SuccessConsole Output

Started by GitHub push by davidsoergel
Building in workspace /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace
Cloning the remote Git repository
Cloning repository https://github.com/davidsoergel/phyloutils.git
 > git init /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace
Fetching upstream changes from https://github.com/davidsoergel/phyloutils.git
 > git --version
 > git fetch --tags --progress https://github.com/davidsoergel/phyloutils.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/davidsoergel/phyloutils.git
 > git config remote.origin.fetch +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/davidsoergel/phyloutils.git
Fetching upstream changes from https://github.com/davidsoergel/phyloutils.git
 > git fetch --tags --progress https://github.com/davidsoergel/phyloutils.git +refs/heads/*:refs/remotes/origin/*
 > git rev-parse origin/master^{commit}
Checking out Revision 772e5873a79aecc9dd81bf4eb60032506fa0db40 (origin/master)
 > git config core.sparsecheckout
 > git checkout -f 772e5873a79aecc9dd81bf4eb60032506fa0db40
First time build. Skipping changelog.
Parsing POMs
[workspace] $ java -Xmx1024M -XX:MaxPermSize=256M -cp /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven31-agent-1.5.jar:/usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/boot/plexus-classworlds-2.5.1.jar:/usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/conf/logging jenkins.maven3.agent.Maven31Main /usr/share/apache-tomcat-7.0.22/.jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1 /usr/share/apache-tomcat-7.0.22/webapps/jenkins/WEB-INF/lib/remoting-2.43.jar /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven31-interceptor-1.5.jar /usr/share/apache-tomcat-7.0.22/.jenkins/plugins/maven-plugin/WEB-INF/lib/maven3-interceptor-commons-1.5.jar 52496
<===[JENKINS REMOTING CAPACITY]===>channel started
Executing Maven:  -B -f /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/pom.xml -U -e clean source:jar package jar:test-jar javadoc:jar
[INFO] Error stacktraces are turned on.
[WARNING] 
[WARNING] Some problems were encountered while building the effective settings
[WARNING] Unrecognised tag: 'scmVersionType' (position: START_TAG seen ...</username>\n    <scmVersionType>... @22:21)  @ /usr/share/apache-tomcat-7.0.22/.m2/settings.xml, line 22, column 21
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[INFO] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.93-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ phyloutils ---
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ phyloutils ---
[INFO] 
[INFO] >>> maven-source-plugin:2.2.1:jar (default-cli) @ phyloutils >>>
[WARNING] Failed to getClass for org.apache.maven.plugin.source.SourceJarMojo
[INFO] 
[INFO] <<< maven-source-plugin:2.2.1:jar (default-cli) @ phyloutils <<<
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar (default-cli) @ phyloutils ---
[INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ phyloutils ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] Compiling 35 source files to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/classes
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[17,45] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[283,12] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ phyloutils ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] Compiling 4 source files to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] Surefire report directory: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestSuite
2014-07-06 17:58:16,528 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2014-07-06 17:58:16,552 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2014-07-06 17:58:16,552 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2014-07-06 17:58:16,668 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2014-07-06 17:58:16,669 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2014-07-06 17:58:16,669 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2014-07-06 17:58:16,669 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2014-07-06 17:58:16,670 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2014-07-06 17:58:16,670 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2014-07-06 17:58:16,670 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2014-07-06 17:58:16,673 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2014-07-06 17:58:16,679 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2014-07-06 17:58:16,679 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2014-07-06 17:58:16,679 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2014-07-06 17:58:16,680 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2014-07-06 17:58:16,680 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2014-07-06 17:58:16,680 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2014-07-06 17:58:16,680 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2014-07-06 17:58:16,681 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2014-07-06 17:58:16,681 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2014-07-06 17:58:16,681 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2014-07-06 17:58:16,681 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2014-07-06 17:58:16,682 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2014-07-06 17:58:16,683 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2014-07-06 17:58:16,683 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2014-07-06 17:58:16,683 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2014-07-06 17:58:16,683 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2014-07-06 17:58:16,684 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2014-07-06 17:58:16,684 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2014-07-06 17:58:16,684 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2014-07-06 17:58:16,684 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2014-07-06 17:58:16,685 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2014-07-06 17:58:16,685 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2014-07-06 17:58:16,686 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2014-07-06 17:58:16,686 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2014-07-06 17:58:16,686 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2014-07-06 17:58:16,687 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2014-07-06 17:58:16,687 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2014-07-06 17:58:16,687 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2014-07-06 17:58:16,687 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2014-07-06 17:58:16,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2014-07-06 17:58:16,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2014-07-06 17:58:16,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2014-07-06 17:58:16,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2014-07-06 17:58:16,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2014-07-06 17:58:16,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2014-07-06 17:58:16,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2014-07-06 17:58:16,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2014-07-06 17:58:16,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2014-07-06 17:58:16,690 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2014-07-06 17:58:16,690 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2014-07-06 17:58:16,694 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2014-07-06 17:58:16,695 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2014-07-06 17:58:16,695 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2014-07-06 17:58:16,695 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2014-07-06 17:58:16,695 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2014-07-06 17:58:16,696 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2014-07-06 17:58:16,696 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2014-07-06 17:58:16,697 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2014-07-06 17:58:16,697 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2014-07-06 17:58:16,698 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2014-07-06 17:58:16,698 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2014-07-06 17:58:16,698 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2014-07-06 17:58:16,699 [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: 1.919 sec

Results :

Tests run: 6, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ phyloutils ---
[INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ phyloutils ---
[INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-tests.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default) @ phyloutils ---
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ phyloutils ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (default-cli) @ phyloutils ---
[INFO] 
Loading source files for package edu.berkeley.compbio.phyloutils...
Loading source files for package edu.berkeley.compbio.phyloutils.alphadiversity...
Loading source files for package edu.berkeley.compbio.phyloutils.betadiversity...
Constructing Javadoc information...
Standard Doclet version 1.6.0_27
Building tree for all the packages and classes...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//CiccarelliTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//EnvironmentParser.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//ExplicitHybridRootedPhylogeny.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//HugenholtzTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//HybridRootedPhylogeny.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//LogTransitionMatrix.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NASTDistanceMapper.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NearestNodeFinder.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NewickIntegerTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NewickParser.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NewickStringTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//NewickWithSynonymsAndRanksTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//PhylogenyTypeConverter.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//PhyloUtilsException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//PhyloUtilsRuntimeException.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//RankedTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//RequiresPreparationTaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//RootedPhylogenyAsService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonMerger.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomyBasedSynonymService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomyService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomySynonymService.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonStringIdMapper.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TraditionalTaxonMerger.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//TransitionMatrix.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//FaithPD.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//PhylogeneticShannon.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//Shannon.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//JDivergence.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//KullbackLeibler.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//NormalizedWeightedUniFrac.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//PhylogeneticJDivergence.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//PhylogeneticKullbackLeibler.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//UnweightedUniFrac.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//WeightedUniFrac.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/overview-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//package-summary.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-frame.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-summary.html...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//package-tree.html...
Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/constant-values.html...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonStringIdMapper.html...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NewickWithSynonymsAndRanksTaxonomyService.html...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/CiccarelliTaxonomyService.html...
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Building index for all the packages and classes...
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Building index for all classes...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/allclasses-noframe.html...
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Generating /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/apidocs/stylesheet.css...
10 warnings
[WARNING] Javadoc Warnings
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:17: warning: sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[WARNING] import sun.reflect.generics.reflectiveObjects.NotImplementedException;
[WARNING] ^
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomyService.java:105: warning - @return tag has no arguments.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/HugenholtzTaxonomyService.java:1121: warning - @return tag has no arguments.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/HybridRootedPhylogeny.java:36: warning - @Author is an unknown tag -- same as a known tag except for case.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/HybridRootedPhylogeny.java:36: warning - @Version is an unknown tag -- same as a known tag except for case.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/NewickParser.java:43: warning - @Author is an unknown tag -- same as a known tag except for case.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/NewickParser.java:43: warning - @Version is an unknown tag -- same as a known tag except for case.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/PhylogenyTypeConverter.java:32: warning - @return tag has no arguments.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomySynonymService.java:31: warning - @return tag has no arguments.
[WARNING] /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomySynonymService.java:43: warning - @return tag has no arguments.
[INFO] Fixed Javadoc frame injection vulnerability (CVE-2013-1571) in 1 files.
[INFO] Building jar: /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-javadoc.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 35.374s
[INFO] Finished at: Sun Jul 06 17:58:33 EDT 2014
[INFO] Final Memory: 17M/41M
[INFO] ------------------------------------------------------------------------
[JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/pom.xml to edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT.pom
[JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT.jar to edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT.jar
[JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-sources.jar to edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT-sources.jar
[JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-tests.jar to edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT-tests.jar
[JENKINS] Archiving /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target/phyloutils-0.93-SNAPSHOT-javadoc.jar to edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT-javadoc.jar
channel stopped
Maven RedeployPublisher use remote  maven settings from : /usr/share/apache-tomcat-7.0.22/.m2/settings.xml
[ERROR] uniqueVersion == false is not anymore supported in maven 3
[INFO] Deployment in dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots (id=dev.davidsoergel.com.snapshot,uniqueVersion=false)
Deploying the main artifact phyloutils-0.93-SNAPSHOT.jar
Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
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Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5.jar
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5.jar (2791 KB at 3925.0 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5.pom
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5.pom (5 KB at 27.0 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml
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Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
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Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml (348 B at 1.7 KB/sec)
Deploying the main artifact phyloutils-0.93-SNAPSHOT-sources.jar
Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-sources.jar
Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-sources.jar (2768 KB at 3902.7 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
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Deploying the main artifact phyloutils-0.93-SNAPSHOT-tests.jar
Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-tests.jar
Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-tests.jar (10 KB at 44.0 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 8.8 KB/sec)
Deploying the main artifact phyloutils-0.93-SNAPSHOT-javadoc.jar
Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-javadoc.jar
Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20140706.215834-5-javadoc.jar (219 KB at 1233.3 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 10.1 KB/sec)
[INFO] Deployment done in 3.6 sec
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of phyloutils-docs-deploy
Triggering a new build of msensr
Finished: SUCCESS