureLoad took 0.002 sec BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 15 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -5564,8 +5611,8 @@ [echo] Using java version 17.0.6 BUILD SUCCESSFUL -Total time: 6 seconds -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +Total time: 8 seconds +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_install @@ -5587,9 +5634,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb'. -dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-8_all.deb'. -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-8_all.deb'. +dpkg-deb: pakket 'libbiojava4.0-java' wordt gebouwd in '../libbiojava4.0-java_4.2.12+dfsg-8_all.deb'. +dpkg-deb: pakket 'libbiojava4-java-doc' wordt gebouwd in '../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb'. +dpkg-deb: pakket 'libbiojava4-java' wordt gebouwd in '../libbiojava4-java_4.2.12+dfsg-8_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava4-live_4.2.12+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../biojava4-live_4.2.12+dfsg-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5597,12 +5644,14 @@ 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/31310/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/31310/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/5065 and its subdirectories -I: Current time: Tue Apr 18 19:15:39 -12 2023 -I: pbuilder-time-stamp: 1681888539 +I: removing directory /srv/workspace/pbuilder/31310 and its subdirectories +I: Current time: Wed May 22 03:57:31 +14 2024 +I: pbuilder-time-stamp: 1716299851