projectStarted edu.berkeley.compbio:ncbitaxonomyServer:0.91-SNAPSHOT [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ncbitaxonomyServer 0.91-SNAPSHOT [INFO] ------------------------------------------------------------------------ mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean) [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ncbitaxonomyServer --- mojoSucceeded org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean) mojoStarted org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean) [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ ncbitaxonomyServer --- mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean) Jul 08, 2012 1:04:18 AM hudson.maven.ExecutedMojo <init> WARNING: Failed to getClass for org.apache.maven.plugin.source.SourceJarMojo mojoStarted org.apache.maven.plugins:maven-source-plugin:2.1.2(default-cli) [INFO] [INFO] --- maven-source-plugin:2.1.2:jar (default-cli) @ ncbitaxonomyServer --- [INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-sources.jar mojoSucceeded org.apache.maven.plugins:maven-source-plugin:2.1.2(default-cli) mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources) [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ncbitaxonomyServer --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 4 resources mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources) mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile) [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ncbitaxonomyServer --- [INFO] Compiling 16 source files to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/classes mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile) mojoStarted org.codehaus.mojo:aspectj-maven-plugin:1.3(default) [INFO] [INFO] --- aspectj-maven-plugin:1.3:compile (default) @ ncbitaxonomyServer --- [WARNING] bad version number found in /home/ec2-user/.m2/repository/org/aspectj/aspectjrt/1.6.10/aspectjrt-1.6.10.jar expected 1.6.7 found 1.6.10 [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean, com.davidsoergel.trees.AbstractRootedPhylogeny$MutualExclusionResolutionMode))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:412) advised by before advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:60(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean, com.davidsoergel.trees.AbstractRootedPhylogeny$MutualExclusionResolutionMode))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:412) advised by afterThrowing advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:67(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean, com.davidsoergel.trees.AbstractRootedPhylogeny$MutualExclusionResolutionMode))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:412) advised by afterReturning advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:77(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean, com.davidsoergel.trees.AbstractRootedPhylogeny$MutualExclusionResolutionMode))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:412) advised by after advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:82(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:421) advised by before advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:60(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:421) advised by afterThrowing advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:67(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:421) advised by afterReturning advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:77(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(com.davidsoergel.trees.BasicRootedPhylogeny edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl.extractTreeWithLeafIDs(java.util.Set, boolean, boolean))' in Type 'edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImpl' (NcbiCiccarelliHybridServiceImpl.java:421) advised by after advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:82(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(boolean edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode.isLeaf())' in Type 'edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode' (NcbiTaxonomyNode.java:636) advised by before advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:60(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(boolean edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode.isLeaf())' in Type 'edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode' (NcbiTaxonomyNode.java:636) advised by afterThrowing advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:67(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(boolean edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode.isLeaf())' in Type 'edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode' (NcbiTaxonomyNode.java:636) advised by afterReturning advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:77(from AbstractTransactionAspect.aj)) [INFO] Join point 'method-execution(boolean edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode.isLeaf())' in Type 'edu.berkeley.compbio.ncbitaxonomy.jpa.NcbiTaxonomyNode' (NcbiTaxonomyNode.java:636) advised by after advice from 'org.springframework.transaction.aspectj.AnnotationTransactionAspect' (spring-aspects-2.5.6.jar!AbstractTransactionAspect.class:82(from AbstractTransactionAspect.aj)) mojoSucceeded org.codehaus.mojo:aspectj-maven-plugin:1.3(default) mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)[debug] execute contextualize [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ncbitaxonomyServer ---[INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources) mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile) [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ncbitaxonomyServer --- [INFO] Compiling 2 source files to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/test-classes mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile) mojoStarted org.codehaus.mojo:aspectj-maven-plugin:1.3(default) [INFO] [INFO] --- aspectj-maven-plugin:1.3:test-compile (default) @ ncbitaxonomyServer --- [WARNING] bad version number found in /home/ec2-user/.m2/repository/org/aspectj/aspectjrt/1.6.10/aspectjrt-1.6.10.jar expected 1.6.7 found 1.6.10 mojoSucceeded org.codehaus.mojo:aspectj-maven-plugin:1.3(default) mojoStarted org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test) [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ncbitaxonomyServer --- [INFO] Surefire report directory: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/surefire-reports ------------------------------------------------------- T E S T S ------------------------------------------------------- Running TestSuite 2012-07-08 01:04:55,985 [main] INFO edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false 2012-07-08 01:04:56,155 [main] INFO com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny 2012-07-08 01:04:57,068 [main] INFO edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false 2012-07-08 01:04:57,223 [main] INFO com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny/ancestorPathCache Tests run: 17, Failures: 13, Errors: 0, Skipped: 0, Time elapsed: 8.507 sec <<< FAILURE! 2012-07-08 01:05:00,458 [Thread-1] WARN com.davidsoergel.dsutils.CacheManager - AccumulatingMap did not change: /tmp/testCacheedu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny/ancestorPathCache Results : Failed tests: edu.berkeley.compbio.phyloutils.HybridRootedPhylogeny(com.davidsoergel.trees.TaxonMergingPhylogenyInterfaceTest) edu.berkeley.compbio.phyloutils.HybridRootedPhylogeny(com.davidsoergel.trees.TaxonMergingPhylogenyInterfaceTest) ciccarelliTreeIsConvertedToTaxIdTree(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) exactDistanceBetweenWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest): No such element: 5664 extractTreeWithLeafIDsForNonCiccarelliNodesWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) extractTreeWithLeafIDsThrowsExceptionForCiccarelliNodesWhenArgumentsAreNotAllLeaves(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest): (..) extractTreeWithLeafIDsWorksForCiccarelliNodes(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) findTaxIDByNameWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) findTaxIDByUnknownNameThrowsException(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest): (..) minDistanceBetweenWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) nearestKnownAncestorIntegerWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) nearestKnownAncestorStringWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest) findTaxonByNameWorks(edu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogenyTest) Tests run: 17, Failures: 13, Errors: 0, Skipped: 0 mojoSucceeded org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)[ERROR] There are test failures. Please refer to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/surefire-reports for the individual test results. [JENKINS] Recording test results mojoStarted org.apache.maven.plugins:maven-war-plugin:2.0(default-war) [INFO] [INFO] --- maven-war-plugin:2.0:war (default-war) @ ncbitaxonomyServer --- [INFO] Exploding webapp... [INFO] Copy webapp webResources to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer [INFO] Assembling webapp ncbitaxonomyServer in /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer [INFO] Generating war /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.war [INFO] Building war: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.war mojoSucceeded org.apache.maven.plugins:maven-war-plugin:2.0(default-war) mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default) [INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-tests.jar [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ncbitaxonomyServer --- mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default) mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default) [INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.jar [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ ncbitaxonomyServer --- mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default) mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli) [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ ncbitaxonomyServer --- [WARNING] Artifact edu.berkeley.compbio:ncbitaxonomyServer:test-jar:tests:0.91-SNAPSHOT already attached to project, ignoring duplicate mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli) projectSucceeded edu.berkeley.compbio:ncbitaxonomyServer:0.91-SNAPSHOT