SuccessConsole Output

Started by user soergel
Building remotely on i-0404a965 in workspace /media/ephemeral0/workspace/phyloutils
[phyloutils] $ hg showconfig paths.default
[phyloutils] $ hg pull --rev default
[phyloutils] $ hg update --clean --rev default
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
[phyloutils] $ hg --config extensions.purge= clean --all
[phyloutils] $ hg log --rev . --template {node}
[phyloutils] $ hg log --rev . --template {rev}
[phyloutils] $ hg log --rev 18728f7ab7c530c15fa9c00edeff0b1d0c23f2be
[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 18728f7ab7c530c15fa9c00edeff0b1d0c23f2be
Parsing POMs
[phyloutils] $ java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 45198
<===[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 -DdevelopmentVersion=0.93-SNAPSHOT -DreleaseVersion=0.921 -U -e clean -Dresume=false release:prepare release:perform
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.93-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ phyloutils ---
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ phyloutils ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.93-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-release-plugin:2.0:prepare (default-cli) @ phyloutils ---
[INFO] Verifying that there are no local modifications...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg status
[INFO] [release.properties:unknown]
[INFO] Checking dependencies and plugins for snapshots ...
[INFO] Transforming 'phyloutils'...
[INFO] Not generating release POMs
[INFO] Executing goals 'clean verify'...
[INFO] [INFO] Scanning for projects...
[INFO] [INFO]                                                                         
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Building phyloutils 0.921
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] 
[INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ phyloutils ---
[INFO] [INFO] 
[INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ phyloutils ---
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Compiling 35 source files to /media/ephemeral0/workspace/phyloutils/target/classes
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[11,45] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[277,12] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 4 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] [INFO] Compiling 4 source files to /media/ephemeral0/workspace/phyloutils/target/test-classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/phyloutils/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 03:02:33,573 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
[INFO] 2013-03-21 03:02:33,787 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
[INFO] 2013-03-21 03:02:34,446 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
[INFO] BasicRootedPhylogeny{root}
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.416 sec
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ phyloutils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.921.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ phyloutils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.921-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ phyloutils ---
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] BUILD SUCCESS
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Total time: 1:00.239s
[INFO] [INFO] Finished at: Thu Mar 21 03:02:40 UTC 2013
[INFO] [INFO] Final Memory: 11M/27M
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] Checking in modified POMs...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg commit --message '[maven-release-plugin] prepare release phyloutils-0.921' /media/ephemeral0/workspace/phyloutils/pom.xml
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg push ssh://dev.davidsoergel.com//home/hg/phyloutils
[INFO] Tagging release with the label phyloutils-0.921...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg tag --message '[maven-release-plugin]  copy for tag phyloutils-0.921' phyloutils-0.921
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg push ssh://dev.davidsoergel.com//home/hg/phyloutils
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg locate
[INFO] Transforming 'phyloutils'...
[INFO] Not removing release POMs
[INFO] Checking in modified POMs...
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg commit --message '[maven-release-plugin] prepare for next development iteration' /media/ephemeral0/workspace/phyloutils/pom.xml
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils && hg push ssh://dev.davidsoergel.com//home/hg/phyloutils
[INFO] Release preparation complete.
[INFO] 
[INFO] --- maven-release-plugin:2.0:perform (default-cli) @ phyloutils ---
[INFO] Checking out the project to perform the release ...
[INFO] Removing /media/ephemeral0/workspace/phyloutils/target/checkout
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils/target && hg clone -r phyloutils-0.921 ssh://dev.davidsoergel.com//home/hg/phyloutils /media/ephemeral0/workspace/phyloutils/target/checkout
[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/phyloutils/target/checkout && hg locate
[INFO] Executing goals 'deploy site-deploy'...
[INFO] [INFO] Scanning for projects...
[INFO] [WARNING] 
[INFO] [WARNING] Some problems were encountered while building the effective model for edu.berkeley.compbio:phyloutils:jar:0.921
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing.
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-deploy-plugin is missing.
[INFO] [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-source-plugin is missing.
[INFO] [WARNING] 
[INFO] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[INFO] [WARNING] 
[INFO] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[INFO] [WARNING] 
[INFO] [INFO]                                                                         
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Building phyloutils 0.921
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Compiling 35 source files to /media/ephemeral0/workspace/phyloutils/target/checkout/target/classes
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[11,45] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[277,12] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 4 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] [INFO] Compiling 4 source files to /media/ephemeral0/workspace/phyloutils/target/checkout/target/test-classes
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/phyloutils/target/checkout/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 03:04:05,446 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
[INFO] 2013-03-21 03:04:05,590 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
[INFO] 2013-03-21 03:04:06,176 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
[INFO] BasicRootedPhylogeny{root}
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.906 sec
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ phyloutils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921.jar
[INFO] [INFO] 
[INFO] [INFO] >>> maven-source-plugin:2.2.1:jar (attach-sources) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-source-plugin:2.2.1:jar (attach-sources) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] --- maven-source-plugin:2.2.1:jar (attach-sources) @ phyloutils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-sources.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-javadoc-plugin:2.9:jar (attach-javadocs) @ phyloutils ---
[INFO] [INFO] 
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils...
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils.betadiversity...
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils.alphadiversity...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.6.0_37
[INFO] Building tree for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//CiccarelliTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//EnvironmentParser.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//ExplicitHybridRootedPhylogeny.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//HugenholtzTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//HybridRootedPhylogeny.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//LogTransitionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NASTDistanceMapper.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NearestNodeFinder.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NewickIntegerTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NewickParser.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NewickStringTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//NewickWithSynonymsAndRanksTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//PhylogenyTypeConverter.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//PhyloUtilsException.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//PhyloUtilsRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//RankedTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//RequiresPreparationTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//RootedPhylogenyAsService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonMerger.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomyBasedSynonymService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonomySynonymService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TaxonStringIdMapper.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TraditionalTaxonMerger.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//TransitionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//JDivergence.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//KullbackLeibler.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//NormalizedWeightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//PhylogeneticJDivergence.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//PhylogeneticKullbackLeibler.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//UnweightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//WeightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//FaithPD.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//PhylogeneticShannon.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//Shannon.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/overview-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/serialized-form.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TransitionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NewickIntegerTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/PhyloUtilsRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/PhyloUtilsException.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonomyBasedSynonymService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonMerger.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/HybridRootedPhylogeny.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NewickWithSynonymsAndRanksTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/ExplicitHybridRootedPhylogeny.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TraditionalTaxonMerger.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/EnvironmentParser.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/RootedPhylogenyAsService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/LogTransitionMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NewickStringTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/HugenholtzTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/CiccarelliTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NearestNodeFinder.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonStringIdMapper.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/RankedTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NewickParser.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/NASTDistanceMapper.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/RequiresPreparationTaxonomyService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/PhylogenyTypeConverter.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//class-use/TaxonomySynonymService.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/KullbackLeibler.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/UnweightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/WeightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/PhylogeneticKullbackLeibler.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/NormalizedWeightedUniFrac.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/JDivergence.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//class-use/PhylogeneticJDivergence.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//class-use/Shannon.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//class-use/PhylogeneticShannon.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//class-use/FaithPD.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils//package-use.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/alphadiversity//package-use.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/edu/berkeley/compbio/phyloutils/betadiversity//package-use.html...
[INFO] Building index for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/overview-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/index-all.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/deprecated-list.html...
[INFO] Building index for all classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/allclasses-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/allclasses-noframe.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/overview-summary.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/help-doc.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/apidocs/stylesheet.css...
[INFO] 10 warnings
[INFO] [WARNING] Javadoc Warnings
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:11: warning: sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] [WARNING] import sun.reflect.generics.reflectiveObjects.NotImplementedException;
[INFO] [WARNING] ^
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomyService.java:99: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/HugenholtzTaxonomyService.java:1115: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/HybridRootedPhylogeny.java:62: warning - @Author is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/HybridRootedPhylogeny.java:62: warning - @Version is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/NewickParser.java:69: warning - @Author is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/NewickParser.java:69: warning - @Version is an unknown tag -- same as a known tag except for case.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/PhylogenyTypeConverter.java:26: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomySynonymService.java:25: warning - @return tag has no arguments.
[INFO] [WARNING] /media/ephemeral0/workspace/phyloutils/target/checkout/src/main/java/edu/berkeley/compbio/phyloutils/TaxonomySynonymService.java:37: warning - @return tag has no arguments.
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-javadoc.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ phyloutils ---
[INFO] [INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ phyloutils ---
[INFO] [INFO] 
[INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ phyloutils ---
[INFO] [INFO] Installing /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/phyloutils/target/checkout/pom.xml to /home/ec2-user/.m2/repository/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.pom
[INFO] [INFO] Installing /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-sources.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-sources.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-javadoc.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-javadoc.jar
[INFO] [INFO] Installing /media/ephemeral0/workspace/phyloutils/target/checkout/target/phyloutils-0.921-tests.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-tests.jar
[INFO] [INFO] 
[INFO] [INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ phyloutils ---
[INFO] WAGON_VERSION: 1.0-beta-2
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.jar (2793 KB at 932.6 KB/sec)
[INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.pom
[INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921.pom (7 KB at 1.2 KB/sec)
[INFO] Downloading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/maven-metadata.xml
[INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/maven-metadata.xml (393 B at 1.6 KB/sec)
[INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/maven-metadata.xml
[INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/maven-metadata.xml (425 B at 0.7 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-sources.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-sources.jar (2779 KB at 735.8 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-javadoc.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-javadoc.jar (217 KB at 109.7 KB/sec)
[INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-tests.jar
[INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/phyloutils/0.921/phyloutils-0.921-tests.jar (11 KB at 14.2 KB/sec)
[INFO] [INFO] 
[INFO] [INFO] --- maven-site-plugin:3.1:site (default-site) @ phyloutils ---
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-javadoc-plugin:2.8.1
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-aggregate (report:test-aggregate) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:test-aggregate (report:test-aggregate) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ phyloutils <<<
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-jxr-plugin:2.3
[INFO] [INFO] configuring report plugin org.codehaus.mojo:cobertura-maven-plugin:2.5.1
[INFO] [INFO] 
[INFO] [INFO] >>> cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- cobertura-maven-plugin:2.5.1:instrument (report:cobertura) @ phyloutils ---
[INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file
[INFO] Instrumenting 38 files to /media/ephemeral0/workspace/phyloutils/target/checkout/target/generated-classes/cobertura
[INFO] Cobertura: Saved information on 38 classes.
[INFO] Instrument time: 3534ms
[INFO] 
[INFO] [INFO] Instrumentation was successful.
[INFO] [INFO] NOT adding cobertura ser file to attached artifacts list.
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 4 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/phyloutils/target/checkout/target/surefire-reports
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
[INFO] 2013-03-21 03:05:31,112 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
[INFO] 2013-03-21 03:05:31,243 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
[INFO] 2013-03-21 03:05:31,950 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Loaded caches for itol090314_name.tree, false
[INFO] BasicRootedPhylogeny{root}
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.715 sec
[INFO] Flushing results...
[INFO] Flushing results done
[INFO] Cobertura: Loaded information on 38 classes.
[INFO] Cobertura: Saved information on 38 classes.
[INFO] 
[INFO] Results :
[INFO] 
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0
[INFO] 
[INFO] [INFO] 
[INFO] [INFO] <<< cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ phyloutils <<<
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-surefire-report-plugin:2.12
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report (report:report) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 7 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ phyloutils ---
[INFO] [debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] [INFO] Copying 4 resources
[INFO] [INFO] 
[INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] [INFO] Nothing to compile - all classes are up to date
[INFO] [INFO] 
[INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] [INFO] Skipping execution of surefire because it has already been run for this configuration
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report (report:report) @ phyloutils <<<
[INFO] [INFO] 
[INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report-only (report:report-only) @ phyloutils >>>
[INFO] [INFO] 
[INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report-only (report:report-only) @ phyloutils <<<
[INFO] [WARNING] Report plugin org.apache.maven.plugins:maven-project-info-reports-plugin has an empty version.
[INFO] [WARNING] 
[INFO] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[INFO] [WARNING] 
[INFO] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[INFO] [INFO] configuring report plugin org.apache.maven.plugins:maven-project-info-reports-plugin:2.6
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.01
[INFO] [WARNING] Unable to find a URL to the parent project. The parent menu will NOT be added.
[INFO] [INFO] Relativizing decoration links with respect to project URL: http://dev.davidsoergel.com/phyloutils
[INFO] [INFO] Rendering site with org.apache.maven.skins:maven-default-skin:jar:1.0 skin.
[INFO] [INFO] Skipped "Test JavaDocs" report, file "testapidocs/index.html" already exists for the English version.
[INFO] [INFO] Skipped "JavaDocs" report, file "apidocs/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Source Xref" report, file "xref/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Test Source Xref" report, file "xref-test/index.html" already exists for the English version.
[INFO] [INFO] Skipped "Surefire Report" report, file "surefire-report.html" already exists for the English version.
[INFO] [INFO] Generating "Test JavaDocs" report    --- maven-javadoc-plugin:2.8.1
[INFO] [INFO] 
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.6.0_37
[INFO] Building tree for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//CiccarelliUtilsTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//HugenholtzTaxonomyServiceTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//HybridRootedPhylogenyTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//NewickParserTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//class-use/HybridRootedPhylogenyTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//class-use/CiccarelliUtilsTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//class-use/NewickParserTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//class-use/HugenholtzTaxonomyServiceTest.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/edu/berkeley/compbio/phyloutils//package-use.html...
[INFO] Building index for all the packages and classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/overview-tree.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/index-all.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/deprecated-list.html...
[INFO] Building index for all classes...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/allclasses-frame.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/allclasses-noframe.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/help-doc.html...
[INFO] Generating /media/ephemeral0/workspace/phyloutils/target/checkout/target/site/testapidocs/stylesheet.css...
[INFO] [INFO] Generating "JavaDocs" report    --- maven-javadoc-plugin:2.8.1
[INFO] [INFO] 
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils...
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils.betadiversity...
[INFO] Loading source files for package edu.berkeley.compbio.phyloutils.alphadiversity...
[INFO] Constructing Javadoc information...
[INFO] Standard Doclet version 1.6.0_37
[INFO] Building tree for all the packages and classes...
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[INFO] [ERROR] Unable to determine if resource com.davidsoergel:dsutils:jar:1.051:compile exists in http://repo.maven.apache.org/maven2
[INFO] [INFO] 
[INFO] [INFO] --- maven-site-plugin:3.1:deploy (default-deploy) @ phyloutils ---
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.01
[INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.01
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[INFO] [INFO]    >>> to scpexe://dev.davidsoergel.com/home/build/mavensites/phyloutils/./
[INFO] Executing command: mkdir -p /home/build/mavensites/phyloutils/./
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "mkdir -p /home/build/mavensites/phyloutils/./"'
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[INFO] Executing command: cd /home/build/mavensites/phyloutils/./; unzip -q -o wagon6734011894586642194.zip; rm -f wagon6734011894586642194.zip
[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "cd /home/build/mavensites/phyloutils/./; unzip -q -o wagon6734011894586642194.zip; rm -f wagon6734011894586642194.zip"'
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[INFO] Executing command: /bin/bash -c 'ssh -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" jenkins@dev.davidsoergel.com "chmod -Rf g+w,a+rX /home/build/mavensites/phyloutils/"'
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[INFO] [INFO] BUILD SUCCESS
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[INFO] [INFO] Total time: 6:09.408s
[INFO] [INFO] Finished at: Thu Mar 21 03:09:22 UTC 2013
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[INFO] Finished at: Thu Mar 21 03:09:23 UTC 2013
[INFO] Final Memory: 9M/25M
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[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.pom
Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
Downloaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 20.9 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.030926-3.pom
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.030926-3.pom (7 KB at 2.4 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml
Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml (348 B at 5.8 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 7.6 KB/sec)
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 2.9 KB/sec)
[INFO] Deployment done in 3.3 sec
msensr #19 is already in the queue
Finished: SUCCESS