SuccessConsole Output

Skipping 20 KB.. Full Log
plexus/plexus-utils/1.5.6/plexus-utils-1.5.6.jar (245 KB at 661.3 KB/sec)
[INFO] Verifying that there are no local modifications...
[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...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/CompleteLinkageAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/ExplicitAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalClusteringStringDistanceMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalExplicitCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/OnlineAgglomerativeClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/OnlineHierarchicalClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/RandomOrderedBatchAgglomerativeClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/SingleLinkageAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/AbundanceModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/ACERichnessEstimate.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/Chao1RichnessEstimate.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/ClusteringSimilarityModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/HierarchicalClusteringStats.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/GrowableKmeansClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/KmeansClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/DataCollector.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/EnergyMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/MonteCarlo.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/MonteCarloState.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/Move.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/MoveNotPossibleException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/MoveTypeSet.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/ProbabilityMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/TextFileDataCollector.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/ChainList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/MetropolisCoupledMonteCarlo.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/MetropolisCoupledSwapMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/DistanceMeasureRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/EuclideanDistance.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/overview-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/distancemeasure/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/package-frame.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/package-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/package-tree.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/constant-values.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/serialized-form.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/class-use/BinaryCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/class-use/MultiClassCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/class-use/CrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AdditiveCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/CentroidClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractUnsupervisedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/Clusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusteringTestResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BatchCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SimpleClusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BatchAdditiveCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/PrototypeBasedCentroidClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BasicCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterableIteratorFactory.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/EmptyPointClusterFilter.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SimpleClusterList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/UnsupervisedClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SupervisedClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractSupervisedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterableDoubleArray.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SampleInitializedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SemisupervisedClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SampleInitializedBatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ProhibitionModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/DistanceMatrixBatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/DistanceBasedMultiClassCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/CentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/OnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterRuntimeException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/PointClusterFilter.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AdditiveClusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/CentroidClusteringUtils.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/Cluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusteringStats.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BasicBatchCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/EmptyProhibitionModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SimpleHierarchicalCentroidClusterList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/NoGoodClusterException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterableIterator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/CollectionClusterableIterator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/class-use/PermutingClusterableIteratorFactory.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/TacoaClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/BayesianClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/LabelDecomposingBayesianClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/MultiNeighborClustering.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/NearestNeighborClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/class-use/KNNClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/CoarseGridSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOM2D.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/NearCurrentPositionSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/WithinCurrentRadiusSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/BruteForceSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOM.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOMCell.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOMnD.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/KohonenSOM2DSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/LabelDiffuser.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/NeighborhoodCollectingLabelDiffuser.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/HillClimbingSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/class-use/DiffusableLabelClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/BatchHierarchicalClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/HierarchicalCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/HierarchicalExplicitCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/RandomOrderedBatchAgglomerativeClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/ExplicitAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/HierarchicalClusteringStringDistanceMatrix.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/class-use/SingleLinkageAgglomerator.html...
[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...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/apidocs/edu/berkeley/compbio/ml/cluster/stats/class-use/ACERichnessEstimate.html...
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[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.
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[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.
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[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.
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[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.
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[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.
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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/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.
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[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.
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[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.
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[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.
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[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
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[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...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/index.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/overview-summary.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/testapidocs/help-doc.html...
[INFO] [INFO] Generating "JavaDocs" report    --- maven-javadoc-plugin:2.8.1
[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/site/apidocs/edu/berkeley/compbio/ml/BinaryCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/CrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/MultiClassCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AbstractCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AbstractCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AbstractClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AbstractSupervisedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AbstractUnsupervisedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AdditiveCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/AdditiveClusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/BasicBatchCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/BasicCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/BatchAdditiveCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/BatchCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/BatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/CentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/CentroidClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/CentroidClusteringUtils.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/Cluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/Clusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableDoubleArray.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableIterator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ClusterableIteratorFactory.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ClusterException.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ClusterMove.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/CollectionClusterableIterator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/DistanceBasedMultiClassCrossValidationResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/DistanceMatrixBatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/EmptyPointClusterFilter.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/EmptyProhibitionModel.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/PermutingClusterableIteratorFactory.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/PointClusterFilter.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/ProhibitionModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/PrototypeBasedCentroidClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SampleInitializedBatchClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SampleInitializedOnlineClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SemisupervisedClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SimpleClusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SimpleClusterList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/SimpleHierarchicalCentroidClusterList.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/KNNClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/LabelDecomposingBayesianClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.BestLabelPair.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/MultiNeighborClustering.VotingResults.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/NearestNeighborClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/bayesian/TacoaClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/BruteForceSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/CoarseGridSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/DiffusableLabelClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/HillClimbingSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2D.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOM2DSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMCell.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/KohonenSOMnD.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/LabelDiffuser.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/NearCurrentPositionSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/NeighborhoodCollectingLabelDiffuser.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kohonen/WithinCurrentRadiusSearchStrategy.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/Agglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/AverageLinkageAgglomerator.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/ExplicitAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalClusteringMethod.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/HierarchicalExplicitCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/OnlineAgglomerativeClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/OnlineHierarchicalClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/RandomOrderedBatchAgglomerativeClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/hierarchical/SingleLinkageAgglomerator.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/stats/AbundanceModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/stats/ACERichnessEstimate.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/stats/Chao1RichnessEstimate.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/stats/ClusteringSimilarityModel.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/stats/HierarchicalClusteringStats.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/GrowableKmeansClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/kmeans/KmeansClustering.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/DataCollector.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/EnergyMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/MonteCarlo.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/MonteCarloState.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/Move.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/MoveNotPossibleException.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/MoveTypeSet.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/ProbabilityMove.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/TextFileDataCollector.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/ChainList.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/mcmc/mcmcmc/MetropolisCoupledMonteCarlo.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AdditiveCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/CentroidClusteringMethod.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractUnsupervisedOnlineClusteringMethod.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusteringTestResults.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SimpleClusterable.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BatchAdditiveCentroidCluster.html...
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[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/BasicCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/ClusterableIteratorFactory.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/AbstractCentroidCluster.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/EmptyPointClusterFilter.html...
[INFO] Generating /media/ephemeral0/workspace/ml/target/checkout/target/site/apidocs/edu/berkeley/compbio/ml/cluster/class-use/SimpleClusterList.html...
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[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.
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[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.
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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
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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
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[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/./"'
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[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"'
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[INFO] [INFO] BUILD SUCCESS
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[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
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[INFO] Cleaning up after release...
mojoSucceeded org.apache.maven.plugins:maven-release-plugin:2.0(default-cli)
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[INFO] Total time: 9:39.811s
[INFO] Finished at: Sun Jul 08 01:24:40 UTC 2012
[INFO] Final Memory: 12M/30M
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Projects to build: [MavenProject: edu.berkeley.compbio:ml:0.912-SNAPSHOT @ /media/ephemeral0/workspace/ml/pom.xml]
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[ERROR] uniqueVersion == false is not anymore supported in maven 3
[INFO] Deployment in dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots (id=dev.davidsoergel.com.snapshot,uniqueVersion=false)
Deploying the main artifact ml-0.912-SNAPSHOT.pom
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Triggering a new build of jlibsvm #16
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