UnstableConsole Output

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 1:20:51 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)
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ncbitaxonomyServer ---
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)
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ncbitaxonomyServer ---
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)
[INFO] Surefire report directory: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/surefire-reports
mojoStarted org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ncbitaxonomyServer ---

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestSuite
2012-07-08 01:21:29,411 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-08 01:21:29,651 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-08 01:21:30,250 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
2012-07-08 01:21:30,289 [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: 7.419 sec <<< FAILURE!
2012-07-08 01:21:32,436 [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

[ERROR] There are test failures.

Please refer to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/surefire-reports for the individual test results.
mojoSucceeded org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[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] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ncbitaxonomyServer ---
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-tests.jar
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default)
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default) @ ncbitaxonomyServer ---
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.jar
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