SuccessConsole Output

Started by an SCM change
Building remotely on i-561eb32e in workspace /media/ephemeral0/workspace/phyloutils
$ hg clone --rev default --noupdate ssh://jenkins@dev.davidsoergel.com//home/hg/phyloutils /media/ephemeral0/workspace/phyloutils
adding changesets
adding manifests
adding file changes
added 414 changesets with 1522 changes to 131 files
[phyloutils] $ hg update --rev default
58 files updated, 0 files merged, 0 files removed, 0 files unresolved
[phyloutils] $ hg log --rev . --template {node}
[phyloutils] $ hg log --rev . --template {rev}
[phyloutils] $ hg log --rev d55deaa8562916b1bccc27debbadf4975e462629
[phyloutils] $ 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 d55deaa8562916b1bccc27debbadf4975e462629
 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
[phyloutils] $ /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 34743
<===[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/phyloutils/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 1.7 KB/sec)
Projects to build: [MavenProject: edu.berkeley.compbio:phyloutils:0.92-SNAPSHOT @ /media/ephemeral0/workspace/phyloutils/pom.xml]
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/plugins/maven-metadata.xml
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Downloading: http://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml
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projectStarted edu.berkeley.compbio:phyloutils:0.92-SNAPSHOT
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/dsutils/1.04-SNAPSHOT/maven-metadata.xml
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.92-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/conja/1.06-SNAPSHOT/maven-metadata.xml
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Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/com/caucho/hessian/3.1.3/hessian-3.1.3.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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Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.023-SNAPSHOT/trees-1.023-20120706.202634-15-tests.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 471.6 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) @ phyloutils ---
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) @ phyloutils ---
mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean)
Jul 07, 2012 5:07:20 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) @ phyloutils ---
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.4.1/maven-archiver-2.4.1.pom
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.4.1/maven-archiver-2.4.1.pom (4 KB at 82.1 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.4.1/maven-archiver-2.4.1.jar
Downloaded: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.4.1/maven-archiver-2.4.1.jar (20 KB at 316.5 KB/sec)
[INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.92-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) @ phyloutils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] Compiling 35 source files to /media/ephemeral0/workspace/phyloutils/target/classes
[WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[11,45] NotImplementedException is internal proprietary API and may be removed in a future release
[WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[277,12] NotImplementedException is internal proprietary API and may be removed in a future release
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) @ phyloutils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)
[INFO] Compiling 4 source files to /media/ephemeral0/workspace/phyloutils/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) @ phyloutils ---
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) @ phyloutils ---
[INFO] Surefire report directory: /media/ephemeral0/workspace/phyloutils/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestSuite
2012-07-07 17:07:43,028 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-07 17:07:43,109 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-07 17:07:43,115 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2012-07-07 17:07:43,247 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2012-07-07 17:07:43,250 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2012-07-07 17:07:43,251 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2012-07-07 17:07:43,251 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2012-07-07 17:07:43,252 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2012-07-07 17:07:43,253 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2012-07-07 17:07:43,253 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2012-07-07 17:07:43,311 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2012-07-07 17:07:43,311 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2012-07-07 17:07:43,311 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2012-07-07 17:07:43,311 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2012-07-07 17:07:43,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2012-07-07 17:07:43,313 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2012-07-07 17:07:43,316 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2012-07-07 17:07:43,317 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2012-07-07 17:07:43,317 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2012-07-07 17:07:43,318 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2012-07-07 17:07:43,342 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2012-07-07 17:07:43,343 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2012-07-07 17:07:43,346 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2012-07-07 17:07:43,346 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2012-07-07 17:07:43,346 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2012-07-07 17:07:43,346 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2012-07-07 17:07:43,346 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2012-07-07 17:07:43,347 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2012-07-07 17:07:43,352 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2012-07-07 17:07:43,352 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2012-07-07 17:07:43,352 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2012-07-07 17:07:43,352 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2012-07-07 17:07:43,352 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2012-07-07 17:07:43,353 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2012-07-07 17:07:43,353 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2012-07-07 17:07:43,353 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2012-07-07 17:07:43,353 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2012-07-07 17:07:43,353 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2012-07-07 17:07:43,358 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2012-07-07 17:07:43,358 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2012-07-07 17:07:43,358 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2012-07-07 17:07:43,358 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2012-07-07 17:07:43,358 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2012-07-07 17:07:43,359 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2012-07-07 17:07:43,359 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2012-07-07 17:07:43,359 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2012-07-07 17:07:43,359 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
BasicRootedPhylogeny{root}
Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.851 sec

Results :

Tests run: 6, 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) @ phyloutils ---
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/org/apache/maven/maven-archiver/2.5/maven-archiver-2.5.pom
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[INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.92-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] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.92-SNAPSHOT-tests.jar

[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ phyloutils ---
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mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default)
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mojoStarted org.apache.maven.plugins:maven-jar-plugin:2.4(default-cli)
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[INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ phyloutils ---
[WARNING] Artifact edu.berkeley.compbio:phyloutils:test-jar:tests:0.92-SNAPSHOT already attached to project, ignoring duplicate
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[INFO] BUILD SUCCESS
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[INFO] Total time: 53.345s
[INFO] Finished at: Sat Jul 07 17:07:51 UTC 2012
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Projects to build: [MavenProject: edu.berkeley.compbio:phyloutils:0.92-SNAPSHOT @ /media/ephemeral0/workspace/phyloutils/pom.xml]
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[JENKINS] Archiving /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.92-SNAPSHOT.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/modules/edu.berkeley.compbio$phyloutils/builds/2012-07-07_13-06-34/archive/edu.berkeley.compbio/phyloutils/0.92-SNAPSHOT/phyloutils-0.92-SNAPSHOT.jar
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[INFO] Deployment done in 6.7 sec
ncbitaxonomy #10 is already in the queue
Finished: SUCCESS