Started by user soergel Building remotely on i-24df0d4c in workspace /media/ephemeral0/workspace/trees [trees] $ hg showconfig paths.default [trees] $ hg pull --rev default [trees] $ hg update --clean --rev default 0 files updated, 0 files merged, 0 files removed, 0 files unresolved [trees] $ hg --config extensions.purge= clean --all [trees] $ hg log --rev . --template {node} [trees] $ hg log --rev . --template {rev} [trees] $ hg log --rev f8504395d61e584c18e6ab4275f509bf35b86e9e [trees] $ 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 f8504395d61e584c18e6ab4275f509bf35b86e9e Parsing POMs [trees] $ 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 46803 <===[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/trees/pom.xml -DdevelopmentVersion=1.04-SNAPSHOT -DreleaseVersion=1.031 -U -e clean -Dresume=false release:prepare release:perform [INFO] Error stacktraces are turned on. [INFO] Scanning for projects... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building trees 1.04-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ trees --- [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ trees --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building trees 1.04-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-release-plugin:2.0:prepare (default-cli) @ trees --- [INFO] Verifying that there are no local modifications... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg status [INFO] [release.properties:unknown] [INFO] Checking dependencies and plugins for snapshots ... [INFO] Transforming 'trees'... [INFO] Not generating release POMs [INFO] Executing goals 'clean verify'... [INFO] [INFO] Scanning for projects... [INFO] [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Building trees 1.031 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ trees --- [INFO] [INFO] [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ trees --- [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [INFO] [INFO] Compiling 44 source files to /media/ephemeral0/workspace/trees/target/classes [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ trees --- [INFO] [INFO] Compiling 12 source files to /media/ephemeral0/workspace/trees/target/test-classes [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ trees --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/trees/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2013-03-20 19:52:01,340 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: root [INFO] 2013-03-20 19:52:01,345 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: a [INFO] 2013-03-20 19:52:01,346 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aa [INFO] 2013-03-20 19:52:01,347 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaa [INFO] 2013-03-20 19:52:01,348 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaaa [INFO] 2013-03-20 19:52:01,348 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ab [INFO] 2013-03-20 19:52:01,351 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: b [INFO] 2013-03-20 19:52:01,352 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ba [INFO] 2013-03-20 19:52:01,353 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: baa [INFO] 2013-03-20 19:52:01,354 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bab [INFO] 2013-03-20 19:52:01,354 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bb [INFO] 2013-03-20 19:52:01,355 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bba [INFO] 2013-03-20 19:52:01,356 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbb [INFO] 2013-03-20 19:52:01,356 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbba [INFO] 2013-03-20 19:52:01,357 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: c [INFO] 2013-03-20 19:52:01,358 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ca [INFO] 2013-03-20 19:52:01,358 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: cb [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.672 sec [INFO] [INFO] Results : [INFO] [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ trees --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/trees-1.031.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ trees --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/trees-1.031-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ trees --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] BUILD SUCCESS [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Total time: 44.433s [INFO] [INFO] Finished at: Wed Mar 20 19:52:04 UTC 2013 [INFO] [INFO] Final Memory: 10M/26M [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Checking in modified POMs... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg commit --message '[maven-release-plugin] prepare release trees-1.031' /media/ephemeral0/workspace/trees/pom.xml [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg push ssh://dev.davidsoergel.com//home/hg/trees [INFO] Tagging release with the label trees-1.031... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg tag --message '[maven-release-plugin] copy for tag trees-1.031' trees-1.031 [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg push ssh://dev.davidsoergel.com//home/hg/trees [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg locate [INFO] Transforming 'trees'... [INFO] Not removing release POMs [INFO] Checking in modified POMs... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg commit --message '[maven-release-plugin] prepare for next development iteration' /media/ephemeral0/workspace/trees/pom.xml [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees && hg push ssh://dev.davidsoergel.com//home/hg/trees [INFO] Release preparation complete. [INFO] Checking out the project to perform the release ... [INFO] Removing /media/ephemeral0/workspace/trees/target/checkout [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees/target && hg clone -r trees-1.031 ssh://dev.davidsoergel.com//home/hg/trees /media/ephemeral0/workspace/trees/target/checkout [INFO] [INFO] --- maven-release-plugin:2.0:perform (default-cli) @ trees --- [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/trees/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 com.davidsoergel:trees:jar:1.031 [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 trees 1.031 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [INFO] [INFO] Compiling 44 source files to /media/ephemeral0/workspace/trees/target/checkout/target/classes [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ trees --- [INFO] [INFO] Compiling 12 source files to /media/ephemeral0/workspace/trees/target/checkout/target/test-classes [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ trees --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/trees/target/checkout/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2013-03-20 19:53:38,023 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: root [INFO] 2013-03-20 19:53:38,042 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: a [INFO] 2013-03-20 19:53:38,043 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aa [INFO] 2013-03-20 19:53:38,044 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaa [INFO] 2013-03-20 19:53:38,044 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaaa [INFO] 2013-03-20 19:53:38,045 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ab [INFO] 2013-03-20 19:53:38,046 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: b [INFO] 2013-03-20 19:53:38,047 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ba [INFO] 2013-03-20 19:53:38,047 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: baa [INFO] 2013-03-20 19:53:38,048 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bab [INFO] 2013-03-20 19:53:38,055 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bb [INFO] 2013-03-20 19:53:38,056 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bba [INFO] 2013-03-20 19:53:38,056 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbb [INFO] 2013-03-20 19:53:38,057 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbba [INFO] 2013-03-20 19:53:38,058 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: c [INFO] 2013-03-20 19:53:38,058 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ca [INFO] 2013-03-20 19:53:38,062 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: cb [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.716 sec [INFO] [INFO] Results : [INFO] [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ trees --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031.jar [INFO] [INFO] [INFO] [INFO] >>> maven-source-plugin:2.2.1:jar (attach-sources) @ trees >>> [INFO] [INFO] [INFO] [INFO] <<< maven-source-plugin:2.2.1:jar (attach-sources) @ trees <<< [INFO] [INFO] [INFO] [INFO] --- maven-source-plugin:2.2.1:jar (attach-sources) @ trees --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-sources.jar [INFO] [INFO] [INFO] [INFO] --- maven-javadoc-plugin:2.9:jar (attach-javadocs) @ trees --- [INFO] [INFO] [INFO] Loading source files for package com.davidsoergel.trees.htpn... [INFO] Loading source files for package com.davidsoergel.trees... [INFO] Loading source files for package com.davidsoergel.trees.dhtpn... [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/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//AbstractExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//AbstractHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//BasicHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//ExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//ExtendedHierarchicalTypedPropertyNodeImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//HierarchicalPropertyNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//HierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//HierarchicalTypedPropertyNode.PropertyConsumerFlags.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//MapToHierarchicalTypedPropertyNodeAdapter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//SerializableHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//AbstractHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//AbstractRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//AbstractRootedPhylogeny.MutualExclusionResolutionMode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//BasicHierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//BasicPhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//BasicRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//DepthFirstTreeIterator.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//DepthFirstTreeIteratorImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//HierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//HierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//ImmutableHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//ImmutableSortedSetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//IntegerGeneratingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//IntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//LengthWeightHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//ListHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//NodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//NoSuchNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//PhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//RequireExistingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//RootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//SerializablePhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//SerializableRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//SetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//StringIntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//StringNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//TaxonMergingPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//TreeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//TreePrinter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//TreeRuntimeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//AbstractDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//AbstractSerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//DoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//ExtendedDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//ResultCollector.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//SerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/overview-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//package-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//package-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//package-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//package-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//package-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//package-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//package-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//package-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//package-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/constant-values.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/serialized-form.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/SerializableHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/ExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/ExtendedHierarchicalTypedPropertyNodeImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/MapToHierarchicalTypedPropertyNodeAdapter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalPropertyNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalTypedPropertyNode.PropertyConsumerFlags.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/AbstractHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/AbstractExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//class-use/BasicHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/SerializableRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/DepthFirstTreeIterator.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/BasicPhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/PhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/HierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/RootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/StringIntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/ImmutableHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/IntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/NodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/LengthWeightHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/NoSuchNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/RequireExistingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/AbstractRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/AbstractRootedPhylogeny.MutualExclusionResolutionMode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/TreePrinter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/DepthFirstTreeIteratorImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/IntegerGeneratingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/TreeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/ListHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/SetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/HierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/TaxonMergingPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/ImmutableSortedSetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/SerializablePhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/BasicRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/AbstractHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/TreeRuntimeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/StringNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//class-use/BasicHierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/DoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/AbstractSerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/SerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/AbstractDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/ExtendedDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//class-use/ResultCollector.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees//package-use.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/dhtpn//package-use.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/com/davidsoergel/trees/htpn//package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/allclasses-noframe.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/index.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/overview-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/help-doc.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/apidocs/stylesheet.css... [INFO] 64 warnings [INFO] [WARNING] Javadoc Warnings [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:66: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:208: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:267: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/HierarchicalTypedPropertyNode.java:116: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:66: warning - Tag @return cannot be used in field documentation. It can only be used in the following types of documentation: method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:566: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/TaxonMergingPhylogeny.java:137: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:359: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:98: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:89: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:107: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:331: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:118: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicRootedPhylogeny.java:64: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicRootedPhylogeny.java:64: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/RootedPhylogeny.java:142: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/HierarchyNode.java:50: warning - @See is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:48: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/NodeNamer.java:44: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:50: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/RootedPhylogeny.java:55: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/TaxonMergingPhylogeny.java:49: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-javadoc.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ trees --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ trees --- [INFO] [INFO] [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ trees --- [INFO] [INFO] Installing /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031.jar to /home/ec2-user/.m2/repository/com/davidsoergel/trees/1.031/trees-1.031.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/trees/target/checkout/pom.xml to /home/ec2-user/.m2/repository/com/davidsoergel/trees/1.031/trees-1.031.pom [INFO] [INFO] Installing /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-sources.jar to /home/ec2-user/.m2/repository/com/davidsoergel/trees/1.031/trees-1.031-sources.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-javadoc.jar to /home/ec2-user/.m2/repository/com/davidsoergel/trees/1.031/trees-1.031-javadoc.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/trees/target/checkout/target/trees-1.031-tests.jar to /home/ec2-user/.m2/repository/com/davidsoergel/trees/1.031/trees-1.031-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ trees --- [INFO] WAGON_VERSION: 1.0-beta-2 [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031.jar (83 KB at 14.8 KB/sec) [INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031.pom [INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031.pom (5 KB at 6.1 KB/sec) [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/maven-metadata.xml [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/maven-metadata.xml (384 B at 0.6 KB/sec) [INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/maven-metadata.xml [INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/maven-metadata.xml (416 B at 0.6 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-sources.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-sources.jar (91 KB at 17.2 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-javadoc.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-javadoc.jar (361 KB at 101.5 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-tests.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/com/davidsoergel/trees/1.031/trees-1.031-tests.jar (28 KB at 9.6 KB/sec) [INFO] [INFO] [INFO] [INFO] --- maven-site-plugin:3.1:site (default-site) @ trees --- [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) @ trees >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [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) @ trees <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ trees >>> [INFO] [INFO] [INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ trees <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ trees >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [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) @ trees <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ trees >>> [INFO] [INFO] [INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ trees <<< [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) @ trees >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:instrument (report:cobertura) @ trees --- [INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file [INFO] Instrumenting 47 files to /media/ephemeral0/workspace/trees/target/checkout/target/generated-classes/cobertura [INFO] Cobertura: Saved information on 47 classes. [INFO] Instrument time: 4028ms [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) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ trees --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ trees --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/trees/target/checkout/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2013-03-20 19:55:27,483 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: root [INFO] 2013-03-20 19:55:27,485 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: a [INFO] 2013-03-20 19:55:27,486 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aa [INFO] 2013-03-20 19:55:27,486 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaa [INFO] 2013-03-20 19:55:27,487 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: aaaa [INFO] 2013-03-20 19:55:27,488 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ab [INFO] 2013-03-20 19:55:27,490 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: b [INFO] 2013-03-20 19:55:27,490 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ba [INFO] 2013-03-20 19:55:27,491 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: baa [INFO] 2013-03-20 19:55:27,491 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bab [INFO] 2013-03-20 19:55:27,492 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bb [INFO] 2013-03-20 19:55:27,493 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bba [INFO] 2013-03-20 19:55:27,493 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbb [INFO] 2013-03-20 19:55:27,495 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: bbba [INFO] 2013-03-20 19:55:27,496 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: c [INFO] 2013-03-20 19:55:27,497 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: ca [INFO] 2013-03-20 19:55:27,497 [main] INFO com.davidsoergel.trees.BasicPhylogenyNodeTest - Tree iterator provided node: cb [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.842 sec [INFO] Flushing results... [INFO] Flushing results done [INFO] Cobertura: Loaded information on 47 classes. [INFO] Cobertura: Saved information on 47 classes. [INFO] [INFO] Results : [INFO] [INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] <<< cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ trees <<< [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) @ trees >>> [INFO] [INFO] [INFO] [INFO] <<< maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ trees <<< [INFO] [INFO] [INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report (report:report) @ trees >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ trees --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ trees --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/trees/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ trees --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ trees --- [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) @ trees <<< [INFO] [INFO] [INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report-only (report:report-only) @ trees >>> [INFO] [INFO] [INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report-only (report:report-only) @ trees <<< [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/trees [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 com.davidsoergel.trees... [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/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//AbstractRootedPhylogenyAbstractTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//BasicPhylogenyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//BasicRootedPhylogenyTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//BasicRootedPhylogenyTest.BasicRootedPhylogenyWithSpecificNodeHandles.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//HierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//ImmutableHierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//ImmutableSortedSetHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//LengthWeightHierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//ListHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//PhylogenyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//RootedPhylogenyInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//SetHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//TaxonMergingPhylogenyInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//package-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//package-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//package-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/constant-values.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/BasicRootedPhylogenyTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/BasicRootedPhylogenyTest.BasicRootedPhylogenyWithSpecificNodeHandles.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/LengthWeightHierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/ImmutableSortedSetHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/BasicPhylogenyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/TaxonMergingPhylogenyInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/HierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/PhylogenyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/RootedPhylogenyInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/ImmutableHierarchyNodeInterfaceTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/AbstractRootedPhylogenyAbstractTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/SetHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//class-use/ListHierarchyNodeTest.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/com/davidsoergel/trees//package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/allclasses-noframe.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/index.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/testapidocs/help-doc.html... [INFO] Generating /media/ephemeral0/workspace/trees/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 com.davidsoergel.trees.htpn... [INFO] Loading source files for package com.davidsoergel.trees... [INFO] Loading source files for package com.davidsoergel.trees.dhtpn... [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/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//AbstractExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//AbstractHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//BasicHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//ExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//ExtendedHierarchicalTypedPropertyNodeImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//HierarchicalPropertyNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//HierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//HierarchicalTypedPropertyNode.PropertyConsumerFlags.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//MapToHierarchicalTypedPropertyNodeAdapter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//SerializableHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//AbstractHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//AbstractRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//AbstractRootedPhylogeny.MutualExclusionResolutionMode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//BasicHierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//BasicPhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//BasicRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//DepthFirstTreeIterator.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//DepthFirstTreeIteratorImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//HierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//HierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//ImmutableHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//ImmutableSortedSetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//IntegerGeneratingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//IntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//LengthWeightHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//ListHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//NodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//NoSuchNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//PhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//RequireExistingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//RootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//SerializablePhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//SerializableRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//SetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//StringIntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//StringNodeNamer.html... 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[INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//DoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//ExtendedDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//ResultCollector.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//SerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/overview-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//package-frame.html... 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[INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/MapToHierarchicalTypedPropertyNodeAdapter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalPropertyNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/HierarchicalTypedPropertyNode.PropertyConsumerFlags.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/AbstractHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/AbstractExtendedHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//class-use/BasicHierarchicalTypedPropertyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/SerializableRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/DepthFirstTreeIterator.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/BasicPhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/PhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/HierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/RootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/StringIntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/ImmutableHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/IntegerNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/NodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/LengthWeightHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/NoSuchNodeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/RequireExistingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/AbstractRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/AbstractRootedPhylogeny.MutualExclusionResolutionMode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/TreePrinter.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/DepthFirstTreeIteratorImpl.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/IntegerGeneratingNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/TreeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/ListHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/SetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/HierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/TaxonMergingPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/ImmutableSortedSetHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/SerializablePhylogenyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/BasicRootedPhylogeny.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/AbstractHierarchyNode.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/TreeRuntimeException.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/StringNodeNamer.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//class-use/BasicHierarchicalStringObjectMap.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/DoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/AbstractSerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/SerializableDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/AbstractDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/ExtendedDoubleHierarchicalTypedProperties.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//class-use/ResultCollector.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees//package-use.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/dhtpn//package-use.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/com/davidsoergel/trees/htpn//package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/allclasses-noframe.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/index.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/overview-summary.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/help-doc.html... [INFO] Generating /media/ephemeral0/workspace/trees/target/checkout/target/site/apidocs/stylesheet.css... [INFO] 64 warnings [INFO] [WARNING] Javadoc Warnings [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:66: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:208: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:267: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/HierarchicalTypedPropertyNode.java:116: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/htpn/AbstractHierarchicalTypedPropertyNode.java:66: warning - Tag @return cannot be used in field documentation. It can only be used in the following types of documentation: method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:566: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/TaxonMergingPhylogeny.java:137: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:359: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:98: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:89: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:107: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:331: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:118: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicRootedPhylogeny.java:64: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicRootedPhylogeny.java:64: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/RootedPhylogeny.java:142: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/HierarchyNode.java:50: warning - @See is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:48: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/NodeNamer.java:44: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:50: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/RootedPhylogeny.java:55: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/TaxonMergingPhylogeny.java:49: warning - @JavadocOK is an unknown tag. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:670: warning - @inheritDoc used but appendToValue(String, NodeNamer<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/PhylogenyNode.java:101: warning - @inheritDoc used but clone() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/AbstractRootedPhylogeny.java:169: warning - @inheritDoc used but commonAncestor(PhylogenyNode<T>, PhylogenyNode<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/BasicPhylogenyNode.java:804: warning - @inheritDoc used but getGreatestNodeDepthBelow() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/trees/target/checkout/src/main/java/com/davidsoergel/trees/LengthWeightHierarchyNode.java:131: warning - @inheritDoc used but toNewick(Writer, String, String, int, double) does not override or implement any method. [INFO] [INFO] Generating "Source Xref" report --- maven-jxr-plugin:2.3 [INFO] [INFO] Generating "Test Source Xref" report --- maven-jxr-plugin:2.3 [INFO] [INFO] Generating "Cobertura Test Coverage" report --- cobertura-maven-plugin:2.5.1 [INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file [INFO] Cobertura: Loaded information on 47 classes. [INFO] Report time: 10795ms [INFO] [INFO] [INFO] Cobertura Report generation was successful. [INFO] [INFO] Generating "Surefire Report" report --- maven-surefire-report-plugin:2.12 [INFO] [INFO] Generating "About" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Project Team" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Dependency Information" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Project Plugins" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Continuous Integration" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Issue Tracking" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Source Repository" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Project License" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Plugin Management" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Distribution Management" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Project Summary" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Mailing Lists" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] Generating "Dependencies" report --- maven-project-info-reports-plugin:2.6 [INFO] [INFO] [INFO] [INFO] --- maven-site-plugin:3.1:deploy (default-deploy) @ trees --- [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 [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/trees/ - Session: Opened [INFO] [INFO] Pushing /media/ephemeral0/workspace/trees/target/checkout/target/site [INFO] [INFO] >>> to scpexe://dev.davidsoergel.com/home/build/mavensites/trees/./ [INFO] Executing command: mkdir -p /home/build/mavensites/trees/./ [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/trees/./"' [INFO] [INFO] [INFO] Executing command: mkdir -p /home/build/mavensites/trees//. [INFO] [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/trees//. [INFO] "' [INFO] [INFO] [INFO] Uploading: ./wagon272017482293222790.zip to scpexe://dev.davidsoergel.com/home/build/mavensites/trees/ [INFO] [INFO] Executing command: /bin/bash -c 'cd /tmp && scp -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" wagon272017482293222790.zip jenkins@dev.davidsoergel.com:/home/build/mavensites/trees//./wagon272017482293222790.zip' [INFO] ############################################################################################################################################################################################################################################### [INFO] Transfer finished. 976328 bytes copied in 0.964 seconds [INFO] Executing command: cd /home/build/mavensites/trees/./; unzip -q -o wagon272017482293222790.zip; rm -f wagon272017482293222790.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/trees/./; unzip -q -o wagon272017482293222790.zip; rm -f wagon272017482293222790.zip"' [INFO] [INFO] [INFO] Executing command: chmod -Rf g+w,a+rX /home/build/mavensites/trees/ [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/trees/"' [INFO] [INFO] [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/trees/ - Session: Disconnecting [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/trees/ - Session: Disconnected [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] BUILD SUCCESS [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Total time: 6:23.959s [INFO] [INFO] Finished at: Wed Mar 20 19:58:49 UTC 2013 [INFO] [INFO] Final Memory: 27M/68M [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Cleaning up after release... [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 8:17.135s [INFO] Finished at: Wed Mar 20 19:58:58 UTC 2013 [INFO] Final Memory: 9M/25M [INFO] ------------------------------------------------------------------------ [JENKINS] Archiving /media/ephemeral0/workspace/trees/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/trees/modules/com.davidsoergel$trees/builds/2013-03-20_15-50-28/archive/com.davidsoergel/trees/1.04-SNAPSHOT/trees-1.04-SNAPSHOT.pom Waiting for Jenkins to finish collecting data channel stopped [M2Release] marking build to keep until the next release build [M2Release] removing keep build from build 11 Maven RedeployPublisher use remote i-24df0d4c maven settings from : /home/ec2-user/.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 trees-1.04-SNAPSHOT.pom Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/maven-metadata.xml Downloaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/maven-metadata.xml (2 KB at 24.3 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/trees-1.04-20130320.195907-3.pom Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/trees-1.04-20130320.195907-3.pom (5 KB at 15.8 KB/sec) Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/maven-metadata.xml Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/maven-metadata.xml (380 B at 6.2 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/1.04-SNAPSHOT/maven-metadata.xml (2 KB at 6.1 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/com/davidsoergel/trees/maven-metadata.xml (380 B at 1.5 KB/sec) [INFO] Deployment done in 1.3 sec Finished: SUCCESS