Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 17:39:21.403478962 +0000 +++ b2/build.log 2024-11-21 17:46:16.240728296 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 24 11:57:54 -12 2025 -I: pbuilder-time-stamp: 1766620674 +I: Current time: Fri Nov 22 07:39:24 +14 2024 +I: pbuilder-time-stamp: 1732210764 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,54 +29,86 @@ 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/101985/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/45565/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Nov 21 17:39 /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/45565/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/45565/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='2d7c6fd74b9a4bc2872553e6adc4e952' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='101985' - PS1='# ' - PS2='> ' + INVOCATION_ID=757e827129694629a75aae5c68e24e5f + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=45565 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.16LFYuzy/pbuilderrc_Pv70 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.16LFYuzy/b1 --logfile b1/build.log biojava-live_1.9.7+dfsg-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.16LFYuzy/pbuilderrc_PQXQ --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.16LFYuzy/b2 --logfile b2/build.log biojava-live_1.9.7+dfsg-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/101985/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/45565/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -415,7 +447,7 @@ Get: 287 http://deb.debian.org/debian trixie/main i386 maven-repo-helper all 1.11 [142 kB] Get: 288 http://deb.debian.org/debian trixie/main i386 unzip i386 6.0-28 [166 kB] Get: 289 http://deb.debian.org/debian trixie/main i386 maven-debian-helper all 2.6.5 [108 kB] -Fetched 273 MB in 3s (83.7 MB/s) +Fetched 273 MB in 11s (24.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:i386. (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 ... 19956 files and directories currently installed.) @@ -1795,7 +1827,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava-live-1.9.7+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_1.9.7+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/45565/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/45565/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava-live-1.9.7+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_1.9.7+dfsg-2_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1855,8 +1891,8 @@ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/MethodRootContext.java:[117,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[83,25] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ChildContext.java:[140,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Some input files use unchecked or unsafe operations. -[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/IntrospectedCodeClass.java: Recompile with -Xlint:unchecked for details. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Some input files use unchecked or unsafe operations. +[INFO] /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/main/java/org/biojava/utils/bytecode/ConstantPool.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.1:testResources (default-testResources) @ bytecode --- [INFO] skip non existing resourceDirectory /build/reproducible-path/biojava-live-1.9.7+dfsg/bytecode/src/test/resources @@ -2139,9 +2175,9 @@ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[352,38] Integer(java.lang.String) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[608,15] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/TaxonSQL.java:[632,17] Integer(int) in java.lang.Integer has been deprecated and marked for removal -[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OracleDBHelper.java:[200,63] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.java:[129,94] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLRichObjectBuilder.java:[154,78] Integer(int) in java.lang.Integer has been deprecated and marked for removal +[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojava/bio/seq/db/biosql/OracleDBHelper.java:[200,63] Long(long) in java.lang.Long has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[602,64] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[976,120] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/biosql/src/main/java/org/biojavax/bio/db/biosql/BioSQLFeatureFilter.java:[978,114] Integer(int) in java.lang.Integer has been deprecated and marked for removal @@ -2304,10 +2340,10 @@ [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/LineInfo.java:[51,28] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,53] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbiTraceRenderer.java:[157,72] Double(double) in java.lang.Double has been deprecated and marked for removal -[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[173,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal -[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[174,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,26] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FilteringRenderer.java:[119,48] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal +[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[173,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal +[WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/FeatureBlockSequenceRenderer.java:[174,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[176,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/AbstractPeptideDigestRenderer.java:[206,27] Integer(int) in java.lang.Integer has been deprecated and marked for removal [WARNING] /build/reproducible-path/biojava-live-1.9.7+dfsg/gui/src/main/java/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:[288,50] Boolean(boolean) in java.lang.Boolean has been deprecated and marked for removal @@ -2396,20 +2432,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] -[INFO] bytecode ........................................... SUCCESS [ 1.873 s] -[INFO] core ............................................... SUCCESS [ 8.090 s] -[INFO] alignment .......................................... SUCCESS [ 0.319 s] -[INFO] biosql ............................................. SUCCESS [ 0.446 s] -[INFO] blast .............................................. SUCCESS [ 0.439 s] -[INFO] sequencing ......................................... SUCCESS [ 0.458 s] -[INFO] gui ................................................ SUCCESS [ 0.485 s] -[INFO] phylo .............................................. SUCCESS [ 0.272 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.003 s] +[INFO] bytecode ........................................... SUCCESS [ 3.162 s] +[INFO] core ............................................... SUCCESS [ 15.138 s] +[INFO] alignment .......................................... SUCCESS [ 0.713 s] +[INFO] biosql ............................................. SUCCESS [ 1.020 s] +[INFO] blast .............................................. SUCCESS [ 0.964 s] +[INFO] sequencing ......................................... SUCCESS [ 0.904 s] +[INFO] gui ................................................ SUCCESS [ 1.038 s] +[INFO] phylo .............................................. SUCCESS [ 0.520 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 12.531 s -[INFO] Finished at: 2025-12-24T23:58:53Z +[INFO] Total time: 23.675 s +[INFO] Finished at: 2024-11-21T17:42:25Z [INFO] ------------------------------------------------------------------------ dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.7\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.7\+dfsg/debian/maven-repo --batch-mode test @@ -2475,69 +2511,389 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.ontology.OntologyTest -[INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest -[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] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +testGetNameClass +testToString +testCompareTo +testSetNameClass +testGetName +testHashCode +testEquals +testSetName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +[INFO] Running org.biojavax.bio.SimpleBioEntryTest +testGetNamespace +testGetNoteSet +testGetRankedDocRefs +testGetRelationships +testGetTaxon +testSetDescription +testGetAccession +testGetRankedCrossRefs +testToString +testCompareTo +testGetName +testRemoveComment +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation +testSetNoteSet +testRemoveRankedCrossRef +testRemoveRankedDocRef +testRemoveRelationship +testGetVersion +testGetDescription +testSetIdentifier +testGetComments +testHashCode +testEquals +testAddRankedCrossRef +testAddRankedDocRef +testAddRelationship +testSetDivision +testGetDivision +testSetTaxon +testAddComment +[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojavax.bio.SimpleBioEntryTest +[INFO] Running org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest +[INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest +testEquals +[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.bio.seq.MultiSourceCompoundRichLocationTest +testEquals +[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: 0.001 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest +Location 467: 467 +Location 340..565: 340..565 +Location <345..500: <345..500 +Location <1..888: <1..888 +Location (102.110): (102.110) +Location (23.45)..600: (23.45)..600 +Location (122.133)..(204.221): (122.133)..(204.221) +Location 123^124: 123^124 +Location 145^177: 145^177 +Location join(12..78,134..202): join(12..78,134..202) +Location complement(1..23): complement(1..23) +Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) +Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) +Location complement(34..(122.126)): complement(34..(122.126)) +Location complement((122.126)..34): complement((122.126)..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: 0.008 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest +[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojavax.bio.seq.io.Bug2250_2256Test +[INFO] Running org.biojavax.bio.seq.io.Bug2255Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.bio.seq.io.Bug2255Test +[INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest +testEquals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Running org.biojavax.SimpleDocRefTest +testGetTitle +testToString +testGetLocation +testSetCrossref +testGetCrossref +testCompareTo +testGetAuthors +testGetAuthorList +testHashCode +testSetRemark +testEquals +testGetCRC +testGetRemark +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.SimpleDocRefTest +[INFO] Running org.biojavax.SimpleRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testToString +testGetNote +testSetNoteSet +testContains +testGetPropertys +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testRemoveProperty2 +testContainsProperty +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojavax.SimpleRichAnnotationTest +[INFO] Running org.biojavax.EmptyRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testGetNote +testSetNoteSet +testContains +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testEquals +testContainsProperty +[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.EmptyRichAnnotationTest +[INFO] Running org.biojavax.SimpleNoteTest +testGetValue +testToString +testCompareTo +testGetRank +testGetTerm +testHashCode +testEquals +testSetRank +testSetTerm +testSetValue +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleNoteTest +[INFO] Running org.biojavax.SimpleNamespaceTest +testGetAuthority +testSetDescription +testToString +testGetAcronym +testCompareTo +testGetName +testSetAuthority +testGetDescription +testHashCode +testSetAcronym +testEquals +testGetURI +testSetURI +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleNamespaceTest +[INFO] Running org.biojavax.SimpleCrossRefTest +testGetNoteSet +testGetAccession +testToString +testCompareTo +testGetAnnotation +testSetNoteSet +testGetVersion +testHashCode +testGetDbname +testEquals +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleCrossRefTest +[INFO] Running org.biojavax.DummyCrossReferenceResolverTest +testGetRemoteBioEntry +testGetRemoteSymbolList +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.DummyCrossReferenceResolverTest +[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Running org.biojavax.SimpleRankedDocRefTest +testGetStart +testSetLocation +testToString +testGetDocumentReference +testCompareTo +testGetRank +testHashCode +testEquals +testGetEnd +testSetRank +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Running org.biojavax.SimpleDocRefAuthorTest +testIsConsortium +testToString +testCompareTo +testGetName +testHashCode +testEquals +testGetExtendedName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.SimpleDocRefAuthorTest +[INFO] Running org.biojavax.SimpleCommentTest +testSetComment +testToString +testCompareTo +testGetRank +testHashCode +testGetComment +testEquals +testSetRank +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleCommentTest +[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest +testGetSubject +testSetDescriptors +testToString +testGetSynonyms +testRemoveDescriptor +testCompareTo +testAddSynonym +testGetName +testGetOntology +testGetPredicate +testGetAnnotation +testGetDescription +testGetDescriptors +testHashCode +testAddDescriptor +testEquals +testGetObject +testRemoveSynonym +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ontology.SimpleComparableTripleTest +[INFO] Running org.biojavax.ontology.SimpleComparableTermTest +testSetDescription +testGetRankedCrossRefs +testToString +testGetSynonyms +testCompareTo +testAddSynonym +testGetName +testGetOntology +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation +testRemoveRankedCrossRef +testGetDescription +testSetIdentifier +testHashCode +testEquals +testAddRankedCrossRef +testRemoveSynonym +testSetObsolete +testGetObsolete +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ontology.SimpleComparableTermTest +[INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest +testSetTripleSet +testCreateTriple +testContainsTriple +testGetTerms +testCreateVariable +testContainsTerm +testGetTermSet +testSetDescription +testToString +testGetOrCreateTerm +testCompareTo +testGetTriples +testGetName +testGetTerm +testGetOrImportTerm +testGetTripleSet +testCreateTerm +testGetDescription +testSetTermSet +testHashCode +testDeleteTerm +testEquals +testGetOps +testImportTerm +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ontology.SimpleComparableOntologyTest +[INFO] Running 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.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.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.001 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[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] 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] 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] Running org.biojavax.ga.util.GAToolsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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 s - in org.biojavax.ga.util.WeightedSetTest +[INFO] Running org.biojavax.SimpleRankedCrossRefTest +testToString +testGetCrossRef +testCompareTo +testGetRank +testHashCode +testEquals +testSetRank +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRankedCrossRefTest +[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 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: 0.011 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Running org.biojava.bio.MergeAnnotationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest +[INFO] Running org.biojava.bio.AnnotationTypeTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.AnnotationTypeTest +[INFO] Running org.biojava.bio.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 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: 0.035 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Running org.biojava.bio.dist.DistributionTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.DistributionTest +[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Running 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.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Running org.biojava.bio.dp.EmissionStateEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.dp.EmissionStateEventTest +[INFO] Running org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Running org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dp.MarkovModelEventTest [INFO] Running org.biojava.bio.program.phred.PhredToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.bio.program.phred.PhredToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 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: 0.085 s - in org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Running org.biojava.bio.seq.ProteinToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.ProteinToolsTest +[INFO] Running org.biojava.bio.seq.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.RNAToolsTest +[INFO] Running org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.seq.FilterUtilsTest +[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] Running org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.CircularSequenceTest [INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[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] Running org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.MergeFeatureHolderTest [INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.HashSequenceDBTest [INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 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: 0.005 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest [INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Running org.biojava.bio.seq.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.bio.seq.SeqSerializationTest -[INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.DNAToolsTest -[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] Running org.biojava.bio.seq.io.SeqIOToolsTest -idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.477 s - in org.biojava.bio.seq.io.SeqIOToolsTest -[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.59 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest -[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] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest [INFO] Running org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.CircularSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.CircularSequenceTest -[INFO] Running org.biojava.bio.seq.FilterUtilsTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.FilterUtilsTest -[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Running org.biojava.bio.seq.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.RNAToolsTest +[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.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.impl.GappedSequenceTest [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} @@ -2545,29 +2901,38 @@ 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: 0.003 s - in org.biojava.bio.seq.impl.ViewSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.impl.ViewSequenceTest [INFO] Running org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 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: 0.05 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest [INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[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.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.filter.FilterTransformerTest -[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] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.dp.MarkovModelEventTest -[INFO] Running org.biojava.bio.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.dp.DPSerializationTest -[INFO] Running org.biojava.bio.AnnotationTypeTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.AnnotationTypeTest -[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) - at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) - at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) - at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.seq.SeqSerializationTest +[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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: 0.047 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest +idb length: 79 +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.857 s - in org.biojava.bio.seq.io.SeqIOToolsTest +[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.226 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest +[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] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 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 s - in org.biojava.bio.proteomics.MassCalcTest +[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) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) @@ -2587,11 +2952,9 @@ 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: 0.005 s - in org.biojava.bio.proteomics.aaindex.AAindexTest -[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) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) +org.biojava.bio.seq.db.IllegalIDException: No table found with name test. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) @@ -2611,9 +2974,9 @@ 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) -org.biojava.bio.seq.db.IllegalIDException: No table found with name test. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) +java.lang.NullPointerException: table is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) @@ -2633,9 +2996,15 @@ 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) -java.lang.NullPointerException: table is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[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) + at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) + at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) + at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at junit.framework.TestCase.runTest(TestCase.java:177) @@ -2655,115 +3024,131 @@ 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: 0.005 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Running org.biojava.bio.proteomics.MassCalcTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.proteomics.MassCalcTest -[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.002 s - in org.biojava.bio.search.SeqContentPatternTest -[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.SimpleSeqSimilaritySearchHitTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Running 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.SimpleSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.symbol.SimpleSymbolEventTest -[INFO] Running 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.SymbolSerializationTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IntegerAlphabetTest -[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] Running org.biojava.bio.symbol.NameTokenizationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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] Running org.biojava.bio.symbol.CircularLocationTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.CircularLocationTest -[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] Running org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.proteomics.aaindex.AAindexTest [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: 0.017 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest -[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: 0.028 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest [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] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.082 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest [INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest symbolForIndex getAlphabet indexForSymbol -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[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] Running org.biojava.bio.symbol.PointLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.PointLocationTest +[INFO] Running org.biojava.bio.symbol.CircularLocationTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CircularLocationTest +[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.222 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IntegerAlphabetTest [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.MotifToolsTest -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.MotifToolsTest +[INFO] Running org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.913 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest [INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.symbol.SimpleCodonPrefTest [INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.AlphabetManagerTest +[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] Running org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Running org.biojava.bio.symbol.MotifToolsTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.MotifToolsTest +[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.RangeLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.RangeLocationTest +[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.CodonPrefToolsTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest [INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Running org.biojava.bio.symbol.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.701 s - in org.biojava.bio.symbol.SymbolListTest -[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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: 0.001 s - in org.biojava.bio.dist.DistributionTest -[INFO] Running org.biojava.bio.dist.DistributionToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.dist.DistributionToolsTest -[INFO] Running org.biojava.bio.dist.DistSerTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.dist.DistSerTest -[INFO] Running org.biojava.bio.MergeAnnotationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.MergeAnnotationTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet +[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] Running org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.ListToolsTest +[INFO] Running org.biojava.utils.SmallMapTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest +[INFO] Running org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 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: 0.036 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Running org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.automata.NfaTest +[INFO] Running org.biojava.utils.RepeatedCharSequenceTest +JAM +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.utils.regex.RegexTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.RegexTest +[INFO] Running org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Running org.biojava.utils.walker.WalkerTest +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: Overlaps([20,50]) +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) +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: 0.01 s - in org.biojava.utils.walker.WalkerTest +[INFO] Running org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Running org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.RegistryConfigurationTest [INFO] Running org.biojava.directory.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.directory.SystemRegistryTest [INFO] Running org.biojava.directory.OBDARegistryParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.OBDARegistryParserTest -[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] 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: 0.002 s - in org.biojava.naming.ObdaUriParserTest [INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest Reached Attributes: No attributes -Binding: urn -> org.biojava.naming.ObdaContext@36c83a +Binding: urn -> org.biojava.naming.ObdaContext@1d5a6fd Reached urn Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@14b8cb6 +Binding: open-bio.org -> org.biojava.naming.ObdaContext@1bcb4ad Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed @@ -2771,7 +3156,7 @@ module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } -Binding: type -> org.biojava.naming.ObdaContext@a930eb +Binding: type -> org.biojava.naming.ObdaContext@157524b Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types @@ -2780,7 +3165,7 @@ type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } -Binding: type -> org.biojava.naming.ObdaContext@ad709 +Binding: type -> org.biojava.naming.ObdaContext@4a287c Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this @@ -2789,7 +3174,7 @@ 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@1e8f5e8 +Binding: format -> org.biojava.naming.ObdaContext@dc86c6 Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this @@ -2800,7 +3185,7 @@ 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@1449465 +Binding: alphabet -> org.biojava.naming.ObdaContext@874f2c Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as @@ -2812,14 +3197,14 @@ 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@3dd5ce +Binding: format -> org.biojava.naming.ObdaContext@13b84bd 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@f7f59f +Binding: enzyme -> org.biojava.naming.ObdaContext@734eee Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from @@ -2835,29 +3220,29 @@ ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } -Binding: genbank -> org.biojava.naming.ObdaContext@e8051c +Binding: genbank -> org.biojava.naming.ObdaContext@191150 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@1125718 +Binding: swissprot -> org.biojava.naming.ObdaContext@fbd390 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@1016b11 +Binding: embl -> org.biojava.naming.ObdaContext@166b11e 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@f327e3 +Binding: alphabet -> org.biojava.naming.ObdaContext@1e68be2 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@3d0d44 +Binding: rna -> org.biojava.naming.ObdaContext@123999f Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry @@ -2865,7 +3250,7 @@ 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@1563e4c +Binding: protein -> org.biojava.naming.ObdaContext@118b738 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, @@ -2873,7 +3258,7 @@ 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@1d79214 +Binding: dna -> org.biojava.naming.ObdaContext@1c20984 Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry @@ -2881,372 +3266,23 @@ 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@14d32bf} +lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@1281d19} My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@e26986} +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1cddaf8} My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@1f2d6eb, format=org.biojava.naming.ObdaContext@16cd1e0, alphabet=org.biojava.naming.ObdaContext@a9a009} +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@1c50f52, format=org.biojava.naming.ObdaContext@cc1026, alphabet=org.biojava.naming.ObdaContext@44589a} My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@1785903, genbank=org.biojava.naming.ObdaContext@9349, swissprot=org.biojava.naming.ObdaContext@168a7f8, embl=org.biojava.naming.ObdaContext@faf1f4} +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@1e35070, genbank=org.biojava.naming.ObdaContext@216f01, swissprot=org.biojava.naming.ObdaContext@901203, embl=org.biojava.naming.ObdaContext@721583} My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.naming.ObdaInitialContextFactoryTest -[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 s - in org.biojava.naming.ObdaUriParserTest -[INFO] Running org.biojava.utils.ListToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 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 s - in org.biojava.utils.regex.RegexTest -[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Running org.biojava.utils.automata.NfaTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.automata.NfaTest -[INFO] Running org.biojava.utils.SmallMapTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest -[INFO] Running org.biojava.utils.RepeatedCharSequenceTest -JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.RepeatedCharSequenceTest -[INFO] Running org.biojava.utils.process.ExternalProcessTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.utils.process.ExternalProcessTest -[INFO] Running org.biojava.utils.process.AllTests -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.utils.process.AllTests -[INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.utils.walker.WalkerFactoryTest -[INFO] Running org.biojava.utils.walker.WalkerTest -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: Overlaps([20,50]) -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) -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: 0.008 s - in org.biojava.utils.walker.WalkerTest -[INFO] Running org.biojavax.EmptyRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testGetNote -testSetNoteSet -testContains -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testEquals -testContainsProperty -[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.EmptyRichAnnotationTest -[INFO] Running org.biojavax.ontology.SimpleComparableTripleTest -testGetSubject -testSetDescriptors -testToString -testGetSynonyms -testRemoveDescriptor -testCompareTo -testAddSynonym -testGetName -testGetOntology -testGetPredicate -testGetAnnotation -testGetDescription -testGetDescriptors -testHashCode -testAddDescriptor -testEquals -testGetObject -testRemoveSynonym -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.ontology.SimpleComparableTripleTest -[INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest -testSetTripleSet -testCreateTriple -testContainsTriple -testGetTerms -testCreateVariable -testContainsTerm -testGetTermSet -testSetDescription -testToString -testGetOrCreateTerm -testCompareTo -testGetTriples -testGetName -testGetTerm -testGetOrImportTerm -testGetTripleSet -testCreateTerm -testGetDescription -testSetTermSet -testHashCode -testDeleteTerm -testEquals -testGetOps -testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.ontology.SimpleComparableOntologyTest -[INFO] Running org.biojavax.ontology.SimpleComparableTermTest -testSetDescription -testGetRankedCrossRefs -testToString -testGetSynonyms -testCompareTo -testAddSynonym -testGetName -testGetOntology -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testRemoveRankedCrossRef -testGetDescription -testSetIdentifier -testHashCode -testEquals -testAddRankedCrossRef -testRemoveSynonym -testSetObsolete -testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ontology.SimpleComparableTermTest -[INFO] Running org.biojavax.SimpleRankedDocRefTest -testGetStart -testSetLocation -testToString -testGetDocumentReference -testCompareTo -testGetRank -testHashCode -testEquals -testGetEnd -testSetRank -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.SimpleRankedDocRefTest -[INFO] Running org.biojavax.DummyCrossReferenceResolverTest -testGetRemoteBioEntry -testGetRemoteSymbolList -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.DummyCrossReferenceResolverTest -[INFO] Running org.biojavax.SimpleRankedCrossRefTest -testToString -testGetCrossRef -testCompareTo -testGetRank -testHashCode -testEquals -testSetRank -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleRankedCrossRefTest -[INFO] Running org.biojavax.SimpleNamespaceTest -testGetAuthority -testSetDescription -testToString -testGetAcronym -testCompareTo -testGetName -testSetAuthority -testGetDescription -testHashCode -testSetAcronym -testEquals -testGetURI -testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleNamespaceTest -[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -testGetNameClass -testToString -testCompareTo -testSetNameClass -testGetName -testHashCode -testEquals -testSetName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 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: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest -[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Running org.biojavax.bio.seq.io.Bug2255Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.bio.seq.io.Bug2255Test -[INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest -Location 467: 467 -Location 340..565: 340..565 -Location <345..500: <345..500 -Location <1..888: <1..888 -Location (102.110): (102.110) -Location (23.45)..600: (23.45)..600 -Location (122.133)..(204.221): (122.133)..(204.221) -Location 123^124: 123^124 -Location 145^177: 145^177 -Location join(12..78,134..202): join(12..78,134..202) -Location complement(1..23): complement(1..23) -Location complement(join(2691..4571,4918..5163): complement(join(2691..4571,4918..5163)) -Location join(complement(4918..5163),complement(2691..4571)): complement(join(2691..4571,4918..5163)) -Location complement(34..(122.126)): complement(34..(122.126)) -Location complement((122.126)..34): complement((122.126)..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 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest -[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] 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] 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] Running org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.bio.seq.RichLocationToolsTest -[INFO] Running org.biojavax.bio.SimpleBioEntryTest -testGetNamespace -testGetNoteSet -testGetRankedDocRefs -testGetRelationships -testGetTaxon -testSetDescription -testGetAccession -testGetRankedCrossRefs -testToString -testCompareTo -testGetName -testRemoveComment -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testSetNoteSet -testRemoveRankedCrossRef -testRemoveRankedDocRef -testRemoveRelationship -testGetVersion -testGetDescription -testSetIdentifier -testGetComments -testHashCode -testEquals -testAddRankedCrossRef -testAddRankedDocRef -testAddRelationship -testSetDivision -testGetDivision -testSetTaxon -testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.SimpleBioEntryTest -[INFO] Running org.biojavax.SimpleDocRefAuthorTest -testIsConsortium -testToString -testCompareTo -testGetName -testHashCode -testEquals -testGetExtendedName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleDocRefAuthorTest -[INFO] Running org.biojavax.SimpleNoteTest -testGetValue -testToString -testCompareTo -testGetRank -testGetTerm -testHashCode -testEquals -testSetRank -testSetTerm -testSetValue -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleNoteTest -[INFO] Running org.biojavax.SimpleCrossRefTest -testGetNoteSet -testGetAccession -testToString -testCompareTo -testGetAnnotation -testSetNoteSet -testGetVersion -testHashCode -testGetDbname -testEquals -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleCrossRefTest -[INFO] Running org.biojavax.SimpleRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testToString -testGetNote -testSetNoteSet -testContains -testGetPropertys -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testRemoveProperty2 -testContainsProperty -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.SimpleRichAnnotationTest -[INFO] Running org.biojavax.SimpleDocRefTest -testGetTitle -testToString -testGetLocation -testSetCrossref -testGetCrossref -testCompareTo -testGetAuthors -testGetAuthorList -testHashCode -testSetRemark -testEquals -testGetCRC -testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleDocRefTest -[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] Running 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] 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] 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] Running org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.ProportionalSelectionTest -[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] 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] 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.SimpleCommentTest -testSetComment -testToString -testCompareTo -testGetRank -testHashCode -testGetComment -testEquals -testSetRank -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.SimpleCommentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.naming.ObdaInitialContextFactoryTest +[INFO] Running org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.ontology.OntologyTest +[INFO] Running org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 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] 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] [INFO] Results: [INFO] @@ -3276,11 +3312,11 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.364 s - in org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.63 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] [INFO] Results: [INFO] @@ -3311,7 +3347,7 @@ [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: 0.021 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3340,42 +3376,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.231 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.bio.program.sax.BlastTest -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.261 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.298 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.116 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.687 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.608 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.584 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.466 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.242 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.811 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.626 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.386 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.626 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.558 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.754 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: 0.096 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Running org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 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: 0.055 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest [INFO] [INFO] Results: [INFO] @@ -3404,32 +3440,32 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.program.fastq.FastqTest -[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 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: 0.041 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.program.fastq.FastqBuilderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.FastqTest +[INFO] Running org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.FastqVariantTest +[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] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.scf.SCFTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 s - in org.biojava.bio.program.scf.SCFTest [INFO] [INFO] Results: [INFO] @@ -3479,7 +3515,7 @@ [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: 0.123 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -3488,20 +3524,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.002 s] -[INFO] bytecode ........................................... SUCCESS [ 0.438 s] -[INFO] core ............................................... SUCCESS [ 35.376 s] -[INFO] alignment .......................................... SUCCESS [ 31.010 s] -[INFO] biosql ............................................. SUCCESS [ 30.606 s] -[INFO] blast .............................................. SUCCESS [ 36.621 s] -[INFO] sequencing ......................................... SUCCESS [ 31.084 s] -[INFO] gui ................................................ SUCCESS [ 0.047 s] -[INFO] phylo .............................................. SUCCESS [ 30.701 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.004 s] +[INFO] bytecode ........................................... SUCCESS [ 0.857 s] +[INFO] core ............................................... SUCCESS [ 40.482 s] +[INFO] alignment .......................................... SUCCESS [ 31.525 s] +[INFO] biosql ............................................. SUCCESS [ 30.819 s] +[INFO] blast .............................................. SUCCESS [ 42.519 s] +[INFO] sequencing ......................................... SUCCESS [ 31.761 s] +[INFO] gui ................................................ SUCCESS [ 0.071 s] +[INFO] phylo .............................................. SUCCESS [ 30.999 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 03:16 min -[INFO] Finished at: 2025-12-25T00:02:10Z +[INFO] Total time: 03:29 min +[INFO] Finished at: 2024-11-21T17:45:57Z [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -3641,20 +3677,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.7: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.271 s] -[INFO] bytecode ........................................... SUCCESS [ 0.034 s] -[INFO] core ............................................... SUCCESS [ 0.025 s] -[INFO] alignment .......................................... SUCCESS [ 0.020 s] -[INFO] biosql ............................................. SUCCESS [ 0.018 s] -[INFO] blast .............................................. SUCCESS [ 0.018 s] -[INFO] sequencing ......................................... SUCCESS [ 0.019 s] -[INFO] gui ................................................ SUCCESS [ 0.030 s] -[INFO] phylo .............................................. SUCCESS [ 0.019 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.535 s] +[INFO] bytecode ........................................... SUCCESS [ 0.061 s] +[INFO] core ............................................... SUCCESS [ 0.044 s] +[INFO] alignment .......................................... SUCCESS [ 0.036 s] +[INFO] biosql ............................................. SUCCESS [ 0.036 s] +[INFO] blast .............................................. SUCCESS [ 0.033 s] +[INFO] sequencing ......................................... SUCCESS [ 0.036 s] +[INFO] gui ................................................ SUCCESS [ 0.049 s] +[INFO] phylo .............................................. SUCCESS [ 0.037 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.614 s -[INFO] Finished at: 2025-12-25T00:02:12Z +[INFO] Total time: 1.165 s +[INFO] Finished at: 2024-11-21T17:46:00Z [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --base-directory=/build/reproducible-path/biojava-live-1.9.7\+dfsg --non-explore Analysing pom.xml... @@ -3704,12 +3740,14 @@ 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/45565/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/45565/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/101985 and its subdirectories -I: Current time: Wed Dec 24 12:02:20 -12 2025 -I: pbuilder-time-stamp: 1766620940 +I: removing directory /srv/workspace/pbuilder/45565 and its subdirectories +I: Current time: Fri Nov 22 07:46:15 +14 2024 +I: pbuilder-time-stamp: 1732211175