| ||||||
| BUILD COMPLETE - build.31 | |
|---|---|
| Date of build: | 2012-03-28T06:26:30 |
| Time to build: | 22 minute(s) 31 second(s) |
| Last changed: | 2012-03-28T05:50:01 |
| Last log entry: | javadoc fixes, incorrect @param --> @throws |
| Build Artifacts |
| Modifications since last successful build: (3) | |||||
| modified | heuermh | /biojava-legacy/trunk/sequencing/src/main/java/org/biojava/bio/program/fastq/AbstractFastqReader.java | 9609 | 2012-03-28T05:50:01 | javadoc fixes, incorrect @param --> @throws |
| modified | heuermh | /biojava-legacy/trunk/sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java | 9609 | 2012-03-28T05:50:01 | javadoc fixes, incorrect @param --> @throws |
| modified | heuermh | /biojava-legacy/trunk/sequencing/src/main/java/org/biojava/bio/program/fastq/ParseListener.java | 9609 | 2012-03-28T05:50:01 | javadoc fixes, incorrect @param --> @throws |
| Initial Messages |
| [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] biojava-legacy [INFO] bytecode [INFO] core [INFO] alignment [INFO] biosql [INFO] blast [INFO] das [INFO] sequencing [INFO] gui [INFO] phylo [INFO] Searching repository for plugin with prefix: 'source'. [INFO] ------------------------------------------------------------------------ [INFO] Building biojava-legacy [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| site:attach-descriptor {execution: default-attach-descriptor} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava-legacy/1.8.3-SNAPSHOT/biojava-legacy-1.8.3-SNAPSHOT.pom [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code>
instead. |
| javadoc:jar {execution: default-cli} |
| [INFO] Not executing Javadoc as the project is not a Java classpath-capable package |
| site:attach-descriptor {execution: default-attach-descriptor} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/pom.xml to /home/andreas/.m2/repository/org/biojava/biojava-legacy/1.8.3-SNAPSHOT/biojava-legacy-1.8.3-SNAPSHOT.pom |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biojava-legacy/1.8.3-SNAPSHOT/biojava-legacy-1.8.3-SNAPSHOT.pom 7K uploaded (biojava-legacy-1.8.3-SNAPSHOT.pom) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biojava-legacy' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biojava-legacy:1.8.3-SNAPSHOT' [INFO] ------------------------------------------------------------------------ [INFO] Building bytecode [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/bytecode/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 44 source files to /opt/cruise/projects/biojava-legacy/bytecode/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] No tests to run. |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.6.0/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.3/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/1.4/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list. Ignored it. [INFO] 5 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.4.2/docs/api/package-list [WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/ByteCode.java:1351: warning - @param argument "lockVar" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/CodeContext.java:139: warning - @for.developer is an unknown tag. [WARNING] /opt/cruise/projects/biojava-legacy/bytecode/src/main/java/org/biojava/utils/bytecode/CodeField.java:79: warning - @return tag has no arguments. [INFO] Building jar: /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/bytecode/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] No tests to run. |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/bytecode/target/bytecode-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT.jar 91K uploaded (bytecode-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:bytecode' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:bytecode:1.8.3-SNAPSHOT' [INFO] Uploading project information for bytecode 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT-sources.jar 59K uploaded (bytecode-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/bytecode/1.8.3-SNAPSHOT/bytecode-1.8.3-SNAPSHOT-javadoc.jar 269K uploaded (bytecode-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building core [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/core/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 29 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 1063 source files to /opt/cruise/projects/biojava-legacy/core/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 51 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 148 source files to /opt/cruise/projects/biojava-legacy/core/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/core/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.utils.lsid.LifeScienceIdentifierTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec Running org.biojava.bio.symbol.SymbolListTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.025 sec Running org.biojavax.ga.functions.SimpleMutationFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojavax.SimpleDocRefAuthorTest testEquals testGetName testToString testCompareTo testHashCode testGetExtendedName testIsConsortium Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.286 sec Running org.biojava.bio.dp.EmissionStateEventTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojava.bio.search.SeqContentPatternTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojavax.EmptyRichAnnotationTest testEquals testContains testKeys testGetProperty testGetNote testSetProperty testSetNoteSet testAddNote testClear testRemoveProperty testRemoveNote testContainsProperty testGetNoteSet testAsMap Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.seq.FeatureFilterTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec Running org.biojavax.bio.seq.io.Bug2255Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec Running org.biojavax.SimpleDocRefTest testEquals testToString testGetLocation testCompareTo testHashCode testSetRemark testSetCrossref testGetAuthors testGetAuthorList testGetCRC testGetRemark testGetCrossref testGetTitle Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava.bio.seq.io.SmartSequenceBuilderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.166 sec Running org.biojava.bio.dist.DistributionTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava.bio.seq.filter.FilterTransformerTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec Running org.biojavax.ontology.SimpleComparableOntologyTest testEquals testGetName testToString testGetDescription testSetDescription testGetTerm testCompareTo testHashCode testContainsTerm testGetOrCreateTerm testGetOrImportTerm testCreateTerm testImportTerm testCreateTriple testDeleteTerm testGetTriples testSetTripleSet testGetTripleSet testGetTerms testSetTermSet testGetTermSet testContainsTriple testCreateVariable testGetOps Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.program.indexdb.IndexToolsTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec Running org.biojava.bio.seq.ProteinToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.bio.SimpleBioEntryTest testEquals testGetAnnotation testGetName testToString testGetDescription testSetDescription testSetNoteSet testGetNoteSet testCompareTo testHashCode testGetAccession testGetDivision testGetIdentifier testGetNamespace testGetTaxon testGetVersion testAddRankedCrossRef testRemoveRankedCrossRef testAddRankedDocRef testRemoveRankedDocRef testAddComment testRemoveComment testAddRelationship testRemoveRelationship testSetRankedCrossRefs testGetRankedCrossRefs testSetTaxon testGetComments testGetRankedDocRefs testGetRelationships testSetIdentifier testSetDivision Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec Running org.biojavax.SimpleRichAnnotationTest testContains testToString testKeys testGetProperty testGetNote testSetProperty testSetNoteSet testAddNote testClear testRemoveProperty testRemoveNote testContainsProperty testGetNoteSet testAsMap testGetPropertys testRemoveProperty2 Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec Running org.biojava.bio.symbol.PointLocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.MergeAnnotationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.dp.DPSerializationTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec Running org.biojava.bio.seq.io.SymbolListCharSequenceTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.CodonPrefToolsTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.seq.io.LocationFormatterTest Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 sec Running org.biojavax.bio.seq.io.Bug2249_2248Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.utils.walker.WalkerFactoryTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojavax.ga.functions.AbstractMutationFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.SimpleCrossRefTest testEquals testGetAnnotation testToString testSetNoteSet testGetNoteSet testCompareTo testHashCode testGetAccession testGetVersion testGetDbname Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.symbol.DoubleAlphabetTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec 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$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} 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} Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec Running org.biojava.bio.symbol.TestSoftMaskedAlphabet Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.symbol.IntegerAlphabetTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.SimpleSymbolListTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.bio.seq.io.EMBLFormatTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.utils.walker.WalkerTest Increasing counter: Overlaps([20,50]) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: ByClass(org.biojava.bio.seq.ComponentFeature) Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec Running org.biojava.bio.symbol.SimpleSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.utils.RepeatedCharSequenceTest JAM Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.seq.FilterUtilsTest Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojavax.bio.db.ncbi.GenbankRichSequenceDBTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.953 sec Running org.biojavax.SimpleRankedDocRefTest testEquals testToString testGetRank testSetRank testCompareTo testHashCode testGetDocumentReference testGetStart testGetEnd testSetLocation Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojavax.bio.seq.RichLocationToolsTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.impl.ViewSeqSerializationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec Running org.biojava.utils.regex.PatternCheckerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.MergeLocationTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.ontology.SimpleComparableTermTest testEquals testGetAnnotation testGetName testToString testGetDescription testSetDescription testCompareTo testHashCode testGetIdentifier testAddRankedCrossRef testRemoveRankedCrossRef testSetRankedCrossRefs testGetRankedCrossRefs testSetIdentifier testAddSynonym testRemoveSynonym testGetSynonyms testGetOntology testGetObsolete testSetObsolete Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.utils.ListToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.seq.db.HashSequenceDBTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.symbol.TranslationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteSymbolList testGetRemoteBioEntry Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.SimpleNamespaceTest testEquals testGetName testToString testGetDescription testSetDescription testCompareTo testHashCode testSetAcronym testSetAuthority testSetURI testGetAcronym testGetAuthority testGetURI Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.AnnotationTypeTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.seq.RNAToolsTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.directory.SystemRegistryTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 sec Running org.biojava.bio.seq.SeqSerializationTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.search.MaxMismatchPatternTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.NewSimpleAssemblyTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojava.bio.seq.io.filterxml.FilterXMLTest Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec Running org.biojava.bio.symbol.CompoundLocationTest Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojavax.ga.functions.ProportionalSelectionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava.bio.symbol.CircularLocationTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava.bio.seq.FeatureHolderUtilsTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.proteomics.IsoelectricPointCalcTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.symbol.AlphabetManagerTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojavax.bio.db.ncbi.GenpeptRichSequenceDBTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 sec Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.CrossProductTokenizationTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.AlphabetSerializationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec Running org.biojava.naming.ObdaUriParserTest oneName :trail lead: urn:obda.org:format:embl/ac Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.naming.ObdaInitialContextFactoryTest lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@6ad3acca} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@5aa33bb4} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@12a4d4e9, format=org.biojava.naming.ObdaContext@396168f, alphabet=org.biojava.naming.ObdaContext@72a3081f} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@2d6a6605, genbank=org.biojava.naming.ObdaContext@244fe98e, swissprot=org.biojava.naming.ObdaContext@7a6e7c41, embl=org.biojava.naming.ObdaContext@6b9fce32} My component is embl Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@1bab2037 Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@7fd00911 Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } Binding: type -> org.biojava.naming.ObdaContext@59298a3b Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types that are given IDs will be very general in nature, such as Sequence and File Format. All types are of type urn:open-bio.org:type:type. Any URN in the type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } Binding: type -> org.biojava.naming.ObdaContext@36325538 Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this may map to the types of data structures, or objects. Alternativel, it may map to a particular set of keys being present in a map, or a term in an 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@2278eb54 Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this type identify a format. The format can be used to choose how to treat a file. The format is not expected to be resolvable to a formal deffinition of the file structure using OBDA-supplied functionality. Different applications may chose to process a stream with the same format URN in different ways. This 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@30a1e97a Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as strings of characters. However, in differnt circumstances, the same characters can represent different things. For example, in DNA, the 't' character represents tyrosine. In Protein, this same character represents tryptophan. Associating alphabets with these sequences disambiguates their interpretation. 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@55e76187 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@49b41220 Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from the ebi at: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ For an example of a file in this format, see: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat The format is described more fully in ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } Binding: genbank -> org.biojava.naming.ObdaContext@4d1218ad 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@5f122d62 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@2261adb1 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@3ad25119 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@45ca5e7a Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides 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@6900bf61 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, read a biochemistry or genetics text book. It is common for protein sequences 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@3014af22 Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides 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. } Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojava.bio.symbol.GappedSymbolListTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava.bio.symbol.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec Running org.biojava.bio.seq.SimpleAssemblyTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojavax.ga.util.WeightedSetTest Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.bio.symbol.SimpleWobbleDistributionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.SimpleNoteTest testEquals testToString testGetTerm testSetTerm testGetValue testSetValue testGetRank testSetRank testCompareTo testHashCode Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.utils.SmallMapTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.dist.TranslatedDistributionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.bio.seq.SimpleRichFeatureTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.RangeLocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.directory.OBDARegistryParserTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.07 sec Running org.biojava.ontology.TripleImplTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.MotifToolsTest Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.utils.regex.RegexTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.CircularSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.SymbolSerializationTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava.bio.seq.DNAToolsTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.seq.db.TestHashSequenceDB Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojavax.bio.seq.io.GenbankFormatTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec Running org.biojava.bio.proteomics.MassCalcTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.dp.MarkovModelEventTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.dist.DistributionToolsTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec Running org.biojava.bio.symbol.LinearAlphabetIndexTest getAlphabet symbolForIndex indexForSymbol Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.SimpleCodonPrefTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.ontology.SimpleComparableTripleTest testEquals testGetAnnotation testGetName testToString testGetDescription testCompareTo testHashCode testAddSynonym testRemoveSynonym testGetSynonyms testGetOntology testGetSubject testGetObject testGetPredicate testAddDescriptor testRemoveDescriptor testGetDescriptors testSetDescriptors Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojavax.bio.seq.io.INSDseqFormatTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec Running org.biojava.bio.program.phred.PhredToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.bio.seq.io.UniProtFormatTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.seq.impl.SubSequenceTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.symbol.NameTokenizationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest testSetName testEquals testGetName testToString testCompareTo testHashCode testSetNameClass testGetNameClass Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.SimpleCommentTest testEquals testToString testGetComment testSetComment testGetRank testSetRank testCompareTo testHashCode Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec 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) Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.MergeFeatureHolderTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.utils.process.ExternalProcessTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 sec Running org.biojavax.SimpleRankedCrossRefTest testEquals testToString testGetRank testSetRank testCompareTo testHashCode testGetCrossRef Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 Testing SP read Testing SP read Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.243 sec Running org.biojava.bio.dist.DistSerTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec Running org.biojava.bio.seq.impl.GappedSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojavax.bio.seq.io.Bug2250_2256Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec Running org.biojavax.CrossReferenceResolutionExceptionTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.ontology.ParseOBOFileTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 sec Running org.biojava.ontology.TermImplTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.BetweenLocationTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec Running org.biojavax.ga.impl.SimplePopulationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.IndexedNoAmbPackTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.ontology.OntologyTest Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.molbio.RestrictionEnzymeTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.utils.automata.NfaTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.directory.RegistryConfigurationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.ga.impl.SimpleOrganismTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.ga.util.GAToolsTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec 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:326) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava.bio.seq.io.MSFAlignmentFormatTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Results : Tests run: 881, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2ee/1.4/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list. Ignored it. [INFO] 8 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.4.2/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.3/docs/api/package-list [WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojava/bio/molbio/RestrictionMapper.java:119: warning - Tag @author cannot be used in constructor documentation. It can only be used in the following types of documentation: overview, package, class/interface. [WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojava/bio/alignment/SimpleAlignment.java:303: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojava/bio/seq/db/GenbankSequenceDB.java:58: warning - @George is an unknown tag. [WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojava/bio/seq/db/GenpeptSequenceDB.java:44: warning - @George is an unknown tag. [WARNING] /opt/cruise/projects/biojava-legacy/core/src/main/java/org/biojavax/bio/seq/io/GenbankLocationParser.java:52: warning - @authour is an unknown tag. [INFO] Building jar: /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 29 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 51 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/core/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.utils.lsid.LifeScienceIdentifierTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec Running org.biojava.bio.symbol.SymbolListTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.984 sec Running org.biojavax.ga.functions.SimpleMutationFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojavax.SimpleDocRefAuthorTest testEquals testGetName testToString testCompareTo testHashCode testGetExtendedName testIsConsortium Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.28 sec Running org.biojava.bio.dp.EmissionStateEventTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec Running org.biojava.bio.search.SeqContentPatternTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.EmptyRichAnnotationTest testEquals testContains testKeys testGetProperty testGetNote testSetProperty testSetNoteSet testAddNote testClear testRemoveProperty testRemoveNote testContainsProperty testGetNoteSet testAsMap Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.seq.FeatureFilterTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec Running org.biojavax.bio.seq.io.Bug2255Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec Running org.biojavax.SimpleDocRefTest testEquals testToString testGetLocation testCompareTo testHashCode testSetRemark testSetCrossref testGetAuthors testGetAuthorList testGetCRC testGetRemark testGetCrossref testGetTitle Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.bio.seq.io.SmartSequenceBuilderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.161 sec Running org.biojava.bio.dist.DistributionTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava.bio.seq.filter.FilterTransformerTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec Running org.biojavax.ontology.SimpleComparableOntologyTest testEquals testGetName testToString testGetDescription testSetDescription testGetTerm testCompareTo testHashCode testContainsTerm testGetOrCreateTerm testGetOrImportTerm testCreateTerm testImportTerm testCreateTriple testDeleteTerm testGetTriples testSetTripleSet testGetTripleSet testGetTerms testSetTermSet testGetTermSet testContainsTriple testCreateVariable testGetOps Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest testEquals Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.program.indexdb.IndexToolsTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec Running org.biojava.bio.seq.ProteinToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.bio.SimpleBioEntryTest testEquals testGetName testGetAnnotation testToString testGetDescription testSetDescription testSetNoteSet testGetNoteSet testCompareTo testHashCode testGetAccession testGetDivision testGetIdentifier testGetNamespace testGetTaxon testGetVersion testAddRankedCrossRef testRemoveRankedCrossRef testAddRankedDocRef testRemoveRankedDocRef testAddComment testRemoveComment testAddRelationship testRemoveRelationship testSetRankedCrossRefs testGetRankedCrossRefs testSetTaxon testGetComments testGetRankedDocRefs testGetRelationships testSetIdentifier testSetDivision Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec Running org.biojavax.SimpleRichAnnotationTest testContains testToString testKeys testGetProperty testGetNote testSetProperty testSetNoteSet testAddNote testClear testRemoveProperty testRemoveNote testContainsProperty testGetNoteSet testAsMap testGetPropertys testRemoveProperty2 Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.symbol.PointLocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.MergeAnnotationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.dp.DPSerializationTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec Running org.biojava.bio.seq.io.SymbolListCharSequenceTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.CodonPrefToolsTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.bio.seq.io.LocationFormatterTest Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 sec Running org.biojavax.bio.seq.io.Bug2249_2248Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.utils.walker.WalkerFactoryTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojavax.ga.functions.AbstractMutationFunctionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.SimpleCrossRefTest testEquals testGetAnnotation testToString testSetNoteSet testGetNoteSet testCompareTo testHashCode testGetAccession testGetVersion testGetDbname Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava.bio.symbol.DoubleAlphabetTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec 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$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} 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} Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec Running org.biojava.bio.symbol.TestSoftMaskedAlphabet Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.symbol.IntegerAlphabetTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.SimpleSymbolListTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.bio.seq.io.EMBLFormatTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.utils.walker.WalkerTest Increasing counter: Overlaps([20,50]) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) Increasing counter: Overlaps([20,50]) Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) OverlapsLocation: Overlaps([20,50]) Feature: ByClass(org.biojava.bio.seq.StrandedFeature) Feature: ByClass(org.biojava.bio.seq.ComponentFeature) Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec Running org.biojava.bio.symbol.SimpleSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.utils.RepeatedCharSequenceTest JAM Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.seq.FilterUtilsTest Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojavax.bio.db.ncbi.GenbankRichSequenceDBTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 sec Running org.biojavax.SimpleRankedDocRefTest testEquals testToString testGetRank testSetRank testCompareTo testHashCode testGetDocumentReference testGetStart testGetEnd testSetLocation Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojavax.bio.seq.RichLocationToolsTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.seq.impl.ViewSeqSerializationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec Running org.biojava.utils.regex.PatternCheckerTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.MergeLocationTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojavax.ontology.SimpleComparableTermTest testEquals testGetName testGetAnnotation testToString testGetDescription testSetDescription testCompareTo testHashCode testGetIdentifier testAddRankedCrossRef testRemoveRankedCrossRef testSetRankedCrossRefs testGetRankedCrossRefs testSetIdentifier testAddSynonym testRemoveSynonym testGetSynonyms testGetOntology testGetObsolete testSetObsolete Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.utils.ListToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.seq.db.HashSequenceDBTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.symbol.TranslationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.DummyCrossReferenceResolverTest testGetRemoteSymbolList testGetRemoteBioEntry Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.SimpleNamespaceTest testEquals testGetName testToString testGetDescription testSetDescription testCompareTo testHashCode testSetAcronym testSetAuthority testSetURI testGetAcronym testGetAuthority testGetURI Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.bio.AnnotationTypeTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.seq.RNAToolsTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec Running org.biojava.directory.SystemRegistryTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec Running org.biojava.bio.seq.SeqSerializationTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.search.MaxMismatchPatternTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.seq.NewSimpleAssemblyTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec Running org.biojava.bio.seq.io.filterxml.FilterXMLTest Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec Running org.biojava.bio.symbol.CompoundLocationTest Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojavax.ga.functions.ProportionalSelectionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec Running org.biojava.bio.symbol.CircularLocationTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec Running org.biojava.bio.seq.FeatureHolderUtilsTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.proteomics.IsoelectricPointCalcTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.AlphabetManagerTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojavax.bio.db.ncbi.GenpeptRichSequenceDBTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.CrossProductTokenizationTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.symbol.AlphabetSerializationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec Running org.biojava.naming.ObdaUriParserTest oneName :trail lead: urn:obda.org:format:embl/ac Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.naming.ObdaInitialContextFactoryTest lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@6ef53890} My component is urn:open-bio.org:format:embl lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@12a4d4e9} My component is open-bio.org:format:embl lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@396168f, format=org.biojava.naming.ObdaContext@72a3081f, alphabet=org.biojava.naming.ObdaContext@2d6a6605} My component is format:embl lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@244fe98e, genbank=org.biojava.naming.ObdaContext@7a6e7c41, swissprot=org.biojava.naming.ObdaContext@6b9fce32, embl=org.biojava.naming.ObdaContext@489a6bd1} My component is embl Reached Attributes: No attributes Binding: urn -> org.biojava.naming.ObdaContext@7fd00911 Reached urn Attributes: No attributes Binding: open-bio.org -> org.biojava.naming.ObdaContext@33037ca5 Reached urn:open-bio.org Attributes: {description=description: This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the module obda-specs in the cvs repository located at pub.open-bio.org:/home/repository/obf-common. } Binding: type -> org.biojava.naming.ObdaContext@36325538 Reached urn:open-bio.org:type Attributes: {description=description: The namespace for URNs that identify data types. It is expected that the types that are given IDs will be very general in nature, such as Sequence and File Format. All types are of type urn:open-bio.org:type:type. Any URN in the type namespace that is not of this type is not conforming to the OBDA specification for this namespace. } Binding: type -> org.biojava.naming.ObdaContext@2278eb54 Reached urn:open-bio.org:type:type Attributes: {description=description: The OBDA URN that identifies the concept of 'type'. In a given language, this may map to the types of data structures, or objects. Alternativel, it may map to a particular set of keys being present in a map, or a term in an 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@30a1e97a Reached urn:open-bio.org:type:format Attributes: {description=description: A file format. Many file formats are used in bioinformatics. Entities of this type identify a format. The format can be used to choose how to treat a file. The format is not expected to be resolvable to a formal deffinition of the file structure using OBDA-supplied functionality. Different applications may chose to process a stream with the same format URN in different ways. This 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@55e76187 Reached urn:open-bio.org:type:alphabet Attributes: {description=description: A biological sequence alphabet. Biological sequences are often represented as strings of characters. However, in differnt circumstances, the same characters can represent different things. For example, in DNA, the 't' character represents tyrosine. In Protein, this same character represents tryptophan. Associating alphabets with these sequences disambiguates their interpretation. 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@49b41220 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@4d1218ad Reached urn:open-bio.org:format:enzyme Attributes: {description=description: The Enzyme database entry format. The enzyme database can be downloaded from the ebi at: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ For an example of a file in this format, see: ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat The format is described more fully in ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt } Binding: genbank -> org.biojava.naming.ObdaContext@5f122d62 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@2261adb1 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@3ad25119 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@45ca5e7a 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@6900bf61 Reached urn:open-bio.org:alphabet:rna Attributes: {description=description: The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides 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@3014af22 Reached urn:open-bio.org:alphabet:protein Attributes: {description=description: The protein alphabet. Proteins are composed from amino-acids. To find out more, read a biochemistry or genetics text book. It is common for protein sequences 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@1df5f9d7 Reached urn:open-bio.org:alphabet:dna Attributes: {description=description: The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry or genetics introductory textbook to find out more. Commonly, the nucleotides 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. } Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojava.bio.symbol.GappedSymbolListTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.bio.symbol.UkkonenSuffixTreeTest Adding symbol list taccaccagga$ Adding symbol list taccaccagga$ Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 sec Running org.biojava.bio.seq.SimpleAssemblyTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojavax.ga.util.WeightedSetTest Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.symbol.SimpleWobbleDistributionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.SimpleNoteTest testEquals testToString testGetTerm testSetTerm testGetValue testSetValue testGetRank testSetRank testCompareTo testHashCode Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.utils.SmallMapTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.dist.TranslatedDistributionTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.bio.seq.SimpleRichFeatureTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.RangeLocationTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.directory.OBDARegistryParserTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.605 sec Running org.biojava.ontology.TripleImplTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.symbol.MotifToolsTest Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.utils.regex.RegexTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.seq.CircularSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.symbol.SymbolSerializationTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec Running org.biojava.bio.seq.DNAToolsTest Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.seq.db.TestHashSequenceDB Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojavax.bio.seq.io.GenbankFormatTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec Running org.biojava.bio.proteomics.MassCalcTest Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.dp.MarkovModelEventTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.dist.DistributionToolsTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec Running org.biojava.bio.symbol.LinearAlphabetIndexTest getAlphabet symbolForIndex indexForSymbol Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.SimpleCodonPrefTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojavax.ontology.SimpleComparableTripleTest testEquals testGetName testGetAnnotation testToString testGetDescription testCompareTo testHashCode testAddSynonym testRemoveSynonym testGetSynonyms testGetOntology testGetSubject testGetObject testGetPredicate testAddDescriptor testRemoveDescriptor testGetDescriptors testSetDescriptors Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojavax.bio.seq.io.INSDseqFormatTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec Running org.biojava.bio.program.phred.PhredToolsTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.bio.seq.io.UniProtFormatTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.seq.impl.SubSequenceTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.symbol.NameTokenizationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest testSetName testEquals testGetName testToString testCompareTo testHashCode testSetNameClass testGetNameClass Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojavax.SimpleCommentTest testEquals testToString testGetComment testSetComment testGetRank testSetRank testCompareTo testHashCode Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec 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) Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.seq.MergeFeatureHolderTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.utils.process.ExternalProcessTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec Running org.biojavax.SimpleRankedCrossRefTest testEquals testToString testGetRank testSetRank testCompareTo testHashCode testGetCrossRef Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.seq.io.SeqIOToolsTest idb length: 79 Testing SP read Testing SP read Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.342 sec Running org.biojava.bio.dist.DistSerTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec Running org.biojava.bio.seq.impl.GappedSequenceTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojavax.bio.seq.io.Bug2250_2256Test Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 sec Running org.biojavax.CrossReferenceResolutionExceptionTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.ontology.ParseOBOFileTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec Running org.biojava.ontology.TermImplTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec Running org.biojava.bio.symbol.BetweenLocationTest Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec Running org.biojavax.ga.impl.SimplePopulationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.bio.symbol.IndexedNoAmbPackTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojava.ontology.OntologyTest Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.bio.molbio.RestrictionEnzymeTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec Running org.biojava.utils.automata.NfaTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.directory.RegistryConfigurationTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.ga.impl.SimpleOrganismTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec Running org.biojavax.ga.util.GAToolsTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec 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:326) 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 sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec Running org.biojava.bio.seq.io.MSFAlignmentFormatTest at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Results : Tests run: 881, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/core/target/core-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT.jar 2413K uploaded (core-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:core:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:core' [INFO] Uploading project information for core 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT-sources.jar 2035K uploaded (core-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/core/1.8.3-SNAPSHOT/core-1.8.3-SNAPSHOT-javadoc.jar 13383K uploaded (core-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building alignment [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/alignment/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/alignment/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 14 source files to /opt/cruise/projects/biojava-legacy/alignment/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 4 source files to /opt/cruise/projects/biojava-legacy/alignment/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/alignment/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.alignment.SubstitutionMatrixTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.223 sec Running org.biojava.bio.alignment.FlexibleAlignmentTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 sec Results : Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2ee/1.4/docs/api/package-list. Ignored it. [INFO] 16 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.5.0/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.3/docs/api/package-list [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AbstractULAlignment.java:207: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:57: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:392: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:532: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:524: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:327: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:335: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:343: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:351: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:359: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:367: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/AlignmentPair.java:226: warning - @param argument "queryLength" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-legacy/alignment/src/main/java/org/biojava/bio/alignment/FlexibleAlignment.java:270: warning - @return tag has no arguments. [INFO] Building jar: /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/alignment/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/alignment/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.alignment.SubstitutionMatrixTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.223 sec Running org.biojava.bio.alignment.FlexibleAlignmentTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 sec Results : Tests run: 3, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/alignment/target/alignment-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT.jar 36K uploaded (alignment-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:alignment:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:alignment' [INFO] Uploading project information for alignment 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT-sources.jar 33K uploaded (alignment-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/alignment/1.8.3-SNAPSHOT/alignment-1.8.3-SNAPSHOT-javadoc.jar 216K uploaded (alignment-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building biosql [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/biosql/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 35 source files to /opt/cruise/projects/biojava-legacy/biosql/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 2 source files to /opt/cruise/projects/biojava-legacy/biosql/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/biosql/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.4.2/docs/api/package-list. Ignored it. [INFO] 2 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.3/docs/api/package-list [INFO] Building jar: /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/biosql/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/biosql/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/biosql/target/biosql-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT.jar 156K uploaded (biosql-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:biosql:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:biosql' [INFO] Uploading project information for biosql 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT-sources.jar 135K uploaded (biosql-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/biosql/1.8.3-SNAPSHOT/biosql-1.8.3-SNAPSHOT-javadoc.jar 692K uploaded (biosql-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building blast [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/blast/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 56 source files to /opt/cruise/projects/biojava-legacy/blast/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 22 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 19 source files to /opt/cruise/projects/biojava-legacy/blast/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/blast/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.522 sec Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 sec Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.278 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.406 sec Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 sec Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.774 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.038 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.92 sec Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 sec Running org.biojava.bio.program.sax.BlastTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.611 sec Running org.biojava.bio.program.sax.blastxml.BlastXMLTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.784 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.635 sec Results : Tests run: 118, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.6.0/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.4.2/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.3/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/1.4/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list. Ignored it. [INFO] 1 warning [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [INFO] Building jar: /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 22 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/blast/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.523 sec Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.375 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.264 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.401 sec Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 sec Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.762 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.029 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.915 sec Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 sec Running org.biojava.bio.program.sax.BlastTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.61 sec Running org.biojava.bio.program.sax.blastxml.BlastXMLTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.783 sec Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 sec Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.636 sec Results : Tests run: 118, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/blast/target/blast-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT.jar 178K uploaded (blast-1.8.3-SNAPSHOT.jar) [INFO] Uploading project information for blast 1.8.3-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:blast:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:blast' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT-sources.jar 128K uploaded (blast-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/blast/1.8.3-SNAPSHOT/blast-1.8.3-SNAPSHOT-javadoc.jar 316K uploaded (blast-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building das [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/das/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/das/src/main/resources [INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from maven2-repository.dev.java.net [INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from maven-repository.dev.java.net [INFO] snapshot org.biojava:biojava:3.0-alpha2-SNAPSHOT: checking for updates from biojava-maven-repo Downloading: http://www.biojava.org/download/maven//org/biojava/biojava/3.0-alpha2-SNAPSHOT/biojava-3.0-alpha2-SNAPSHOT.pom |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 91 source files to /opt/cruise/projects/biojava-legacy/das/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 9 source files to /opt/cruise/projects/biojava-legacy/das/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/das/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.dasobert.TestRegistry unsupported capability: das1:cors unsupported capability: das1:unknown-segment unsupported capability: das1:cors unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:cors unsupported capability: das1:cors unsupported capability: das1:cors unsupported capability: das1:bigfile-bam unsupported capability: das1:cors unsupported capability: das1:bigfile-bam unsupported capability: das1:bigfile-bam unsupported capability: das1:cors unsupported capability: das1:cors Das2SourceHandler: source size: 2098 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.116 sec Running org.biojava.dasobert.TestInteractionParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava.dasobert.TestExternalSource Das2SourceHandler: source size: 33 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.251 sec Running org.biojava.dasobert.TestSisyphusServer Mar 27, 2012 11:39:13 PM org.biojava.dasobert.das.AlignmentThread retrieveAlignments INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468 object: CONSTRUCT:35 object: CONSTRUCT:36 object: CONSTRUCT:37 object: CONSTRUCT:38 object: CONSTRUCT:39 object: CONSTRUCT:40 object: CONSTRUCT:41 object: CONSTRUCT:42 object: CONSTRUCT:43 object: CONSTRUCT:44 object: CONSTRUCT:45 object: CONSTRUCT:46 object: CONSTRUCT:47 object: CONSTRUCT:48 object: CONSTRUCT:49 object: CONSTRUCT:50 object: CONSTRUCT:51 object: CONSTRUCT:52 object: CONSTRUCT:53 object: CONSTRUCT:54 object: CONSTRUCT:55 number of blocks: 4 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.552 sec Running org.biojava.dasobert.TestSequenceParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec Running org.biojava.dasobert.server.TestServers started getInteractions method java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:150) at java.net.SocketInputStream.read(SocketInputStream.java:121) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:641) at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:589) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1319) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:163) at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:136) at org.biojava.dasobert.das.InteractionThread.retrieveInteractions(InteractionThread.java:163) at org.biojava.dasobert.das.InteractionThread.getInteractions(InteractionThread.java:134) at org.biojava.dasobert.server.TestServers.testInteractionServer(TestServers.java:86) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Mar 27, 2012 11:39:30 PM org.biojava.dasobert.das.SequenceThread retrieveSequence INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225 MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFVVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.441 sec Running org.biojava.dasobert.TestUCSCFeatures Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec Running org.biojava.dasobert.TestSourcesParse unsupported capability: das1:dna Das2SourceHandler: source size: 267 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec Running org.biojava.dasobert.TestFeatureParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Results : Tests run: 10, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.6.0/docs/api/package-list. Ignored it. [INFO] 10 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.5.0/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2ee/1.4/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/org/biojava/dasobert/das2/io/DASRegistryCoordinatesReaderXML.java:56: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/org/biojava/dasobert/das/Capabilities.java:58: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Detail.java:143: warning - @return tag has no arguments. [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:178: warning - @param argument "interactors" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interaction.java:187: warning - @param argument "ref" is not a parameter name. [WARNING] /opt/cruise/projects/biojava-legacy/das/src/main/java/de/mpg/mpiinf/ag3/dasmi/model/Interactor.java:237: warning - @returntrue is an unknown tag. [INFO] Building jar: /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/das/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/das/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.dasobert.TestRegistry unsupported capability: das1:cors unsupported capability: das1:unknown-segment unsupported capability: das1:cors unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:unknown-segment unsupported capability: das1:cors unsupported capability: das1:cors unsupported capability: das1:cors unsupported capability: das1:bigfile-bam unsupported capability: das1:cors unsupported capability: das1:bigfile-bam unsupported capability: das1:bigfile-bam unsupported capability: das1:cors unsupported capability: das1:cors Das2SourceHandler: source size: 2098 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.407 sec Running org.biojava.dasobert.TestInteractionParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec Running org.biojava.dasobert.TestExternalSource Das2SourceHandler: source size: 33 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.879 sec Running org.biojava.dasobert.TestSisyphusServer Mar 27, 2012 11:41:36 PM org.biojava.dasobert.das.AlignmentThread retrieveAlignments INFO: requesting alignment http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query%3DAL10057468 object: CONSTRUCT:35 object: CONSTRUCT:36 object: CONSTRUCT:37 object: CONSTRUCT:38 object: CONSTRUCT:39 object: CONSTRUCT:40 object: CONSTRUCT:41 object: CONSTRUCT:42 object: CONSTRUCT:43 object: CONSTRUCT:44 object: CONSTRUCT:45 object: CONSTRUCT:46 object: CONSTRUCT:47 object: CONSTRUCT:48 object: CONSTRUCT:49 object: CONSTRUCT:50 object: CONSTRUCT:51 object: CONSTRUCT:52 object: CONSTRUCT:53 object: CONSTRUCT:54 object: CONSTRUCT:55 number of blocks: 4 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.82 sec Running org.biojava.dasobert.TestSequenceParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec Running org.biojava.dasobert.server.TestServers started getInteractions method java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) at java.net.SocketInputStream.read(SocketInputStream.java:150) at java.net.SocketInputStream.read(SocketInputStream.java:121) at java.io.BufferedInputStream.fill(BufferedInputStream.java:235) at java.io.BufferedInputStream.read1(BufferedInputStream.java:275) at java.io.BufferedInputStream.read(BufferedInputStream.java:334) at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:641) at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:589) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1319) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468) at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:163) at org.biojava.dasobert.util.HttpConnectionTools.getInputStream(HttpConnectionTools.java:136) at org.biojava.dasobert.das.InteractionThread.retrieveInteractions(InteractionThread.java:163) at org.biojava.dasobert.das.InteractionThread.getInteractions(InteractionThread.java:134) at org.biojava.dasobert.server.TestServers.testInteractionServer(TestServers.java:86) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at junit.framework.TestCase.runTest(TestCase.java:168) at junit.framework.TestCase.runBare(TestCase.java:134) at junit.framework.TestResult$1.protect(TestResult.java:110) at junit.framework.TestResult.runProtected(TestResult.java:128) at junit.framework.TestResult.run(TestResult.java:113) at junit.framework.TestCase.run(TestCase.java:124) at junit.framework.TestSuite.runTest(TestSuite.java:232) at junit.framework.TestSuite.run(TestSuite.java:227) at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:83) at org.apache.maven.surefire.junit4.JUnit4TestSet.execute(JUnit4TestSet.java:59) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) Mar 27, 2012 11:41:52 PM org.biojava.dasobert.das.SequenceThread retrieveSequence INFO: requesting sequence from http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/sequence?segment=P50225 MELIQDTSRPPLEYVKGVPLIKYFAEALGPLQSFQARPDDLLISTYPKSGTTWVSQILDMIYQGGDLEKCHRAPIFMRVPFLEFKAPGIPSGMETLKDTPAPRLLKTHLPLALLPQTLLDQKVKVVYVARNAKDVAVSYYHFYHMAKVHPEPGTWDSFLEKFMVGEVSYGSWYQHVQEWWELSRTHPVLYLFYEDMKENPKREIQKILEFVGRSLPEETVDFVVQHTSFKEMKKNPMTNYTTVPQEFMDHSISPFMRKGMAGDWKTTFTVAQNERFDADYAEKMAGCSLSFRSEL Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.711 sec Running org.biojava.dasobert.TestUCSCFeatures Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec Running org.biojava.dasobert.TestSourcesParse unsupported capability: das1:dna Das2SourceHandler: source size: 267 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec Running org.biojava.dasobert.TestFeatureParse Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec Results : Tests run: 10, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/das/target/das-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT.jar 170K uploaded (das-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:das:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:das' [INFO] Uploading project information for das 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT-sources.jar 142K uploaded (das-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/das/1.8.3-SNAPSHOT/das-1.8.3-SNAPSHOT-javadoc.jar 841K uploaded (das-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building sequencing [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/sequencing/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/sequencing/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 33 source files to /opt/cruise/projects/biojava-legacy/sequencing/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 74 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 13 source files to /opt/cruise/projects/biojava-legacy/sequencing/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/sequencing/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.program.fastq.SolexaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec Running org.biojava.bio.program.fastq.FastqBuilderTest Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec Running org.biojava.bio.program.fastq.SangerFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava.bio.program.fastq.SangerFastqReaderTest Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec Running org.biojava.bio.program.fastq.FastqToolsTest Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.445 sec Running org.biojava.bio.program.fastq.SolexaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec Running org.biojava.bio.program.fastq.FastqVariantTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Running org.biojava.bio.program.fastq.FastqTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.program.fastq.StreamingFastqParserTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec Results : Tests run: 167, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2ee/1.4/docs/api/package-list. Ignored it. [INFO] 4 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.3/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list [INFO] Building jar: /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/sequencing/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-legacy/sequencing/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 74 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/sequencing/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojava.bio.program.fastq.SolexaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 sec Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec Running org.biojava.bio.program.fastq.FastqBuilderTest Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec Running org.biojava.bio.program.fastq.SangerFastqWriterTest Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec Running org.biojava.bio.program.fastq.SangerFastqReaderTest Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec Running org.biojava.bio.program.fastq.FastqToolsTest Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec Running org.biojava.bio.program.fastq.SolexaFastqReaderTest Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec Running org.biojava.bio.program.fastq.FastqVariantTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Running org.biojava.bio.program.fastq.FastqTest Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec Running org.biojava.bio.program.fastq.StreamingFastqParserTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec Results : Tests run: 167, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/sequencing/target/sequencing-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT.jar 83K uploaded (sequencing-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:sequencing' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:sequencing:1.8.3-SNAPSHOT' [INFO] Uploading project information for sequencing 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT-sources.jar 69K uploaded (sequencing-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/sequencing/1.8.3-SNAPSHOT/sequencing-1.8.3-SNAPSHOT-javadoc.jar 412K uploaded (sequencing-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building gui [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/gui/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 99 source files to /opt/cruise/projects/biojava-legacy/gui/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] No tests to run. |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.4.2/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.3/docs/api/package-list. Ignored it. [INFO] 3 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/package-list [WARNING] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.5.0/docs/api/package-list [INFO] Building jar: /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/gui/src/test/resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] No tests to run. |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/gui/target/gui-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT.jar 223K uploaded (gui-1.8.3-SNAPSHOT.jar) [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:gui' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:gui:1.8.3-SNAPSHOT' [INFO] Uploading project information for gui 1.8.3-SNAPSHOT [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT-sources.jar 170K uploaded (gui-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/gui/1.8.3-SNAPSHOT/gui-1.8.3-SNAPSHOT-javadoc.jar 1092K uploaded (gui-1.8.3-SNAPSHOT-javadoc.jar) [INFO] ------------------------------------------------------------------------ [INFO] Building phylo [INFO] task-segment: [clean, install, source:jar, javadoc:jar, deploy] [INFO] ------------------------------------------------------------------------ |
| clean:clean {execution: default-clean} |
| [INFO] Deleting /opt/cruise/projects/biojava-legacy/phylo/target |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/phylo/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Compiling 37 source files to /opt/cruise/projects/biojava-legacy/phylo/target/classes |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Compiling 1 source file to /opt/cruise/projects/biojava-legacy/phylo/target/test-classes |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/phylo/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 sec Results : Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT.jar |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT.jar [INFO] Preparing source:jar [INFO] No goals needed for project - skipping |
| source:jar {execution: default-cli} |
| [INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT-sources.jar [WARNING] DEPRECATED [aggregate]: since 2.5. Use the goals <code>javadoc:aggregate</code> and <code>javadoc:test-aggregate</code> instead. |
| javadoc:jar {execution: default-cli} |
| [ERROR] Error fetching link: http://java.sun.com/j2se/1.6.0/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.4.2/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2se/1.3/docs/api/package-list. Ignored it. [ERROR] Error fetching link: http://java.sun.com/j2ee/sdk_1.3/techdocs/api/package-list. Ignored it. [INFO] 2 warnings [WARNING] Javadoc Warnings [WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [WARNING] /opt/cruise/projects/biojava-legacy/phylo/src/main/java/org/biojavax/bio/phylo/io/nexus/TreesBlock.java:640: warning - Tag @link: can't find getTreeAsJGraphT(java.lang.String) in org.biojavax.bio.phylo.io.nexus.TreesBlock [INFO] Building jar: /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT-javadoc.jar |
| resources:resources {execution: default-resources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/cruise/projects/biojava-legacy/phylo/src/main/resources |
| compiler:compile {execution: default-compile} |
| [INFO] Nothing to compile - all classes are up to date |
| resources:testResources {execution: default-testResources} |
| [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources |
| compiler:testCompile {execution: default-testCompile} |
| [INFO] Nothing to compile - all classes are up to date |
| surefire:test {execution: default-test} |
| [INFO] Surefire report directory: /opt/cruise/projects/biojava-legacy/phylo/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 sec Results : Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 |
| jar:jar {execution: default-jar} |
| install:install {execution: default-install} |
| [INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT-sources.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT-sources.jar [INFO] Installing /opt/cruise/projects/biojava-legacy/phylo/target/phylo-1.8.3-SNAPSHOT-javadoc.jar to /home/andreas/.m2/repository/org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT-javadoc.jar |
| deploy:deploy {execution: default-deploy} |
| [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT.jar 75K uploaded (phylo-1.8.3-SNAPSHOT.jar) [INFO] Uploading project information for phylo 1.8.3-SNAPSHOT [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'snapshot org.biojava:phylo:1.8.3-SNAPSHOT' [INFO] Retrieving previous metadata from biojava-maven-repo [INFO] Uploading repository metadata for: 'artifact org.biojava:phylo' [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT-sources.jar 60K uploaded (phylo-1.8.3-SNAPSHOT-sources.jar) [INFO] Retrieving previous build number from biojava-maven-repo Uploading: scp://portal.open-bio.org/home/websites/biojava.org/html/static/download/maven//org/biojava/phylo/1.8.3-SNAPSHOT/phylo-1.8.3-SNAPSHOT-javadoc.jar 427K uploaded (phylo-1.8.3-SNAPSHOT-javadoc.jar) [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] ------------------------------------------------------------------------ [INFO] biojava-legacy ........................................ SUCCESS [1:03.914s] [INFO] bytecode .............................................. SUCCESS [1:27.826s] [INFO] core .................................................. SUCCESS [5:00.040s] [INFO] alignment ............................................. SUCCESS [1:46.200s] [INFO] biosql ................................................ SUCCESS [1:38.323s] [INFO] blast ................................................. SUCCESS [1:33.343s] [INFO] das ................................................... SUCCESS [3:30.314s] [INFO] sequencing ............................................ SUCCESS [2:14.258s] [INFO] gui ................................................... SUCCESS [2:54.790s] [INFO] phylo ................................................. SUCCESS [1:19.547s] [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 22 minutes 30 seconds [INFO] Finished at: Tue Mar 27 23:49:02 PDT 2012 [INFO] Final Memory: 130M/2244M [INFO] ------------------------------------------------------------------------ |
| Unit Tests: (0) | |||
| No Tests Run | |||
| This project doesn't have any tests | |||
|
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