See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/2170/changes>
Changes: [kono] Changed 2D visual lexicon to to minimal lexicon. ------------------------------------------ [...truncated 13 lines...] AU src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.java A src/test/java/org/cytoscape/io/internal/read/datatable A src/test/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderTest.java A src/test/java/org/cytoscape/io/internal/read/sif A src/test/java/org/cytoscape/io/internal/read/sif/InteractionTest.java A src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java A src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java A src/test/java/org/cytoscape/io/internal/read/xgmml A src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java A src/test/resources A src/test/resources/META-INF A src/test/resources/META-INF/spring A src/test/resources/testData A src/test/resources/testData/gml A src/test/resources/testData/gml/example1.gml A src/test/resources/testData/datatable A src/test/resources/testData/datatable/table_space.txt A src/test/resources/testData/datatable/table_comma.txt A src/test/resources/testData/datatable/blank_delimiter.txt A src/test/resources/testData/datatable/table_tab.txt A src/test/resources/testData/sif A src/test/resources/testData/sif/sample.sif A src/test/resources/testData/sif/degenerate.sif A src/test/resources/testData/sif/multiWordProteinsFileTrailingSpaces.sif A src/test/resources/testData/sif/multiWordProteins.sif A src/test/resources/testData/xgmml AU src/test/resources/testData/xgmml/galFiltered.xgmml A src/main A src/main/java A src/main/java/org A src/main/java/org/cytoscape A src/main/java/org/cytoscape/io A src/main/java/org/cytoscape/io/internal A src/main/java/org/cytoscape/io/internal/CyFileFilterImpl.java A src/main/java/org/cytoscape/io/internal/write A src/main/java/org/cytoscape/io/internal/write/gml A src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax A src/main/java/org/cytoscape/io/internal/write/cysession A src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterFactoryImpl.java A src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterImpl.java A src/main/java/org/cytoscape/io/internal/write/sif AU src/main/java/org/cytoscape/io/internal/write/sif/SifNetworkWriterFactory.java AU src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java A src/main/java/org/cytoscape/io/internal/write/datatable A src/main/java/org/cytoscape/io/internal/write/datatable/CyAttributesWriter.java.asdf A src/main/java/org/cytoscape/io/internal/write/session A src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java A src/main/java/org/cytoscape/io/internal/write/session/SessionWriterFactoryImpl.java A src/main/java/org/cytoscape/io/internal/write/xgmml A src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java A src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLNetworkViewWriterFactory.java A src/main/java/org/cytoscape/io/internal/write/bookmarks A src/main/java/org/cytoscape/io/internal/write/bookmarks/BookmarksWriterFactoryImpl.java A src/main/java/org/cytoscape/io/internal/write/bookmarks/BookmarksWriterImpl.java A src/main/java/org/cytoscape/io/internal/write/properties A src/main/java/org/cytoscape/io/internal/write/properties/PropertiesWriterFactoryImpl.java A src/main/java/org/cytoscape/io/internal/write/properties/PropertiesWriterImpl.java A src/main/java/org/cytoscape/io/internal/write/graphics A src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriterFactory.java A src/main/java/org/cytoscape/io/internal/write/graphics/PDFExporter.java A src/main/java/org/cytoscape/io/internal/write/graphics/Exporter.java A src/main/java/org/cytoscape/io/internal/write/graphics/SVGExporter.java A src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java A src/main/java/org/cytoscape/io/internal/write/graphics/PSExporter.java A src/main/java/org/cytoscape/io/internal/write/PresentationWriterManagerImpl.java A src/main/java/org/cytoscape/io/internal/write/AbstractCyNetworkViewWriterFactory.java A src/main/java/org/cytoscape/io/internal/write/CyNetworkViewWriterManagerImpl.java A src/main/java/org/cytoscape/io/internal/write/AbstractWriterManager.java A src/main/java/org/cytoscape/io/internal/write/SessionWriterManagerImpl.java A src/main/java/org/cytoscape/io/internal/write/CyTableWriterManagerImpl.java A src/main/java/org/cytoscape/io/internal/write/AbstractPropertyWriterFactory.java A src/main/java/org/cytoscape/io/internal/write/PropertyWriterManagerImpl.java A src/main/java/org/cytoscape/io/internal/read A src/main/java/org/cytoscape/io/internal/read/cysession A src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReader.java A src/main/java/org/cytoscape/io/internal/read/cysession/CysessionFileFilter.java A src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/gml AU src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java AU src/main/java/org/cytoscape/io/internal/read/gml/GMLFileFilter.java A src/main/java/org/cytoscape/io/internal/read/gml/KeyValue.java A src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java A src/main/java/org/cytoscape/io/internal/read/gml/GMLParser.java A src/main/java/org/cytoscape/io/internal/read/datatable A src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java.asdf A src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java A src/main/java/org/cytoscape/io/internal/read/datatable/TextDataTableReader.java A src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/sif A src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java A src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java A src/main/java/org/cytoscape/io/internal/read/session A src/main/java/org/cytoscape/io/internal/read/session/SessionReaderFactoryImpl.java A src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java A src/main/java/org/cytoscape/io/internal/read/xgmml A src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLParser.java A src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/xgmml/HandlerFactory.java A src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectTypeMap.java A src/main/java/org/cytoscape/io/internal/read/xgmml/ObjectType.java A src/main/java/org/cytoscape/io/internal/read/xgmml/MetadataEntries.java A src/main/java/org/cytoscape/io/internal/read/xgmml/RDFTags.java A src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLFileFilter.java A src/main/java/org/cytoscape/io/internal/read/xgmml/ParseState.java A src/main/java/org/cytoscape/io/internal/read/xgmml/SAXState.java A src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java A src/main/java/org/cytoscape/io/internal/read/xgmml/Handler.java A src/main/java/org/cytoscape/io/internal/read/xgmml/MetadataParser.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFFormat.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AbstractHandler.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroup.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFSource.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroupNode.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGroupDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleListAttributeDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraphics.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDate.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDF.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandleList.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNetworkAttribute.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFTitle.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFType.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFIdentifier.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleRDFDescription.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeHandle.java A src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java A src/main/java/org/cytoscape/io/internal/read/CopyInputStream.java A src/main/java/org/cytoscape/io/internal/read/bookmarks A src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReader.java A src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkFileFilter.java A src/main/java/org/cytoscape/io/internal/read/properties A src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReader.java A src/main/java/org/cytoscape/io/internal/read/properties/PropertiesFileFilter.java A src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/attrs A src/main/java/org/cytoscape/io/internal/read/CySessionReaderManagerImpl.java A src/main/java/org/cytoscape/io/internal/read/expression A src/main/java/org/cytoscape/io/internal/read/expression/mRNAMeasurement.java A src/main/java/org/cytoscape/io/internal/read/expression/ExpressionData.java A src/main/java/org/cytoscape/io/internal/read/CyPropertyReaderManagerImpl.java A src/main/java/org/cytoscape/io/internal/read/CyNetworkViewReaderManagerImpl.java A src/main/java/org/cytoscape/io/internal/read/CyTableReaderManagerImpl.java A src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java A src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java A src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReader.java A src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java A src/main/java/org/cytoscape/io/internal/read/MarkSupportedInputStream.java A src/main/java/org/cytoscape/io/internal/read/AbstractTableReader.java A src/main/java/org/cytoscape/io/internal/util A src/main/java/org/cytoscape/io/internal/util/StreamUtilImpl.java A src/main/java/org/cytoscape/io/internal/util/ReadUtils.java A src/main/resources A src/main/resources/META-INF A src/main/resources/META-INF/spring A src/main/resources/META-INF/spring/bundle-context-osgi.xml A src/main/resources/META-INF/spring/bundle-context.xml A pom.xml U . At revision 24636 WARNING: clock of the subversion server appears to be out of sync. This can result in inconsistent check out behavior. Found mavenVersion 3.0.3 from file jar:file:/R1/tools/maven/apache-maven-3.0.3/lib/maven-core-3.0.3.jar!/META-INF/maven/org.apache.maven/maven-core/pom.properties No emails were triggered. Parsing POMs [trunk] $ java -cp /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven3-agent-1.401.jar:/R1/tools/maven/apache-maven-3.0.3/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /R1/tools/maven/apache-maven-3.0.3 /R1/resources/webservers/tomcat_2/webapps/jenkins/WEB-INF/lib/remoting-1.401.jar /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven3-interceptor-1.401.jar 54742 <===[HUDSON REMOTING CAPACITY]===> channel started Executing Maven: -B -f <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.io-impl [org.cytoscape.io] 3.0.0-alpha2-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ io-impl --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] Copying 0 resource [INFO] [INFO] --- maven-pax-plugin:1.5-SNAPSHOT:compile (default-compile) @ io-impl --- [INFO] Compiling 108 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/target/classes> [INFO] [recovering meta-data] mojoFailed org.ops4j:maven-pax-plugin:1.5-SNAPSHOT(default-compile) projectFailed org.cytoscape:io-impl:3.0.0-alpha2-SNAPSHOT [JENKINS] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20IO%20impl/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 IO impl/modules/org.cytoscape$io-impl/builds/2011-03-30_22-17-52/archive/org.cytoscape/io-impl/3.0.0-alpha2-SNAPSHOT/pom.xml sessionEnded [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.493s [INFO] Finished at: Wed Mar 30 22:17:59 EDT 2011 [INFO] Final Memory: 19M/219M [INFO] ------------------------------------------------------------------------ maven builder waiting mavenExecutionResult exceptions not empty org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.ops4j:maven-pax-plugin:1.5-SNAPSHOT:compile (default-compile) on project io-impl: Compilation failure at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59) at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:319) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156) at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239) at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:146) at hudson.maven.Maven3Builder.call(Maven3Builder.java:124) at hudson.maven.Maven3Builder.call(Maven3Builder.java:71) at hudson.remoting.UserRequest.perform(UserRequest.java:114) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:270) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:516) at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:114) at org.ops4j.pax.construct.lifecycle.BundleCompilerMojo.execute(BundleCompilerMojo.java:74) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Sending e-mails to: [email protected] channel stopped Skipping sonar analysis due to snapshot dependency build trigger -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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