Started by user soergel Building remotely on i-2c07a854 in workspace /media/ephemeral0/workspace/ml [ml] $ hg showconfig paths.default [ml] $ hg pull --rev default [ml] $ hg update --clean --rev default 2 files updated, 0 files merged, 0 files removed, 0 files unresolved [ml] $ hg --config extensions.purge= clean --all [ml] $ hg log --rev . --template {node} [ml] $ hg log --rev . --template {rev} [ml] $ hg log --rev 933d3b3e5b6c4f4afd2bc6f117f89a7551d4d857 [ml] $ 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 933d3b3e5b6c4f4afd2bc6f117f89a7551d4d857 your Apache Maven build is setup to use a config with id org.jenkinsci.plugins.configfiles.maven.MavenSettingsConfig1337980147845 but cannot find the config Parsing POMs Modules changed, recalculating dependency graph [ml] $ /usr/java/default/bin/java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/Maven/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/Maven/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 34623 <===[JENKINS REMOTING CAPACITY]===>channel started Executing Maven: -B -f /media/ephemeral0/workspace/ml/pom.xml -DdevelopmentVersion=0.93-SNAPSHOT -DreleaseVersion=0.92 -U -e clean -Dresume=false release:prepare release:perform log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. [INFO] Error stacktraces are turned on. [INFO] Scanning for projects... Projects to build: [MavenProject: edu.berkeley.compbio:ml:0.912-SNAPSHOT @ /media/ephemeral0/workspace/ml/pom.xml] projectStarted edu.berkeley.compbio:ml:0.912-SNAPSHOT [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building ml 0.912-SNAPSHOT [INFO] ------------------------------------------------------------------------ mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean) [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ml --- mojoSucceeded org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean) mojoStarted org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean) [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ ml --- mojoSucceeded org.codehaus.mojo:cobertura-maven-plugin:2.5.1(clean) projectSucceeded edu.berkeley.compbio:ml:0.912-SNAPSHOT projectStarted edu.berkeley.compbio:ml:0.912-SNAPSHOT [INFO] [INFO] ------------------------------------------------------------------------ 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[INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg status [INFO] [release.properties:unknown] [INFO] Checking dependencies and plugins for snapshots ... [INFO] Transforming 'ml'... [INFO] Not generating release POMs [INFO] Executing goals 'clean verify'... [INFO] [INFO] Scanning for projects... [INFO] [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Building ml 0.92 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ml --- [INFO] [INFO] [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ ml --- [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [INFO] [INFO] Compiling 103 source files to /media/ephemeral0/workspace/ml/target/classes [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ml --- [INFO] [INFO] Compiling 5 source files to /media/ephemeral0/workspace/ml/target/test-classes [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ml --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/ml/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2012-07-08 01:17:01,851 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAgglomerativeClustering - Batch clustering remaining 6 nodes [INFO] 2012-07-08 01:17:01,987 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - [INFO] l=nu w=6.00 [Cluster 10] n=6 sd=0.00 [INFO] | l=29.91 w=1.00 [Cluster 5] n=1 sd=0.00 [INFO] | l=29.91 w=5.00 [Cluster 9] n=5 sd=0.00 [INFO] | | l=22.45 w=1.00 [Cluster 4] n=1 sd=0.00 [INFO] | | l=22.45 w=4.00 [Cluster 8] n=4 sd=0.00 [INFO] | | | l=15.73 w=1.00 [Cluster 3] n=1 sd=0.00 [INFO] | | | l=15.73 w=3.00 [Cluster 7] n=3 sd=0.00 [INFO] | | | | l=10.07 w=1.00 [Cluster 2] n=1 sd=0.00 [INFO] | | | | l=10.07 w=2.00 [Cluster 6] n=2 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 0] n=1 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 1] n=1 sd=0.00 [INFO] [INFO] 2012-07-08 01:17:01,991 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - found largestLengthSpan = 108.56383323669434 [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.691 sec [INFO] [INFO] Results : [INFO] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ml --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/ml-0.92.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ml --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/ml-0.92-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ ml --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] BUILD SUCCESS [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Total time: 1:01.006s [INFO] [INFO] Finished at: Sun Jul 08 01:17:06 UTC 2012 [INFO] [INFO] Final Memory: 14M/35M [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Checking in modified POMs... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg commit --message '[maven-release-plugin] prepare release ml-0.92' /media/ephemeral0/workspace/ml/pom.xml [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg push ssh://dev.davidsoergel.com//home/hg/ml [INFO] Tagging release with the label ml-0.92... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg tag --message '[maven-release-plugin] copy for tag ml-0.92' ml-0.92 [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg push ssh://dev.davidsoergel.com//home/hg/ml [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg locate [INFO] Transforming 'ml'... [INFO] Not removing release POMs [INFO] Checking in modified POMs... [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg commit --message '[maven-release-plugin] prepare for next development iteration' /media/ephemeral0/workspace/ml/pom.xml [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml && hg push ssh://dev.davidsoergel.com//home/hg/ml [INFO] Release preparation complete. mojoSucceeded org.apache.maven.plugins:maven-release-plugin:2.0(default-cli) mojoStarted org.apache.maven.plugins:maven-release-plugin:2.0(default-cli) [INFO] [INFO] --- maven-release-plugin:2.0:perform (default-cli) @ ml --- [INFO] Checking out the project to perform the release ... [INFO] Removing /media/ephemeral0/workspace/ml/target/checkout [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml/target && hg clone -r ml-0.92 ssh://dev.davidsoergel.com//home/hg/ml /media/ephemeral0/workspace/ml/target/checkout [INFO] EXECUTING: /bin/sh -c cd /media/ephemeral0/workspace/ml/target/checkout && hg locate [INFO] Executing goals 'deploy site-deploy'... [INFO] [INFO] Scanning for projects... [INFO] [WARNING] [INFO] [WARNING] Some problems were encountered while building the effective model for edu.berkeley.compbio:ml:jar:0.92 [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 ml 0.92 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [INFO] [INFO] Compiling 103 source files to /media/ephemeral0/workspace/ml/target/checkout/target/classes [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ml --- [INFO] [INFO] Compiling 5 source files to /media/ephemeral0/workspace/ml/target/checkout/target/test-classes [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ml --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/ml/target/checkout/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2012-07-08 01:18:54,846 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAgglomerativeClustering - Batch clustering remaining 6 nodes [INFO] 2012-07-08 01:18:54,974 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - [INFO] l=nu w=6.00 [Cluster 10] n=6 sd=0.00 [INFO] | l=29.91 w=1.00 [Cluster 5] n=1 sd=0.00 [INFO] | l=29.91 w=5.00 [Cluster 9] n=5 sd=0.00 [INFO] | | l=22.45 w=1.00 [Cluster 4] n=1 sd=0.00 [INFO] | | l=22.45 w=4.00 [Cluster 8] n=4 sd=0.00 [INFO] | | | l=15.73 w=1.00 [Cluster 3] n=1 sd=0.00 [INFO] | | | l=15.73 w=3.00 [Cluster 7] n=3 sd=0.00 [INFO] | | | | l=10.07 w=1.00 [Cluster 2] n=1 sd=0.00 [INFO] | | | | l=10.07 w=2.00 [Cluster 6] n=2 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 0] n=1 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 1] n=1 sd=0.00 [INFO] [INFO] 2012-07-08 01:18:54,975 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - found largestLengthSpan = 108.56383323669434 [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.578 sec [INFO] [INFO] Results : [INFO] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ml --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92.jar [INFO] [INFO] [INFO] [INFO] >>> maven-source-plugin:2.1.2:jar (attach-sources) @ ml >>> [INFO] [INFO] [INFO] [INFO] <<< maven-source-plugin:2.1.2:jar (attach-sources) @ ml <<< [INFO] [INFO] [INFO] [INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ ml --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-sources.jar [INFO] [INFO] [INFO] [INFO] --- maven-javadoc-plugin:2.8.1:jar (attach-javadocs) @ ml --- [INFO] [INFO] [INFO] Loading source files for package edu.berkeley.compbio.ml... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.bayesian... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.kohonen... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.hierarchical... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.stats... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.kmeans... [INFO] Loading source files for package edu.berkeley.compbio.ml.mcmc... [INFO] Loading source files for package edu.berkeley.compbio.ml.mcmc.mcmcmc... [INFO] Loading source files for package edu.berkeley.compbio.ml.distancemeasure... [INFO] Constructing Javadoc information... [INFO] Standard Doclet version 1.7.0_04 [INFO] Building tree for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/BinaryCrossValidationResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/CrossValidationResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/MultiClassCrossValidationResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AbstractCentroidCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AbstractCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AbstractSupervisedOnlineClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AbstractUnsupervisedOnlineClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AdditiveCentroidCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/AdditiveClusterable.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/BasicBatchCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/BatchAdditiveCentroidCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/BatchCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/BatchClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/CentroidCluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/CentroidClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/Cluster.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/Clusterable.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableIterator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableIteratorFactory.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterException.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusteringStats.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusteringTestResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterList.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterMove.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ClusterRuntimeException.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/CollectionClusterableIterator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/DistanceBasedMultiClassCrossValidationResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/DistanceMatrixBatchClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/EmptyPointClusterFilter.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/EmptyProhibitionModel.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/NoGoodClusterException.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/OnlineClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/PermutingClusterableIteratorFactory.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/PointClusterFilter.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/ProhibitionModel.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/PrototypeBasedCentroidClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SampleInitializedBatchClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SampleInitializedOnlineClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SemisupervisedClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SimpleClusterable.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SimpleClusterList.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SimpleHierarchicalCentroidClusterList.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/UnsupervisedClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/BayesianClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/KNNClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.BestLabelPair.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.VotingResults.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/NearestNeighborClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/TacoaClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/BruteForceSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/CoarseGridSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/DiffusableLabelClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/HillClimbingSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2DSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMCell.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/LabelDiffuser.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/NearCurrentPositionSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/WithinCurrentRadiusSearchStrategy.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/Agglomerator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/AverageLinkageAgglomerator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/BatchAgglomerativeClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/BatchHierarchicalClusteringMethod.html... 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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/Agglomerator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/BatchAgglomerativeClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/CompleteLinkageAgglomerator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/OnlineHierarchicalClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/AverageLinkageAgglomerator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/HierarchicalClusteringMethod.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/OnlineAgglomerativeClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/ACERichnessEstimate.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/Chao1RichnessEstimate.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/HierarchicalClusteringStats.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/AbundanceModel.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/ClusteringSimilarityModel.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/class-use/KmeansClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/class-use/GrowableKmeansClustering.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/Move.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/MoveTypeSet.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/MonteCarlo.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/MoveNotPossibleException.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/TextFileDataCollector.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/EnergyMove.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/MonteCarloState.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/DataCollector.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/class-use/ProbabilityMove.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/class-use/ChainList.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/class-use/MetropolisCoupledMonteCarlo.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/class-use/MetropolisCoupledSwapMove.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/class-use/EuclideanDistance.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/class-use/DistanceMeasureRuntimeException.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/allclasses-noframe.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/index.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/overview-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/help-doc.html... [INFO] 70 warnings [INFO] [WARNING] Javadoc Warnings [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/BinaryCrossValidationResults.java:89: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.java:666: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.java:309: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AdditiveClusterable.java:84: warning - @param argument "object" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BatchClusteringMethod.java:64: warning - @param argument "testIterator" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:197: warning - @return tag cannot be used in method with void return type. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SampleInitializedBatchClusteringMethod.java:25: warning - @param argument "initSamples" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "trainingCollectionIteratorFactory" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "prototypeFactory" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "trainingEpochs" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/UnsupervisedClusteringMethod.java:40: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/KNNClustering.java:106: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:294: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:223: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/TacoaClustering.java:168: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/BruteForceSearchStrategy.java:61: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/CoarseGridSearchStrategy.java:80: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/HillClimbingSearchStrategy.java:74: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:82: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:82: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:243: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:463: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:78: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:78: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:353: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NearCurrentPositionSearchStrategy.java:71: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.java:55: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.java:55: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/BatchHierarchicalClusteringMethod.java:64: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/BatchHierarchicalClusteringMethod.java:64: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalCentroidCluster.java:316: warning - @return tag cannot be used in method with void return type. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see: missing '#': "MonteCarloState.writeToDataCollector()" [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see: can't find MonteCarloState.writeToDataCollector() in edu.berkeley.compbio.ml.mcmc.DataCollector [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/MonteCarloState.java:54: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-javadoc.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ ml --- [INFO] [INFO] Building jar: /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default) @ ml --- [INFO] [INFO] [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ml --- [INFO] [INFO] Installing /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/ml/0.92/ml-0.92.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/ml/target/checkout/pom.xml to /home/ec2-user/.m2/repository/edu/berkeley/compbio/ml/0.92/ml-0.92.pom [INFO] [INFO] Installing /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-sources.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/ml/0.92/ml-0.92-sources.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-javadoc.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/ml/0.92/ml-0.92-javadoc.jar [INFO] [INFO] Installing /media/ephemeral0/workspace/ml/target/checkout/target/ml-0.92-tests.jar to /home/ec2-user/.m2/repository/edu/berkeley/compbio/ml/0.92/ml-0.92-tests.jar [INFO] [INFO] [INFO] [INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ ml --- [INFO] WAGON_VERSION: 1.0-beta-2 [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92.jar (195 KB at 49.6 KB/sec) [INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92.pom [INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92.pom (7 KB at 1.1 KB/sec) [INFO] Downloading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/maven-metadata.xml [INFO] Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/maven-metadata.xml (344 B at 1.4 KB/sec) [INFO] Uploading: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/maven-metadata.xml [INFO] Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/maven-metadata.xml (354 B at 0.5 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-sources.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-sources.jar (187 KB at 99.8 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-javadoc.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-javadoc.jar (688 KB at 131.7 KB/sec) [INFO] Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-tests.jar [INFO] Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/releases/edu/berkeley/compbio/ml/0.92/ml-0.92-tests.jar (17 KB at 10.4 KB/sec) [INFO] [INFO] [INFO] [INFO] --- maven-site-plugin:3.1:site (default-site) @ ml --- [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) @ ml >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [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) @ ml <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ ml >>> [INFO] [INFO] [INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:javadoc (report:javadoc) @ ml <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:test-javadoc (report:test-javadoc) @ ml >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [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) @ ml <<< [INFO] [INFO] [INFO] [INFO] >>> maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ ml >>> [INFO] [INFO] [INFO] [INFO] <<< maven-javadoc-plugin:2.8.1:aggregate (report:aggregate) @ ml <<< [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) @ ml >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- cobertura-maven-plugin:2.5.1:instrument (report:cobertura) @ ml --- [INFO] [INFO] Cobertura 1.9.4.1 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file [INFO] Instrumenting 124 files to /media/ephemeral0/workspace/ml/target/checkout/target/generated-classes/cobertura [INFO] [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class edu.berkeley.compbio.ml.cluster.kohonen.KohonenSOM2D$1. Perhaps you need to compile with debug=true? [INFO] [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class edu.berkeley.compbio.ml.cluster.kohonen.KohonenSOMnD$1. Perhaps you need to compile with debug=true? [INFO] [cobertura] WARN [main] net.sourceforge.cobertura.instrument.ClassInstrumenter - No line number information found for class edu.berkeley.compbio.ml.cluster.stats.ClusteringSimilarityModel$1. Perhaps you need to compile with debug=true? [INFO] Cobertura: Saved information on 124 classes. [INFO] Instrument time: 4940ms [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) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ml --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ml --- [INFO] [INFO] Surefire report directory: /media/ephemeral0/workspace/ml/target/checkout/target/surefire-reports [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite [INFO] 2012-07-08 01:21:24,619 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAgglomerativeClustering - Batch clustering remaining 6 nodes [INFO] 2012-07-08 01:21:24,743 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - [INFO] l=nu w=6.00 [Cluster 10] n=6 sd=0.00 [INFO] | l=29.91 w=1.00 [Cluster 5] n=1 sd=0.00 [INFO] | l=29.91 w=5.00 [Cluster 9] n=5 sd=0.00 [INFO] | | l=22.45 w=1.00 [Cluster 4] n=1 sd=0.00 [INFO] | | l=22.45 w=4.00 [Cluster 8] n=4 sd=0.00 [INFO] | | | l=15.73 w=1.00 [Cluster 3] n=1 sd=0.00 [INFO] | | | l=15.73 w=3.00 [Cluster 7] n=3 sd=0.00 [INFO] | | | | l=10.07 w=1.00 [Cluster 2] n=1 sd=0.00 [INFO] | | | | l=10.07 w=2.00 [Cluster 6] n=2 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 0] n=1 sd=0.00 [INFO] | | | | | l=0.50 w=1.00 [Cluster 1] n=1 sd=0.00 [INFO] [INFO] 2012-07-08 01:21:24,745 [main] INFO edu.berkeley.compbio.ml.cluster.hierarchical.OnlineAverageLinkageTest - found largestLengthSpan = 108.56383323669434 [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.596 sec [INFO] Flushing results... [INFO] Flushing results done [INFO] Cobertura: Loaded information on 124 classes. [INFO] Cobertura: Saved information on 124 classes. [INFO] [INFO] Results : [INFO] [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] [INFO] [INFO] <<< cobertura-maven-plugin:2.5.1:cobertura (report:cobertura) @ ml <<< [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) @ ml >>> [INFO] [INFO] [INFO] [INFO] <<< maven-surefire-report-plugin:2.12:failsafe-report-only (report:failsafe-report-only) @ ml <<< [INFO] [INFO] [INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report (report:report) @ ml >>> [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/main/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ml --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ml --- [INFO] [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] skip non existing resourceDirectory /media/ephemeral0/workspace/ml/target/checkout/src/test/resources [INFO] [INFO] [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ml --- [INFO] [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ml --- [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) @ ml <<< [INFO] [INFO] [INFO] [INFO] >>> maven-surefire-report-plugin:2.12:report-only (report:report-only) @ ml >>> [INFO] [INFO] [INFO] [INFO] <<< maven-surefire-report-plugin:2.12:report-only (report:report-only) @ ml <<< [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:2.4 [INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0 [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/ml [INFO] [INFO] Rendering site with org.apache.maven.skins:maven-default-skin:jar:1.0 skin. [INFO] [INFO] Skipped "Test JavaDocs" report, file "testapidocs/index.html" already exists for the English version. [INFO] [INFO] Skipped "JavaDocs" report, file "apidocs/index.html" already exists for the English version. [INFO] [INFO] Skipped "Source Xref" report, file "xref/index.html" already exists for the English version. [INFO] [INFO] Skipped "Test Source Xref" report, file "xref-test/index.html" already exists for the English version. [INFO] [INFO] Skipped "Surefire Report" report, file "surefire-report.html" already exists for the English version. [INFO] [INFO] Generating "Test JavaDocs" report --- maven-javadoc-plugin:2.8.1 [INFO] [INFO] [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.kohonen... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.hierarchical... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.stats... [INFO] Loading source files for package edu.berkeley.compbio.ml.cluster.kmeans... [INFO] Constructing Javadoc information... [INFO] Standard Doclet version 1.7.0_04 [INFO] Building tree for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2DTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/OnlineAverageLinkageTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/MockClusterableIterator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/ClusteringSimilarityModelTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/KmeansClusteringTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/overview-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/package-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/package-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/package-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/package-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/package-summary.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/package-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/constant-values.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOM2DTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/OnlineAverageLinkageTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/class-use/MockClusterableIterator.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/ClusteringSimilarityModelTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/class-use/KmeansClusteringTest.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-use.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/edu/berkeley/compbio/ml/cluster/stats/package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/allclasses-noframe.html... 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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/package-use.html... [INFO] Building index for all the packages and classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/overview-tree.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/index-all.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/deprecated-list.html... [INFO] Building index for all classes... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/allclasses-frame.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/allclasses-noframe.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/index.html... [INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/overview-summary.html... 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[INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.java:666: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.java:309: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/AdditiveClusterable.java:84: warning - @param argument "object" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BatchClusteringMethod.java:64: warning - @param argument "testIterator" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:197: warning - @return tag cannot be used in method with void return type. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SampleInitializedBatchClusteringMethod.java:25: warning - @param argument "initSamples" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "trainingCollectionIteratorFactory" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "prototypeFactory" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/SupervisedClusteringMethod.java:27: warning - @param argument "trainingEpochs" is not a parameter name. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/UnsupervisedClusteringMethod.java:40: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/KNNClustering.java:106: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:294: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:223: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/TacoaClustering.java:168: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/BruteForceSearchStrategy.java:61: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/CoarseGridSearchStrategy.java:80: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/HillClimbingSearchStrategy.java:74: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:82: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:82: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:243: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.java:463: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:78: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:78: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.java:353: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NearCurrentPositionSearchStrategy.java:71: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.java:55: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.java:55: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/BatchHierarchicalClusteringMethod.java:64: warning - @Author is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/BatchHierarchicalClusteringMethod.java:64: warning - @Version is an unknown tag -- same as a known tag except for case. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidCluster.java:147: warning - Tag @see: reference not found: ClusteringMethod.computeClusterStdDevs [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalCentroidCluster.java:316: warning - @return tag cannot be used in method with void return type. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see: missing '#': "MonteCarloState.writeToDataCollector()" [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see: can't find MonteCarloState.writeToDataCollector() in edu.berkeley.compbio.ml.mcmc.DataCollector [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/MonteCarloState.java:54: warning - @return tag has no arguments. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/mcmc/DataCollector.java:58: warning - Tag @see cannot be used in inline documentation. It can only be used in the following types of documentation: overview, package, class/interface, constructor, field, method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:87: warning - @inheritDoc used but addAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.java:168: warning - @inheritDoc used but addUpNeighborVotes(TreeMultimap<Double, ClusterMove<T, CentroidCluster<T>>>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.java:221: warning - @inheritDoc used but getExclusiveLabel() does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.java:112: warning - @inheritDoc used but initializeWithSamples(ClusterableIterator<T>, int) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.java:95: warning - @inheritDoc used but removeAll(CentroidCluster<T>) does not override or implement any method. [INFO] [WARNING] /media/ephemeral0/workspace/ml/target/checkout/src/main/java/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.java:143: warning - @inheritDoc used but shortClusteringStats(Collection<? extends CentroidCluster<T>>, DissimilarityMeasure<T>) 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 124 classes. [INFO] Report time: 24745ms [INFO] [INFO] [INFO] Cobertura Report generation was successful. [INFO] [INFO] Generating "Surefire Report" report --- maven-surefire-report-plugin:2.12 [INFO] [INFO] Generating "Distribution Management" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "About" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Dependencies" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Issue Tracking" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Project Plugins" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Continuous Integration" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Project License" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Mailing Lists" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Project Team" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Source Repository" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Plugin Management" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] Generating "Project Summary" report --- maven-project-info-reports-plugin:2.4 [INFO] [INFO] [INFO] [INFO] --- maven-site-plugin:3.1:deploy (default-deploy) @ ml --- [INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0 [INFO] [INFO] Parent project loaded from repository: com.davidsoergel:basepom:pom:1.0 [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/ml/ - Session: Opened [INFO] [INFO] Pushing /media/ephemeral0/workspace/ml/target/checkout/target/site [INFO] [INFO] >>> to scpexe://dev.davidsoergel.com/home/build/mavensites/ml/./ [INFO] Executing command: mkdir -p /home/build/mavensites/ml/./ [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/ml/./"' [INFO] [INFO] [INFO] Executing command: mkdir -p /home/build/mavensites/ml//. [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/ml//. [INFO] "' [INFO] [INFO] [INFO] Uploading: ./wagon8336940533939689292.zip to scpexe://dev.davidsoergel.com/home/build/mavensites/ml/ [INFO] [INFO] Executing command: /bin/bash -c 'cd /tmp && scp -i /home/ec2-user/.ssh/id_rsa -o "BatchMode yes" wagon8336940533939689292.zip jenkins@dev.davidsoergel.com:/home/build/mavensites/ml//./wagon8336940533939689292.zip' [INFO] ################################################################################################################################################################################################################################################################################################################################################################################################################################ [INFO] Transfer finished. 1701770 bytes copied in 0.978 seconds [INFO] Executing command: cd /home/build/mavensites/ml/./; unzip -q -o wagon8336940533939689292.zip; rm -f wagon8336940533939689292.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/ml/./; unzip -q -o wagon8336940533939689292.zip; rm -f wagon8336940533939689292.zip"' [INFO] [INFO] [INFO] Executing command: chmod -Rf g+w,a+rX /home/build/mavensites/ml/ [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/ml/"' [INFO] [INFO] [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/ml/ - Session: Disconnecting [INFO] scpexe://dev.davidsoergel.com/home/build/mavensites/ml/ - Session: Disconnected [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] BUILD SUCCESS [INFO] [INFO] ------------------------------------------------------------------------ [INFO] [INFO] Total time: 7:04.786s [INFO] [INFO] Finished at: Sun Jul 08 01:24:38 UTC 2012 [INFO] [INFO] Final Memory: 30M/79M [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Cleaning up after release... mojoSucceeded org.apache.maven.plugins:maven-release-plugin:2.0(default-cli) projectSucceeded edu.berkeley.compbio:ml:0.912-SNAPSHOT sessionEnded [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 9:39.811s [INFO] Finished at: Sun Jul 08 01:24:40 UTC 2012 [INFO] Final Memory: 12M/30M [INFO] ------------------------------------------------------------------------ Projects to build: [MavenProject: edu.berkeley.compbio:ml:0.912-SNAPSHOT @ /media/ephemeral0/workspace/ml/pom.xml] [JENKINS] Archiving /media/ephemeral0/workspace/ml/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/ml/modules/edu.berkeley.compbio$ml/builds/2012-07-07_21-14-41/archive/edu.berkeley.compbio/ml/0.912-SNAPSHOT/ml-0.912-SNAPSHOT.pom Waiting for Jenkins to finish collecting data channel stopped [M2Release] marking build to keep until the next release build your Apache Maven build is setup to use a config with id org.jenkinsci.plugins.configfiles.maven.MavenSettingsConfig1337980147845 but cannot find the config Maven RedeployPublished use remote i-2c07a854 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 ml-0.912-SNAPSHOT.pom Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/maven-metadata.xml Downloaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/maven-metadata.xml (2 KB at 11.3 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/ml-0.912-20120708.012447-18.pom Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/ml-0.912-20120708.012447-18.pom (7 KB at 28.7 KB/sec) Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/maven-metadata.xml Downloaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/maven-metadata.xml (282 B at 0.4 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/0.912-SNAPSHOT/maven-metadata.xml (2 KB at 2.9 KB/sec) Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/maven-metadata.xml Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/ml/maven-metadata.xml (282 B at 0.0 KB/sec) [INFO] Deployment done in 7.3 sec Sending e-mails to: dev@davidsoergel.com Triggering a new build of jlibsvm #16 Triggering a new build of pmax #15 Finished: SUCCESS