SuccessConsole Output

Started by GitHub push by davidsoergel
Building in workspace /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace
 > git rev-parse --is-inside-work-tree
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/davidsoergel/phyloutils.git
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 rev-parse origin/master^{commit}
Checking out Revision 6a257425e3a24e3de857198f9d3ed6bfefb6e5df (origin/master)
 > git config core.sparsecheckout
 > git checkout -f 6a257425e3a24e3de857198f9d3ed6bfefb6e5df
 > git rev-list 772e5873a79aecc9dd81bf4eb60032506fa0db40
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 53437
<===[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] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.93-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ phyloutils ---
[INFO] Deleting /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/workspace/target
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ phyloutils ---
[INFO] 
[INFO] >>> maven-source-plugin:2.3:jar (default-cli) @ phyloutils >>>
[WARNING] Failed to getClass for org.apache.maven.plugin.source.SourceJarMojo
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[INFO] <<< maven-source-plugin:2.3:jar (default-cli) @ phyloutils <<<
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[INFO] --- maven-source-plugin:2.3:jar (default-cli) @ phyloutils ---
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[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] NotImplementedException is internal 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] NotImplementedException is internal 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
2014-07-12 20:39:44,607 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2014-07-12 20:39:44,650 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2014-07-12 20:39:44,872 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
BasicRootedPhylogeny{root}
Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.956 sec
[JENKINS] Recording test results
Results :

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


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 1.7.0_60
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...
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[INFO] Finished at: Sat Jul 12 20:40:05 EDT 2014
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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 4.8 KB/sec)
[INFO] Deployment done in 12 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 msensr
Triggering a new build of phyloutils-docs-deploy
Finished: SUCCESS