See <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20application/6/>
------------------------------------------ [...truncated 1598 lines...] testGetColorBypass(cytoscape.visual.BypassHelperTest) testParseColorText(cytoscape.util.ColorUtilTest) testGetColorAsText(cytoscape.util.ColorUtilTest) testBug925(cytoscape.view.CytoscapeViewTest) testFilterToViewSelect(cytoscape.view.CytoscapeViewTest) testViewToFilterSelect(cytoscape.view.CytoscapeViewTest) testGetReader(cytoscape.util.GMLFileFilterTest) testWriter(cytoscape.visual.mappings.discrete.DiscreteMappingWriterTest) testControllerTypeWriting(cytoscape.visual.mappings.discrete.DiscreteMappingWriterTest) testControllerTypeWritingWithAttr(cytoscape.visual.mappings.discrete.DiscreteMappingWriterTest) testPassThrough(cytoscape.visual.mappings.PassthroughMappingTest) testNestedNetworkReconstruction1(cytoscape.data.readers.CytoscapeSessionReaderTest) testNestedNetworkReconstruction2(cytoscape.data.readers.CytoscapeSessionReaderTest) testGetImportHandler(cytoscape.CytoscapeTest) testNullNetwork(cytoscape.CytoscapeTest) testCreateNonexistentNetwork(cytoscape.CytoscapeTest) testBug839(cytoscape.CytoscapeTest) testgetCyEdgeWithStrings(cytoscape.CytoscapeTest) testgetCyEdgeWithNodes(cytoscape.CytoscapeTest) testGetCyEdgeWithBadNodeStrings(cytoscape.CytoscapeTest) testSetNestedNetworkAndGetNestedNetwork(cytoscape.CytoscapeTest) testSetNestedNetwork_before(cytoscape.CyNodeTest) testSetNestedNetwork_after(cytoscape.CyNodeTest) testGMLImport(cytoscape.data.readers.FileImporterTest) testXGMMLImport(cytoscape.data.readers.FileImporterTest) testSIFImport(cytoscape.data.readers.FileImporterTest) testReadFromTypicalFile(cytoscape.data.readers.InteractionsReaderTest) testReadFileWithNoInteractions(cytoscape.data.readers.InteractionsReaderTest) testGetGraph(cytoscape.data.readers.InteractionsReaderTest) testGetGraphAndEdgeAttributes(cytoscape.data.readers.InteractionsReaderTest) testReadMultiWordProteinsFile(cytoscape.data.readers.InteractionsReaderTest) testReadMultiWordProteinsFileWithErrantSpaces(cytoscape.data.readers.InteractionsReaderTest) testProperties(cytoscape.visual.VizMapPropertiesTest) testVisualStyle(cytoscape.visual.VizMapPropertiesTest) testDefaultAppearance(cytoscape.visual.NodeAppearanceCalculatorTest) testApplyProperties(cytoscape.visual.NodeAppearanceCalculatorTest) testNodeSizeLock(cytoscape.visual.NodeAppearanceCalculatorTest) testBypass(cytoscape.visual.NodeAppearanceCalculatorTest) testGood1(cytoscape.data.readers.NNFReaderTest) testGood2(cytoscape.data.readers.NNFReaderTest) testGood3(cytoscape.data.readers.NNFReaderTest) testGood4(cytoscape.data.readers.NNFReaderTest) testGood5(cytoscape.data.readers.NNFReaderTest) testGood6(cytoscape.data.readers.NNFReaderTest) testBad1(cytoscape.data.readers.NNFReaderTest) testBad2(cytoscape.data.readers.NNFReaderTest) testMultipleFiles(cytoscape.data.readers.NNFReaderTest) testCtor(cytoscape.data.SelectEventTest) testSmallGraphRead(cytoscape.data.readers.GMLReaderTest) testMediumGraphRead(cytoscape.data.readers.GMLReaderTest) testIllFormattedGML(cytoscape.data.readers.GMLReaderTest) testBug1565(cytoscape.data.readers.GMLReaderTest) testFilterToView(cytoscape.view.FlagAndSelectionHandlerTest) testViewToFilter(cytoscape.view.FlagAndSelectionHandlerTest) testParseRGBTest(cytoscape.util.MiscTest) testGetName(cytoscape.data.ontology.OntologyTest) testGetCurator(cytoscape.data.ontology.OntologyTest) testAdd(cytoscape.data.ontology.OntologyTest) testSize(cytoscape.data.ontology.OntologyTest) testGetTerms(cytoscape.data.ontology.OntologyTest) testContainsTerm(cytoscape.data.ontology.OntologyTest) testGetTerm(cytoscape.data.ontology.OntologyTest) testToString(cytoscape.data.ontology.OntologyTest) testContainsTriple(cytoscape.data.ontology.OntologyTest) testCreateTermStringString(cytoscape.data.ontology.OntologyTest) testCreateTermStringStringObjectArray(cytoscape.data.ontology.OntologyTest) testCreateTriple(cytoscape.data.ontology.OntologyTest) testDeleteTerm(cytoscape.data.ontology.OntologyTest) testGetDescription(cytoscape.data.ontology.OntologyTest) testGetTriples(cytoscape.data.ontology.OntologyTest) testGetXrefMap(cytoscape.data.ontology.readers.DBCrossReferenceReaderTest) testBug(cytoscape.BugHideNodeEventFiringTest) testBasic(cytoscape.data.CyNetworkEventTest) testSetNodeAttributeValue(cytoscape.data.NetworkDataTest) testSingleFlags(cytoscape.data.SelectFilterTest) testGroupFlags(cytoscape.data.SelectFilterTest) testFlagAll(cytoscape.data.SelectFilterTest) testListeners(cytoscape.data.SelectFilterTest) testMakeNewMetadataMap(cytoscape.data.readers.MetadataParserTest) testSetMetadata(cytoscape.data.readers.MetadataParserTest) testToString(cytoscape.data.CyAttributesUtilsTest) testTraverseAttributeValues(cytoscape.data.CyAttributesUtilsTest) testCopyAttributes(cytoscape.data.CyAttributesUtilsTest) testCopyAttribute(cytoscape.data.CyAttributesUtilsTest) testCopyAttribute2(cytoscape.data.CyAttributesUtilsTest) testNetwork(cytoscape.util.GraphSetUtilsTest) testIntersection(cytoscape.util.GraphSetUtilsTest) testDifference(cytoscape.util.GraphSetUtilsTest) testDifference2(cytoscape.util.GraphSetUtilsTest) testDifference_2(cytoscape.util.GraphSetUtilsTest) testDifference2_2(cytoscape.util.GraphSetUtilsTest) testUnion(cytoscape.util.GraphSetUtilsTest) testReader(cytoscape.visual.mappings.continuous.TestContinuousMappingReader) testPluginFileReader(cytoscape.plugin.PluginFileReaderTest) testGetProjectName(cytoscape.plugin.PluginFileReaderTest) testGetProjectDescription(cytoscape.plugin.PluginFileReaderTest) testGetProjectUrl(cytoscape.plugin.PluginFileReaderTest) testGetPlugins(cytoscape.plugin.PluginFileReaderTest) testGetPluginsLicense(cytoscape.plugin.PluginFileReaderTest) testGetThemes(cytoscape.plugin.PluginFileReaderTest) testReadFileMissingThemes(cytoscape.plugin.PluginFileReaderTest) testVersionReads(cytoscape.plugin.PluginFileReaderTest) testThemePlugins(cytoscape.plugin.PluginFileReaderTest) testDownloadPluginWebstart(cytoscape.plugin.PluginManagerTest) testInquireString(cytoscape.plugin.PluginManagerTest) testInquirePartialXML(cytoscape.plugin.PluginManagerTest) testInstallTheme(cytoscape.plugin.PluginManagerTest) testInstallPlugin(cytoscape.plugin.PluginManagerTest) testInstallPluginZip(cytoscape.plugin.PluginManagerTest) testInstallIncorrectFileType(cytoscape.plugin.PluginManagerTest) testDeletePluginInfo(cytoscape.plugin.PluginManagerTest) testDeletePlugin(cytoscape.plugin.PluginManagerTest) testDeleteTheme(cytoscape.plugin.PluginManagerTest) testFindThemeUpdates(cytoscape.plugin.PluginManagerTest) testFindPluginUpdates(cytoscape.plugin.PluginManagerTest) testUpdateTheme(cytoscape.plugin.PluginManagerTest) testUpdatePlugin(cytoscape.plugin.PluginManagerTest) testDownloadGoodTheme(cytoscape.plugin.PluginManagerTest) testDownloadGoodPlugin(cytoscape.plugin.PluginManagerTest) testDownloadBadPlugin(cytoscape.plugin.PluginManagerTest) testDuplicates(cytoscape.plugin.PluginManagerTest) Tests run: 344, Failures: 0, Errors: 178, Skipped: 0 [HUDSON] Recording test results [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20application/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cytoscape 2.X application/modules/cytoscape$application/builds/2010-08-04_15-05-44/archive/cytoscape/application/2.8.0-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] There are test failures. Please refer to <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20application/ws/trunk/target/surefire-reports> for the individual test results. [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1 minute 36 seconds [INFO] Finished at: Wed Aug 04 15:07:23 EDT 2010 [INFO] Final Memory: 73M/674M [INFO] ------------------------------------------------------------------------ Waiting for Hudson to finish collecting data Maven failed with error. Sending e-mails to: [email protected] channel stopped [trunk] $ /R1/tools/maven/apache-maven-2.1.0/bin/mvn org.codehaus.sonar:sonar-maven-plugin:1.8:sonar -Dsonar.jdbc.driver=com.mysql.jdbc.Driver -Dsonar.jdbc.username=sonar -Dsonar.jdbc.password=deploysonar -Dsonar.jdbc.url=jdbc:mysql://10.20.1.1:7070/sonar -Dsonar.host.url=http://localhost:8021/sonar/ -Dsonar.skipInstall=true [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Application [INFO] task-segment: [org.codehaus.sonar:sonar-maven-plugin:1.8:sonar] (aggregator-style) [INFO] ------------------------------------------------------------------------ [INFO] [sonar:sonar] [INFO] Sonar host: http://localhost:8021/sonar [INFO] Sonar version: 1.8 [INFO] [sonar-core:internal] [INFO] Sonar JDBC URL: jdbc:mysql://10.20.1.1:7070/sonar [INFO] Sonar JDBC login: sonar [INFO] Sonar JDBC driver: com.mysql.jdbc.Driver [INFO] Sonar branch: [INFO] ------------------------------------------------------------------------ [ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Can not execute Sonar Embedded error: can not autodetect the dialect Communications link failure due to underlying exception: ** BEGIN NESTED EXCEPTION ** java.net.ConnectException MESSAGE: Connection refused STACKTRACE: java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) at java.net.Socket.connect(Socket.java:529) at java.net.Socket.connect(Socket.java:478) at java.net.Socket.<init>(Socket.java:375) at java.net.Socket.<init>(Socket.java:218) at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256) at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:271) at com.mysql.jdbc.Connection.createNewIO(Connection.java:2771) at com.mysql.jdbc.Connection.<init>(Connection.java:1555) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:285) at java.sql.DriverManager.getConnection(DriverManager.java:582) at java.sql.DriverManager.getConnection(DriverManager.java:185) at org.sonar.commons.database.DriverDatabaseConnector.getConnection(DriverDatabaseConnector.java:90) at org.sonar.commons.database.AbstractDatabaseConnector.getDialect(AbstractDatabaseConnector.java:167) at org.sonar.commons.database.DriverDatabaseConnector.getEntityManagerFactory(DriverDatabaseConnector.java:111) at org.sonar.commons.database.DriverDatabaseConnector.createEntityManager(DriverDatabaseConnector.java:139) at org.sonar.commons.database.DatabaseSession.start(DatabaseSession.java:55) at org.sonar.commons.database.ThreadLocalDatabaseSessionFactory.getSession(ThreadLocalDatabaseSessionFactory.java:35) at org.sonar.commons.database.DatabaseSessionProvider.provide(DatabaseSessionProvider.java:28) 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.picocontainer.injectors.MethodInjector.invokeMethod(MethodInjector.java:137) at org.picocontainer.injectors.MethodInjector.access$000(MethodInjector.java:39) at org.picocontainer.injectors.MethodInjector$2.run(MethodInjector.java:123) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:289) at org.picocontainer.injectors.MethodInjector.decorateComponentInstance(MethodInjector.java:130) at org.picocontainer.injectors.CompositeInjector.decorateComponentInstance(CompositeInjector.java:59) at org.picocontainer.injectors.Reinjector.reinject(Reinjector.java:99) at org.picocontainer.injectors.ProviderAdapter.getComponentInstance(ProviderAdapter.java:84) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:573) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:534) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:546) at org.sonar.mojo.MavenExtensionsContainer.stop(MavenExtensionsContainer.java:91) at org.sonar.mojo.InternalMojo.execute(InternalMojo.java:153) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:483) at org.sonar.mojo.bootstrap.Bootstraper.executeMojo(Bootstraper.java:76) at org.sonar.mojo.bootstrap.Bootstraper.start(Bootstraper.java:62) at org.sonar.mojo.bootstrap.SonarMojo.execute(SonarMojo.java:112) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:483) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:678) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:553) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:523) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:371) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:268) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:181) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:356) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:137) at org.apache.maven.cli.MavenCli.main(MavenCli.java:356) 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.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) at org.codehaus.classworlds.Launcher.main(Launcher.java:375) ** END NESTED EXCEPTION ** Last packet sent to the server was 1 ms ago. [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2 seconds [INFO] Finished at: Wed Aug 04 15:07:32 EDT 2010 [INFO] Final Memory: 21M/338M [INFO] ------------------------------------------------------------------------ -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
