UnstableConsole Output

Started by an SCM change
Started by upstream project "phyloutils" build number 8
Building remotely on i-6001ac18 in workspace /media/ephemeral0/workspace/ncbitaxonomy
$ hg clone --rev default --noupdate ssh://jenkins@dev.davidsoergel.com//home/hg/ncbitaxonomy /media/ephemeral0/workspace/ncbitaxonomy
adding changesets
adding manifests
adding file changes
added 274 changesets with 797 changes to 114 files
[ncbitaxonomy] $ hg update --rev default
61 files updated, 0 files merged, 0 files removed, 0 files unresolved
[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 58100
<===[JENKINS REMOTING CAPACITY]===>channel started
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 -e clean source:jar package jar:test-jar
[INFO] Error stacktraces are turned on.
[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://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/mojo/maven-metadata.xml
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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 07, 2012 5:09:22 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] [WARNING] JAR will be empty - no content was marked for inclusion!

[INFO] --- maven-jar-plugin:2.4:jar (default) @ ncbitaxonomy ---
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/target/ncbitaxonomy-0.91-SNAPSHOT.jar
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli)
[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
[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
projectStarted edu.berkeley.compbio:ncbitaxonomyClient:0.91-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ncbitaxonomyClient 0.91-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/com/caucho/hessian/3.1.3/hessian-3.1.3.pom
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Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120707.170808-11.pom (7 KB at 42.4 KB/sec)
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Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/maven-metadata.xml
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Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/stats/0.93-SNAPSHOT/maven-metadata.xml
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/springframework/spring/2.5.6/spring-2.5.6.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/com/caucho/hessian/3.1.3/hessian-3.1.3.jar
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Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-20120707.170808-11.jar (2793 KB at 2134.7 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 07, 2012 5:09:38 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)
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ncbitaxonomyClient ---
[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
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: 2.058 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] --- maven-jar-plugin:2.4:jar (default-jar) @ ncbitaxonomyClient ---
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT.jar
mojoSucceeded org.apache.maven.plugins:maven-jar-plugin:2.4(default-jar)
mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default)
[INFO] Building jar: /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-tests.jar
[INFO] 
[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)
[WARNING] Artifact edu.berkeley.compbio:ncbitaxonomyClient:test-jar:tests:0.91-SNAPSHOT already attached to project, ignoring duplicate
[INFO] 
[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] ------------------------------------------------------------------------
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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 07, 2012 5:10:25 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.
[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)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/aspectj/aspectjtools/1.6.7/aspectjtools-1.6.7.pom
mojoStarted org.codehaus.mojo:aspectj-maven-plugin:1.3(default)
[INFO] 
[INFO] --- aspectj-maven-plugin:1.3:compile (default) @ ncbitaxonomyServer ---
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/aspectj/aspectjtools/1.6.7/aspectjtools-1.6.7.pom (881 B at 2.5 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-api/2.0/maven-reporting-api-2.0.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-api/2.0/maven-reporting-api-2.0.pom (2 KB at 4.1 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting/2.0/maven-reporting-2.0.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting/2.0/maven-reporting-2.0.pom (504 B at 0.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-sink-api/1.0-alpha-4/doxia-sink-api-1.0-alpha-4.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-sink-api/1.0-alpha-4/doxia-sink-api-1.0-alpha-4.pom (2 KB at 5.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-impl/2.0/maven-reporting-impl-2.0.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-impl/2.0/maven-reporting-impl-2.0.pom (3 KB at 0.7 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/commons-validator/commons-validator/1.1.4/commons-validator-1.1.4.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/commons-validator/commons-validator/1.1.4/commons-validator-1.1.4.pom (168 B at 0.3 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/oro/oro/2.0.7/oro-2.0.7.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/oro/oro/2.0.7/oro-2.0.7.pom (141 B at 0.5 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-core/1.0-alpha-4/doxia-core-1.0-alpha-4.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-core/1.0-alpha-4/doxia-core-1.0-alpha-4.pom (5 KB at 1.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/aspectj/aspectjtools/1.6.7/aspectjtools-1.6.7.jar
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-api/2.0/maven-reporting-api-2.0.jar
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-impl/2.0/maven-reporting-impl-2.0.jar
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-sink-api/1.0-alpha-4/doxia-sink-api-1.0-alpha-4.jar
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/reporting/maven-reporting-api/2.0/maven-reporting-api-2.0.jar (7 KB at 26.0 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/commons-validator/commons-validator/1.1.4/commons-validator-1.1.4.jar
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/oro/oro/2.0.7/oro-2.0.7.jar
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-core/1.0-alpha-4/doxia-core-1.0-alpha-4.jar
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Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/doxia/doxia-sink-api/1.0-alpha-4/doxia-sink-api-1.0-alpha-4.jar (5 KB at 4.4 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar (223 KB at 159.1 KB/sec)
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/aspectj/aspectjtools/1.6.7/aspectjtools-1.6.7.jar (8707 KB at 6223.7 KB/sec)
[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] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources

[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ncbitaxonomyServer ---
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)
[INFO] Compiling 2 source files to /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/test-classes
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ncbitaxonomyServer ---
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)
[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
mojoStarted org.codehaus.mojo:aspectj-maven-plugin:1.3(default)
[INFO] 
[INFO] --- aspectj-maven-plugin:1.3:test-compile (default) @ ncbitaxonomyServer ---
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
2012-07-07 17:11:04,022 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-07 17:11:04,104 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-07 17:11:04,105 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2012-07-07 17:11:04,130 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2012-07-07 17:11:04,131 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2012-07-07 17:11:04,131 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2012-07-07 17:11:04,132 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2012-07-07 17:11:04,136 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2012-07-07 17:11:04,136 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2012-07-07 17:11:04,137 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2012-07-07 17:11:04,137 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2012-07-07 17:11:04,138 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2012-07-07 17:11:04,138 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2012-07-07 17:11:04,138 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2012-07-07 17:11:04,139 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2012-07-07 17:11:04,139 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2012-07-07 17:11:04,142 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2012-07-07 17:11:04,143 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2012-07-07 17:11:04,143 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2012-07-07 17:11:04,143 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2012-07-07 17:11:04,236 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2012-07-07 17:11:04,236 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2012-07-07 17:11:04,237 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2012-07-07 17:11:04,237 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2012-07-07 17:11:04,238 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2012-07-07 17:11:04,238 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2012-07-07 17:11:04,239 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2012-07-07 17:11:04,242 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2012-07-07 17:11:04,242 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2012-07-07 17:11:04,243 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2012-07-07 17:11:04,243 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2012-07-07 17:11:04,244 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2012-07-07 17:11:04,244 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2012-07-07 17:11:04,245 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2012-07-07 17:11:04,245 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2012-07-07 17:11:04,246 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2012-07-07 17:11:04,250 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2012-07-07 17:11:04,250 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2012-07-07 17:11:04,251 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2012-07-07 17:11:04,251 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2012-07-07 17:11:04,251 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2012-07-07 17:11:04,252 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2012-07-07 17:11:04,252 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2012-07-07 17:11:04,253 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2012-07-07 17:11:04,253 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2012-07-07 17:11:04,254 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2012-07-07 17:11:04,256 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2012-07-07 17:11:04,256 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2012-07-07 17:11:04,257 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2012-07-07 17:11:04,261 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2012-07-07 17:11:04,261 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2012-07-07 17:11:04,262 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2012-07-07 17:11:04,262 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2012-07-07 17:11:04,262 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2012-07-07 17:11:04,263 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2012-07-07 17:11:04,263 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2012-07-07 17:11:04,263 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2012-07-07 17:11:04,266 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2012-07-07 17:11:04,266 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2012-07-07 17:11:04,266 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2012-07-07 17:11:04,267 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2012-07-07 17:11:04,274 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2012-07-07 17:11:04,274 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2012-07-07 17:11:04,275 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
2012-07-07 17:11:05,254 [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: 6.323 sec <<< FAILURE!
2012-07-07 17:11:07,229 [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] Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.0.1/maven-archiver-2.0.1.pom

[INFO] --- maven-war-plugin:2.0:war (default-war) @ ncbitaxonomyServer ---
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.0.1/maven-archiver-2.0.1.pom (912 B at 0.2 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven/2.0.1/maven-2.0.1.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven/2.0.1/maven-2.0.1.pom (12 KB at 52.5 KB/sec)
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-profile/2.0.1/maven-profile-2.0.1.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-model/2.0.1/maven-model-2.0.1.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-utils/1.0.5/plexus-utils-1.0.5.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-utils/1.0.5/plexus-utils-1.0.5.pom (918 B at 3.3 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-artifact-manager/2.0.1/maven-artifact-manager-2.0.1.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-artifact-manager/2.0.1/maven-artifact-manager-2.0.1.pom (2 KB at 7.4 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-repository-metadata/2.0.1/maven-repository-metadata-2.0.1.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-artifact/2.0.1/maven-artifact-2.0.1.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-archiver/1.0-alpha-4/plexus-archiver-1.0-alpha-4.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-archiver/1.0-alpha-4/plexus-archiver-1.0-alpha-4.pom (439 B at 2.9 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-components/1.1.4/plexus-components-1.1.4.pom
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.0.1/maven-archiver-2.0.1.jar
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Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/codehaus/plexus/plexus-archiver/1.0-alpha-4/plexus-archiver-1.0-alpha-4.jar (128 KB at 423.2 KB/sec)
[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 [32.604s]
[INFO] ncbitaxonomyClient ................................ SUCCESS [41.476s]
[INFO] ncbitaxonomyServer ................................ SUCCESS [1:17.466s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:46.650s
[INFO] Finished at: Sat Jul 07 17:11:31 UTC 2012
[INFO] Final Memory: 24M/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$ncbitaxonomyServer/builds/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT.pom
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-07_13-08-28/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$ncbitaxonomyServer/builds/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT-sources.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyServer/target/ncbitaxonomyServer-tests.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyServer/builds/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomyServer/0.91-SNAPSHOT/ncbitaxonomyServer-0.91-SNAPSHOT-tests.jar
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[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$ncbitaxonomyClient/builds/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/ncbitaxonomyClient/target/ncbitaxonomyClient-0.91-SNAPSHOT-sources.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomyClient/builds/2012-07-07_13-08-28/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$ncbitaxonomyClient/builds/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomyClient/0.91-SNAPSHOT/ncbitaxonomyClient-0.91-SNAPSHOT-tests.jar
[JENKINS] Archiving /media/ephemeral0/workspace/ncbitaxonomy/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ncbitaxonomy/modules/edu.berkeley.compbio$ncbitaxonomy/builds/2012-07-07_13-08-28/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/2012-07-07_13-08-28/archive/edu.berkeley.compbio/ncbitaxonomy/0.91-SNAPSHOT/ncbitaxonomy-0.91-SNAPSHOT-tests.jar
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channel stopped
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Finished: SUCCESS