UnstableConsole Output

Started by upstream project "phyloutils" build number 7
Building remotely on i-94d275ec in workspace /media/ephemeral0/workspace/ncbitaxonomy
[ncbitaxonomy] $ hg showconfig paths.default
[ncbitaxonomy] $ hg pull --rev default
[ncbitaxonomy] $ hg update --clean --rev default
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
[ncbitaxonomy] $ hg --config extensions.purge= clean --all
[ncbitaxonomy] $ hg log --rev . --template {node}
[ncbitaxonomy] $ hg log --rev . --template {rev}
[ncbitaxonomy] $ hg log --rev bbd8573409c1ad3d8972974726192a463ec07acf
[ncbitaxonomy] $ hg log --template "<changeset node='{node}' author='{author|xmlescape}' rev='{rev}' date='{date}'><msg>{desc|xmlescape}</msg><added>{file_adds|stringify|xmlescape}</added><deleted>{file_dels|stringify|xmlescape}</deleted><files>{files|stringify|xmlescape}</files><parents>{parents}</parents></changeset>\n" --rev default:0 --follow --prune bbd8573409c1ad3d8972974726192a463ec07acf
 your Apache Maven build is setup to use a config with id org.jenkinsci.plugins.configfiles.maven.MavenSettingsConfig1337980147845 but cannot find the config
Parsing POMs
Downloaded artifact http://dev.davidsoergel.com/nexus/content/repositories/snapshots//com/davidsoergel/basepom/0.99-SNAPSHOT/maven-metadata.xml
[ncbitaxonomy] $ /usr/java/default/bin/java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/Maven/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/Maven/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 45101
channel started
<===[JENKINS REMOTING CAPACITY]===>log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
Executing Maven:  -B -f /media/ephemeral0/workspace/ncbitaxonomy/pom.xml -U -cpu -e clean source:jar package jar:test-jar
[INFO] Error stacktraces are turned on.
[WARNING] Command line option -cpu is deprecated and will be removed in future Maven versions.
[INFO] Scanning for projects...
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/basepom/0.99-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/basepom/0.99-SNAPSHOT/maven-metadata.xml (809 B at 0.6 KB/sec)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ncbitaxonomy
[INFO] ncbitaxonomyClient
[INFO] ncbitaxonomyServer
Projects to build: [MavenProject: edu.berkeley.compbio:ncbitaxonomy:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/pom.xml, MavenProject: edu.berkeley.compbio:ncbitaxonomyClient:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/pom.xml, MavenProject: edu.berkeley.compbio:ncbitaxonomyServer:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/pom.xml]
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/mojo/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml (11 KB at 9.6 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/mojo/maven-metadata.xml (21 KB at 21.8 KB/sec)
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml (11 KB at 7.6 KB/sec)
Downloaded: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml (21 KB at 12.1 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml
Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml (632 B at 6.7 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-source-plugin/maven-metadata.xml (632 B at 5.8 KB/sec)
projectStarted edu.berkeley.compbio:ncbitaxonomy:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ncbitaxonomy 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) @ ncbitaxonomy ---
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) @ ncbitaxonomy ---
[INFO] Skipping cobertura mojo for project with packaging type 'pom'
mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean)
Jul 06, 2012 8:29:40 PM 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) @ ncbitaxonomy ---
mojoSucceeded org.apache.maven.plugins:maven-source-plugin:2.1.2(default-cli)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default)
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ncbitaxonomy ---
[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/target/ncbitaxonomy-0.91-SNAPSHOT-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) @ ncbitaxonomy ---
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) @ ncbitaxonomy ---
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli)
projectSucceeded edu.berkeley.compbio:ncbitaxonomy:0.91-SNAPSHOT[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/target/ncbitaxonomy-0.91-SNAPSHOT.jar
[WARNING] JAR will be empty - no content was marked for inclusion!
[WARNING] Artifact edu.berkeley.compbio:ncbitaxonomy:test-jar:tests:0.91-SNAPSHOT already attached to project, ignoring duplicate

projectStarted edu.berkeley.compbio:ncbitaxonomyClient:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ncbitaxonomyClient 0.91-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/dsutils/1.04-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/dsutils/1.04-SNAPSHOT/maven-metadata.xml (2 KB at 11.4 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/maven-metadata.xml (2 KB at 2.8 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10.pom (7 KB at 16.6 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/conja/1.06-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/conja/1.06-SNAPSHOT/maven-metadata.xml (2 KB at 1.4 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/maven-metadata.xml (2 KB at 9.5 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/stats/0.93-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/stats/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 3.7 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10.jar
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10.jar (2793 KB at 6539.0 KB/sec)
mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ncbitaxonomyClient ---
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) @ ncbitaxonomyClient ---
mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean)
Jul 06, 2012 8:29:58 PM 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) @ ncbitaxonomyClient ---
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-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) @ ncbitaxonomyClient ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
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) @ ncbitaxonomyClient ---
[INFO] Compiling 10 source files to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/classes
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/src/test/resources

[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ncbitaxonomyClient ---
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) @ ncbitaxonomyClient ---
[INFO] Compiling 1 source file to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/test-classes
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)
mojoStarted org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ncbitaxonomyClient ---
[INFO] Surefire report directory: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestSuite
Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.439 sec

Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

mojoSucceeded org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[JENKINS] Recording test results
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default-jar)
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT.jar

[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ncbitaxonomyClient ---
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default-jar)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default)
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-tests.jar

[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ncbitaxonomyClient ---
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) @ ncbitaxonomyClient ---
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli)
[INFO] [WARNING] Artifact edu.berkeley.compbio:ncbitaxonomyClient:test-jar:tests:0.91-SNAPSHOT already attached to project, ignoring duplicate

[INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ ncbitaxonomyClient ---
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli)
projectSucceeded edu.berkeley.compbio:ncbitaxonomyClient:0.91-SNAPSHOT
projectStarted edu.berkeley.compbio:ncbitaxonomyServer:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ncbitaxonomyServer 0.91-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/maven-metadata.xml (2 KB at 9.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/springjpautils-0.9-20120706.202205-15.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/springjpautils-0.9-20120706.202205-15.pom (7 KB at 13.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10-tests.jar
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/trees-1.023-20120706.202634-15-tests.jar
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/springjpautils-0.9-20120706.202205-15.jar
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/trees-1.023-20120706.202634-15-tests.jar (28 KB at 138.9 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/springjpautils/0.9-SNAPSHOT/springjpautils-0.9-20120706.202205-15.jar (11 KB at 56.5 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120706.202817-10-tests.jar (11 KB at 50.4 KB/sec)
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 06, 2012 8:30:39 PM 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.
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)[INFO] Copying 4 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] Compiling 2 source files to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/test-classes

[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ncbitaxonomyServer ---
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
2012-07-06 20:31:16,733 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-06 20:31:16,837 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-06 20:31:17,437 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
2012-07-06 20:31:17,574 [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: 7.343 sec <<< FAILURE!
2012-07-06 20:31:19,703 [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] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-tests.jar

[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] 
[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
sessionEnded
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ncbitaxonomy ...................................... SUCCESS [36.377s]
[INFO] ncbitaxonomyClient ................................ SUCCESS [42.506s]
[INFO] ncbitaxonomyServer ................................ SUCCESS [58.664s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:36.041s
[INFO] Finished at: Fri Jul 06 20:31:35 UTC 2012
[INFO] Final Memory: 25M/60M
[INFO] ------------------------------------------------------------------------
Projects to build: [MavenProject: edu.berkeley.compbio:ncbitaxonomy:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/pom.xml, MavenProject: edu.berkeley.compbio:ncbitaxonomyClient:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/pom.xml, MavenProject: edu.berkeley.compbio:ncbitaxonomyServer:0.91-SNAPSHOT @ /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/pom.xml]
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT.pom
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT.war
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-sources.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT-sources.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-tests.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT-tests.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyClient/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT.pom
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyClient/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-sources.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyClient/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT-sources.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-tests.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyClient/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT-tests.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomy/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomy/0.91-SNAPSHOT/ncbitaxonomy-0.91-SNAPSHOT.pom
[JENKINS] Re-archiving /media/ephemeral0/workspace/ncbitaxonomy/target/ncbitaxonomy-0.91-SNAPSHOT.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/target/ncbitaxonomy-0.91-SNAPSHOT-tests.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomy/builds/2012-07-06_16-28-32/archive/edu.berkeley.compbio/ncbitaxonomy/0.91-SNAPSHOT/ncbitaxonomy-0.91-SNAPSHOT-tests.jar
Waiting for Jenkins to finish collecting data
channel stopped
Sending e-mails to: dev@davidsoergel.com
Finished: SUCCESS