Diff of the two buildlogs: -- --- b1/build.log 2023-05-20 15:39:53.222019445 +0000 +++ b2/build.log 2023-05-20 15:55:13.829707372 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 20 03:24:18 -12 2023 -I: pbuilder-time-stamp: 1684596258 +I: Current time: Sat Jun 22 12:02:58 +14 2024 +I: pbuilder-time-stamp: 1719007378 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./biojava-live_1.9.5+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.5+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu May 11 21:19:05 2023 -12 +gpgv: Signature made Fri May 12 23:19:05 2023 +14 gpgv: using RSA key B8CE4DE21080DCF903E16C40F513C419E4B9D0AC gpgv: issuer "ebourg@apache.org" gpgv: Can't check signature: No public key @@ -28,52 +28,84 @@ dpkg-source: info: applying omit_tests_with_problematic_data.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17770/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19779/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 Jun 22 12:03 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/19779/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19779/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='17770' - 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=19779 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.KXBtM2Xc/pbuilderrc_86lu --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.KXBtM2Xc/b1 --logfile b1/build.log biojava-live_1.9.5+dfsg-3.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.KXBtM2Xc/pbuilderrc_axvG --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.KXBtM2Xc/b2 --logfile b2/build.log --extrapackages usrmerge biojava-live_1.9.5+dfsg-3.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 codethink14-arm64 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 18 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17770/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 21 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/19779/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -395,7 +427,7 @@ Get: 266 http://deb.debian.org/debian bookworm/main arm64 maven all 3.8.7-1 [18.9 kB] Get: 267 http://deb.debian.org/debian bookworm/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 268 http://deb.debian.org/debian bookworm/main arm64 maven-debian-helper all 2.6.3 [108 kB] -Fetched 402 MB in 1min 43s (3903 kB/s) +Fetched 402 MB in 38s (10.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sgml-base. (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.) @@ -1667,8 +1699,17 @@ 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/biojava-live-1.9.5+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 > ../biojava-live_1.9.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/19779/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/19779/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/biojava-live-1.9.5+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 > ../biojava-live_1.9.5+dfsg-3_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -2939,20 +2980,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [01:56 min] -[INFO] bytecode ........................................... SUCCESS [ 32.981 s] -[INFO] core ............................................... SUCCESS [02:44 min] -[INFO] alignment .......................................... SUCCESS [ 18.360 s] -[INFO] biosql ............................................. SUCCESS [ 22.276 s] -[INFO] blast .............................................. SUCCESS [ 17.155 s] -[INFO] sequencing ......................................... SUCCESS [ 12.779 s] -[INFO] gui ................................................ SUCCESS [ 27.000 s] -[INFO] phylo .............................................. SUCCESS [ 10.144 s] +[INFO] biojava-legacy ..................................... SUCCESS [02:10 min] +[INFO] bytecode ........................................... SUCCESS [ 28.526 s] +[INFO] core ............................................... SUCCESS [02:27 min] +[INFO] alignment .......................................... SUCCESS [ 17.779 s] +[INFO] biosql ............................................. SUCCESS [ 23.186 s] +[INFO] blast .............................................. SUCCESS [ 21.440 s] +[INFO] sequencing ......................................... SUCCESS [ 22.484 s] +[INFO] gui ................................................ SUCCESS [ 31.095 s] +[INFO] phylo .............................................. SUCCESS [ 18.182 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 07:08 min -[INFO] Finished at: 2023-05-20T03:35:06-12:00 +[INFO] Total time: 07:25 min +[INFO] Finished at: 2024-06-22T12:13:04+14:00 [INFO] ------------------------------------------------------------------------  dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/biojava-live-1.9.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/biojava-live-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode test @@ -3026,7 +3067,7 @@ testEquals testGetEnd testSetRank -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojavax.SimpleRankedDocRefTest [INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest [INFO] Running org.biojavax.SimpleDocRefTest @@ -3043,11 +3084,11 @@ testEquals testGetCRC testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.SimpleDocRefTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.SimpleDocRefTest [INFO] Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteBioEntry testGetRemoteSymbolList -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.64 s - in org.biojavax.DummyCrossReferenceResolverTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.277 s - in org.biojavax.DummyCrossReferenceResolverTest [INFO] Running org.biojavax.SimpleNoteTest testGetValue testToString @@ -3059,7 +3100,7 @@ testSetRank testSetTerm testSetValue -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojavax.SimpleNoteTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.SimpleNamespaceTest testGetAuthority testSetDescription @@ -3074,7 +3115,7 @@ testEquals testGetURI testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.SimpleNamespaceTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojavax.SimpleNamespaceTest [INFO] Running org.biojavax.EmptyRichAnnotationTest testGetNoteSet testAddNote @@ -3090,7 +3131,7 @@ testRemoveProperty testEquals testContainsProperty -[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.EmptyRichAnnotationTest +[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojavax.EmptyRichAnnotationTest [INFO] Running org.biojavax.SimpleDocRefAuthorTest testIsConsortium testToString @@ -3109,7 +3150,7 @@ testGetComment testEquals testSetRank -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojavax.SimpleCommentTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.SimpleCommentTest [INFO] Running org.biojavax.ontology.SimpleComparableTermTest testSetDescription testGetRankedCrossRefs @@ -3131,7 +3172,7 @@ testRemoveSynonym testSetObsolete testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojavax.ontology.SimpleComparableTermTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojavax.ontology.SimpleComparableTermTest [INFO] Running org.biojavax.ontology.SimpleComparableTripleTest testGetSubject testSetDescriptors @@ -3177,7 +3218,7 @@ testEquals testGetOps testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojavax.ontology.SimpleComparableOntologyTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] Running org.biojavax.SimpleRankedCrossRefTest testToString testGetCrossRef @@ -3198,7 +3239,7 @@ testHashCode testGetDbname testEquals -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.SimpleCrossRefTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.SimpleCrossRefTest [INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest testGetNameClass testToString @@ -3208,7 +3249,7 @@ testHashCode testEquals testSetName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [INFO] Running org.biojavax.bio.SimpleBioEntryTest testGetNamespace testGetNoteSet @@ -3242,25 +3283,25 @@ testGetDivision testSetTaxon testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojavax.bio.SimpleBioEntryTest +[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojavax.bio.SimpleBioEntryTest [INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojavax.bio.seq.SimpleRichFeatureTest [INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojavax.bio.seq.CompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.io.Bug2255Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojavax.bio.seq.io.Bug2255Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 s - in org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.237 s - in org.biojavax.bio.seq.io.INSDseqFormatTest [INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest Location 467: 467 Location 340..565: 340..565 @@ -3280,34 +3321,34 @@ Location J00194:100..202: J00194:100..202 Location (8298.8300)..10206: (8298.8300)..10206 Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojavax.bio.seq.io.Bug2249_2248Test [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojavax.bio.seq.io.EMBLFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 s - in org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.874 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.SimpleRichLocationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichLocationTest [INFO] Running org.biojavax.ga.util.GAToolsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.util.GAToolsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.ga.util.GAToolsTest [INFO] Running org.biojavax.ga.util.WeightedSetTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojavax.ga.util.WeightedSetTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.WeightedSetTest [INFO] Running org.biojavax.ga.impl.SimplePopulationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimplePopulationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimplePopulationTest [INFO] Running org.biojavax.ga.impl.SimpleOrganismTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimpleOrganismTest [INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojavax.ga.functions.ProportionalSelectionTest [INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest [INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest [INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest [INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest [INFO] Running org.biojavax.SimpleRichAnnotationTest testGetNoteSet testAddNote @@ -3325,21 +3366,21 @@ testRemoveProperty testRemoveProperty2 testContainsProperty -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.SimpleRichAnnotationTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojavax.SimpleRichAnnotationTest [INFO] Running org.biojava.naming.ObdaUriParserTest urn:obda.org:format:embl/ac :trail oneName lead: -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.naming.ObdaUriParserTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes -Binding: urn -> org.biojava.naming.ObdaContext@130f889 +Binding: urn -> org.biojava.naming.ObdaContext@2f490758 Reached urn Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@1188e820 +Binding: open-bio.org -> org.biojava.naming.ObdaContext@101df177 Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed @@ -3347,7 +3388,7 @@ module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } -Binding: type -> org.biojava.naming.ObdaContext@166fa74d +Binding: type -> org.biojava.naming.ObdaContext@276438c9 Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types @@ -3356,7 +3397,7 @@ type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } -Binding: type -> org.biojava.naming.ObdaContext@40f08448 +Binding: type -> org.biojava.naming.ObdaContext@588df31b Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this @@ -3365,7 +3406,7 @@ ontology. This is not important. The important thing is that we have unique identifiers for common types that all projects use and interact with. } -Binding: format -> org.biojava.naming.ObdaContext@276438c9 +Binding: format -> org.biojava.naming.ObdaContext@33b37288 Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this @@ -3376,7 +3417,7 @@ type of URN is purely there to identify the format of the stream, not the manner in which it should be processed. } -Binding: alphabet -> org.biojava.naming.ObdaContext@588df31b +Binding: alphabet -> org.biojava.naming.ObdaContext@77a57272 Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as @@ -3388,14 +3429,14 @@ Alphabets do not define a mapping to or from strings, but should be used wherever the type of the content of a sequence needs to be stated. } -Binding: format -> org.biojava.naming.ObdaContext@33b37288 +Binding: format -> org.biojava.naming.ObdaContext@7181ae3f Reached urn:open-bio.org:format Attributes: {description=description: A namespace for OBDA URNs that define formats. All URNs within this namespace must be of the type urn:open-bio.org:type:format. Any URN in this namespace that is not of that type is not a valid OBDA URN. } -Binding: enzyme -> org.biojava.naming.ObdaContext@77a57272 +Binding: enzyme -> org.biojava.naming.ObdaContext@46238e3f Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from @@ -3411,29 +3452,29 @@ ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } -Binding: genbank -> org.biojava.naming.ObdaContext@7181ae3f +Binding: genbank -> org.biojava.naming.ObdaContext@6e2c9341 Reached urn:open-bio.org:format:genbank Attributes: {description=description: The GENBANK file format associated with the GENBANK sequence database. } -Binding: swissprot -> org.biojava.naming.ObdaContext@46238e3f +Binding: swissprot -> org.biojava.naming.ObdaContext@32464a14 Reached urn:open-bio.org:format:swissprot Attributes: {description=description: The SWISSPROT file format as used in the SWISSPROT sequence database. } -Binding: embl -> org.biojava.naming.ObdaContext@6e2c9341 +Binding: embl -> org.biojava.naming.ObdaContext@4e4aea35 Reached urn:open-bio.org:format:embl Attributes: {description=description: The EMBL file format associated with entries in the EMBL sequence database. } -Binding: alphabet -> org.biojava.naming.ObdaContext@32464a14 +Binding: alphabet -> org.biojava.naming.ObdaContext@1442d7b5 Reached urn:open-bio.org:alphabet Attributes: {description=description: A namespace within which to store alphabet identifiers. Alphabets should represent URNs that represent objects of the type identified by urn:open-bio.org:type:alphabet, and any useage outside of this is not supported. } -Binding: rna -> org.biojava.naming.ObdaContext@4e4aea35 +Binding: rna -> org.biojava.naming.ObdaContext@1efee8e7 Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry @@ -3441,7 +3482,7 @@ are reprsented by the four letters a, g, c and u. However, this is not a formal requirement for a resource to declare this alphabet as its type. } -Binding: protein -> org.biojava.naming.ObdaContext@1442d7b5 +Binding: protein -> org.biojava.naming.ObdaContext@1ee807c6 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, @@ -3449,7 +3490,7 @@ to be represented by characters, but this is not a formal requirement for a resource to publish an alphabet equal to this identifier. } -Binding: dna -> org.biojava.naming.ObdaContext@1efee8e7 +Binding: dna -> org.biojava.naming.ObdaContext@76a4d6c Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry @@ -3457,167 +3498,167 @@ are reprsented by the four letters a, g, c and t. However, this is not a formal requirement for a resource to declare this alphabet as its type. } -lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@d6da883} +lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@799d4f69} My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@799d4f69} +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@290dbf45} My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@49c43f4e, format=org.biojava.naming.ObdaContext@290dbf45, alphabet=org.biojava.naming.ObdaContext@12028586} +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@12028586, format=org.biojava.naming.ObdaContext@17776a8, alphabet=org.biojava.naming.ObdaContext@69a10787} My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@17776a8, genbank=org.biojava.naming.ObdaContext@69a10787, swissprot=org.biojava.naming.ObdaContext@2d127a61, embl=org.biojava.naming.ObdaContext@2bbaf4f0} +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@2d127a61, genbank=org.biojava.naming.ObdaContext@2bbaf4f0, swissprot=org.biojava.naming.ObdaContext@11c20519, embl=org.biojava.naming.ObdaContext@70beb599} My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.189 s - in org.biojava.naming.ObdaInitialContextFactoryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.naming.ObdaInitialContextFactoryTest [INFO] Running org.biojava.utils.RepeatedCharSequenceTest JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.utils.RepeatedCharSequenceTest [INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.utils.walker.WalkerFactoryTest [INFO] Running org.biojava.utils.walker.WalkerTest Increasing counter: Overlaps([20,50]) -Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Increasing counter: Overlaps([20,50]) Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: ByClass(org.biojava.bio.seq.ComponentFeature) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +OverlapsLocation: Overlaps([20,50]) Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.utils.walker.WalkerTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.utils.walker.WalkerTest [INFO] Running org.biojava.utils.process.AllTests -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 s - in org.biojava.utils.process.AllTests [INFO] Running org.biojava.utils.process.ExternalProcessTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.utils.process.ExternalProcessTest [INFO] Running org.biojava.utils.ListToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.ListToolsTest [INFO] Running org.biojava.utils.regex.PatternCheckerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.utils.regex.PatternCheckerTest [INFO] Running org.biojava.utils.regex.RegexTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.utils.regex.RegexTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.utils.regex.RegexTest [INFO] Running org.biojava.utils.automata.NfaTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.utils.automata.NfaTest [INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest [INFO] Running org.biojava.utils.SmallMapTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.utils.SmallMapTest [INFO] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.948 s - in org.biojava.ontology.ParseOBOFileTest [INFO] Running org.biojava.ontology.TermImplTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.ontology.TermImplTest [INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.ontology.OntologyTest [INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.ontology.TripleImplTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest [INFO] Running org.biojava.bio.AnnotationTypeTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.AnnotationTypeTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.AnnotationTypeTest [INFO] Running org.biojava.bio.search.MaxMismatchPatternTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.MaxMismatchPatternTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [INFO] Running org.biojava.bio.search.SeqContentPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.search.SeqContentPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SeqContentPatternTest [INFO] Running org.biojava.bio.MergeAnnotationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.MergeAnnotationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.MergeAnnotationTest [INFO] Running org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.dist.TranslatedDistributionTest [INFO] Running org.biojava.bio.dist.DistributionTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.dist.DistributionTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.dist.DistributionTest [INFO] Running org.biojava.bio.dist.DistSerTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.381 s - in org.biojava.bio.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 s - in org.biojava.bio.dist.DistSerTest [INFO] Running org.biojava.bio.dist.DistributionToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.bio.dist.DistributionToolsTest [INFO] Running org.biojava.bio.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 s - in org.biojava.bio.dp.DPSerializationTest [INFO] Running org.biojava.bio.dp.EmissionStateEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.dp.EmissionStateEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.dp.EmissionStateEventTest [INFO] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.dp.MarkovModelEventTest [INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.25 s - in org.biojava.bio.symbol.AlphabetSerializationTest [INFO] Running org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.symbol.GappedSymbolListTest [INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.symbol.IntegerAlphabetTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.symbol.BetweenLocationTest [INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.bio.symbol.CompoundLocationTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.NameTokenizationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.symbol.NameTokenizationTest [INFO] Running org.biojava.bio.symbol.RangeLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.symbol.RangeLocationTest [INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet [INFO] Running org.biojava.bio.symbol.CircularLocationTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.CircularLocationTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.symbol.CircularLocationTest [INFO] Running org.biojava.bio.symbol.MergeLocationTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.symbol.MergeLocationTest [INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest [INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.715 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.487 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.MotifToolsTest -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.symbol.MotifToolsTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.MotifToolsTest [INFO] Running org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.symbol.SymbolSerializationTest [INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest [INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CrossProductTokenizationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CrossProductTokenizationTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolListTest [INFO] Running org.biojava.bio.symbol.PointLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.PointLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.PointLocationTest [INFO] Running org.biojava.bio.symbol.TranslationTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.TranslationTest [INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleSymbolEventTest [INFO] Running org.biojava.bio.symbol.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.575 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.006 s - in org.biojava.bio.symbol.SymbolListTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.DoubleAlphabetTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Running org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.AlphabetManagerTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.bio.molbio.RestrictionEnzymeTest [INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.phred.PhredToolsTest [INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 s - in org.biojava.bio.program.indexdb.IndexToolsTest [INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest [INFO] Running org.biojava.bio.proteomics.MassCalcTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.proteomics.MassCalcTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.proteomics.MassCalcTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) @@ -3645,9 +3686,9 @@ at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.proteomics.aaindex.AAindexTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest [INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest java.lang.NullPointerException: name is null. at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) @@ -3721,54 +3762,54 @@ at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest [INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.seq.DNAToolsTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.SimpleAssemblyTest [INFO] Running org.biojava.bio.seq.FilterUtilsTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.FilterUtilsTest [INFO] Running org.biojava.bio.seq.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.RNAToolsTest [INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.filter.FilterTransformerTest [INFO] Running org.biojava.bio.seq.CircularSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.FeatureFilterTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.FeatureFilterTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.FeatureFilterTest [INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest [INFO] Running org.biojava.bio.seq.ProteinToolsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.ProteinToolsTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest [INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 s - in org.biojava.bio.seq.io.LocationFormatterTest [INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.239 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest [INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.532 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.034 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest [INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest [INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.839 s - in org.biojava.bio.seq.io.SeqIOToolsTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.846 s - in org.biojava.bio.seq.io.SeqIOToolsTest [INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.NewSimpleAssemblyTest [INFO] Running org.biojava.bio.seq.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.279 s - in org.biojava.bio.seq.SeqSerializationTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.seq.FeatureHolderUtilsTest [INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.seq.impl.GappedSequenceTest [INFO] Running org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.bio.seq.impl.SubSequenceTest [INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} @@ -3776,25 +3817,25 @@ template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.impl.ViewSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.seq.db.TestHashSequenceDB [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Running org.biojava.directory.OBDARegistryParserTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.directory.OBDARegistryParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.directory.OBDARegistryParserTest [INFO] Running org.biojava.directory.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.directory.RegistryConfigurationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.directory.RegistryConfigurationTest [INFO] [INFO] Results: [INFO] @@ -3823,11 +3864,11 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.923 s - in org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.48 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 s - in org.biojava.bio.alignment.SubstitutionMatrixTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.064 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] [INFO] Results: [INFO] @@ -3857,7 +3898,7 @@ [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. -[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.195 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3886,41 +3927,41 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.606 s - in org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.756 s - in org.biojava.bio.program.sax.BlastTest [INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.603 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.463 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.865 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.915 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.495 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.571 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.251 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.218 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.551 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.604 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.588 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.661 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.4 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.821 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.338 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.389 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.069 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.237 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.841 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.401 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.004 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.612 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.045 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.689 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.845 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.612 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.835 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] [INFO] Results: [INFO] @@ -3949,31 +3990,31 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.685 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.506 s - in org.biojava.bio.program.fastq.FastqToolsTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.276 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.bio.program.fastq.ConvertTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.program.fastq.FastqTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojava.bio.program.fastq.FastqVariantTest [INFO] Running org.biojava.bio.program.scf.SCFTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] @@ -4021,7 +4062,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.424 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -4030,20 +4071,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.007 s] -[INFO] bytecode ........................................... SUCCESS [ 3.147 s] -[INFO] core ............................................... SUCCESS [ 21.758 s] -[INFO] alignment .......................................... SUCCESS [ 10.233 s] -[INFO] biosql ............................................. SUCCESS [ 10.355 s] -[INFO] blast .............................................. SUCCESS [ 30.217 s] -[INFO] sequencing ......................................... SUCCESS [ 10.369 s] -[INFO] gui ................................................ SUCCESS [ 0.131 s] -[INFO] phylo .............................................. SUCCESS [ 10.237 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.012 s] +[INFO] bytecode ........................................... SUCCESS [ 2.955 s] +[INFO] core ............................................... SUCCESS [ 31.599 s] +[INFO] alignment .......................................... SUCCESS [ 10.381 s] +[INFO] biosql ............................................. SUCCESS [ 10.309 s] +[INFO] blast .............................................. SUCCESS [ 30.362 s] +[INFO] sequencing ......................................... SUCCESS [ 10.304 s] +[INFO] gui ................................................ SUCCESS [ 0.198 s] +[INFO] phylo .............................................. SUCCESS [ 10.378 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:37 min -[INFO] Finished at: 2023-05-20T03:36:50-12:00 +[INFO] Total time: 01:47 min +[INFO] Finished at: 2024-06-22T12:14:58+14:00 [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -4174,20 +4215,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 1.001 s] -[INFO] bytecode ........................................... SUCCESS [ 0.135 s] -[INFO] core ............................................... SUCCESS [ 0.064 s] -[INFO] alignment .......................................... SUCCESS [ 0.061 s] -[INFO] biosql ............................................. SUCCESS [ 0.081 s] -[INFO] blast .............................................. SUCCESS [ 0.094 s] -[INFO] sequencing ......................................... SUCCESS [ 0.083 s] -[INFO] gui ................................................ SUCCESS [ 0.072 s] -[INFO] phylo .............................................. SUCCESS [ 0.074 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 1.998 s] +[INFO] bytecode ........................................... SUCCESS [ 0.249 s] +[INFO] core ............................................... SUCCESS [ 0.152 s] +[INFO] alignment .......................................... SUCCESS [ 0.173 s] +[INFO] biosql ............................................. SUCCESS [ 0.148 s] +[INFO] blast .............................................. SUCCESS [ 0.184 s] +[INFO] sequencing ......................................... SUCCESS [ 0.136 s] +[INFO] gui ................................................ SUCCESS [ 0.144 s] +[INFO] phylo .............................................. SUCCESS [ 0.127 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 2.247 s -[INFO] Finished at: 2023-05-20T03:36:56-12:00 +[INFO] Total time: 4.249 s +[INFO] Finished at: 2024-06-22T12:15:09+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/biojava-live-1.9.5\+dfsg --non-explore Analysing pom.xml... @@ -4272,8 +4313,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.5+dfsg-3_all.deb'. -dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.5+dfsg-3_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.5+dfsg-3_all.deb'. +dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.5+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.5+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.5+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4281,12 +4322,14 @@ 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/19779/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19779/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/17770 and its subdirectories -I: Current time: Sat May 20 03:39:52 -12 2023 -I: pbuilder-time-stamp: 1684597192 +I: removing directory /srv/workspace/pbuilder/19779 and its subdirectories +I: Current time: Sat Jun 22 12:18:12 +14 2024 +I: pbuilder-time-stamp: 1719008292