See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/62/changes>
Changes: [kono] Changed method calls for new CyTable parameter. [kono] fixes #377 #457 SUID is supported in Discrete and Passthrough mappings. New parameter had been added for VisualMappingFunctions to allow users to use specific CyTable in addition to Default one. ------------------------------------------ [...truncated 8892 lines...] [INFO] META-INF/spring/bundle-context.xml-legacy already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] org/cytoscape/equations/ already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] org/cytoscape/event/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] META-INF/maven/org.cytoscape/ already added, skipping [INFO] META-INF/maven/org.cytoscape/event-api/ already added, skipping [INFO] META-INF/maven/org.cytoscape/event-api/pom.xml already added, skipping [INFO] META-INF/maven/org.cytoscape/event-api/pom.properties already added, skipping [INFO] META-INF/ already 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already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] META-INF/maven/org.cytoscape/ already added, skipping [INFO] META-INF/spring/ already added, skipping [INFO] META-INF/spring/bundle-context-osgi.xml-legacy already added, skipping [INFO] META-INF/spring/bundle-context.xml-legacy already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] org/cytoscape/util/ already added, skipping [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] META-INF/maven/org.cytoscape/ already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] org/cytoscape/view/ already added, skipping [INFO] org/cytoscape/view/vizmap/ already added, skipping [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [INFO] META-INF/maven/org.cytoscape/ already added, skipping [INFO] org/ already added, skipping [INFO] org/cytoscape/ already added, skipping [INFO] org/cytoscape/work/ already added, skipping [INFO] META-INF/MANIFEST.MF already added, skipping [INFO] META-INF/ already added, skipping [INFO] META-INF/maven/ already added, skipping [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/performance/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$io-impl-performance/builds/2011-11-21_18-06-56/archive/org.cytoscape/io-impl-performance/3.0.0-alpha8-SNAPSHOT/io-impl-performance-3.0.0-alpha8-SNAPSHOT.pom [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/performance/target/io-impl-performance-3.0.0-alpha8-SNAPSHOT.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$io-impl-performance/builds/2011-11-21_18-06-56/archive/org.cytoscape/io-impl-performance/3.0.0-alpha8-SNAPSHOT/io-impl-performance-3.0.0-alpha8-SNAPSHOT.jar [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/performance/target/io-impl-performance-3.0.0-alpha8-SNAPSHOT-sources.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$io-impl-performance/builds/2011-11-21_18-06-56/archive/org.cytoscape/io-impl-performance/3.0.0-alpha8-SNAPSHOT/io-impl-performance-3.0.0-alpha8-SNAPSHOT-sources.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [4.603s] [INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] .. SUCCESS [8.759s] [INFO] Command Executor .................................. SUCCESS [4.743s] [INFO] org.cytoscape.equations-impl ...................... SUCCESS [11.820s] [INFO] model-impl-parent ................................. SUCCESS [1.151s] [INFO] org.cytoscape.model-impl .......................... SUCCESS [17.993s] [INFO] viewmodel-impl-parent ............................. SUCCESS [0.550s] [INFO] org.cytoscape.viewmodel-impl ...................... SUCCESS [6.015s] [INFO] Ding Implementation Parent Pom .................... SUCCESS [0.432s] [INFO] org.cytoscape.util-intr ........................... SUCCESS [6.518s] [INFO] org.cytoscape.spacial ............................. SUCCESS [6.419s] [INFO] org.cytoscape.graph-render ........................ SUCCESS [7:23.287s] [INFO] org.cytoscape.ding-presentation-impl .............. SUCCESS [22.872s] [INFO] org.cytoscape.core-task-impl ...................... SUCCESS [34.863s] [INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] .. SUCCESS [17.511s] [INFO] org.cytoscape.ding-customgraphics-manager-impl .... SUCCESS [6.046s] [INFO] io-impl-parent .................................... SUCCESS [0.457s] [INFO] org.cytoscape.io-impl [org.cytoscape.io] .......... SUCCESS [22.049s] [INFO] event-impl-parent ................................. SUCCESS [0.550s] [INFO] org.cytoscape.event-impl .......................... SUCCESS [14.253s] [INFO] org.cytoscape.layout-impl ......................... SUCCESS [4.826s] [INFO] org.cytoscape.ding-impl-performance-debug ......... SUCCESS [35.131s] [INFO] org.cytoscape.editor-impl ......................... SUCCESS [6.634s] [INFO] org.cytoscape.equations-functions-impl ............ SUCCESS [9.683s] [INFO] org.cytoscape.event-impl-it ....................... SUCCESS [8.776s] [INFO] org.cytoscape.filter-impl [org.cytoscape.filter] .. SUCCESS [9.527s] [INFO] GraphML Reader and Writer for Cytoscape 3 ......... SUCCESS [6.002s] [INFO] org.cytoscape.io-impl-performance ................. FAILURE [26.450s] [INFO] org.cytoscape.layout-cytoscape-impl [csplugins.layout] SKIPPED [INFO] org.cytoscape.layout-jgraph-impl [csplugins.layout] SKIPPED [INFO] org.cytoscape.layout-prefuse-impl [org.cytoscape.prefuse.layouts.internal] SKIPPED [INFO] org.cytoscape.linkout-impl [org.cytoscape.linkout.internal] SKIPPED [INFO] org.cytoscape.log-swing-impl [org.cytoscape.log] .. SKIPPED [INFO] Manual Layout ..................................... SKIPPED [INFO] NetworkAnalyzer ................................... SKIPPED [INFO] Advanced Network Merge ............................ SKIPPED [INFO] org.cytoscape.plugin-impl ......................... SKIPPED [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation] SKIPPED [INFO] org.cytoscape.property.internal ................... SKIPPED [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi] .. SKIPPED [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml] ...... SKIPPED [INFO] org.cytoscape.search-impl [org.cytoscape.search] .. SKIPPED [INFO] org.cytoscape.session-impl ........................ SKIPPED [INFO] Cytoscape Swing Application Impl .................. SKIPPED [INFO] Cytoscape Table Browser Implementation ............ SKIPPED [INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport] SKIPPED [INFO] org.cytoscape.vizmap-gui-impl ..................... SKIPPED [INFO] vizmap-impl-parent ................................ SKIPPED [INFO] org.cytoscape.view.vizmap-impl .................... SKIPPED [INFO] org.cytoscape.io.webservice-biomart-client-impl [org.cytoscape.io.webservice.biomart] SKIPPED [INFO] org.cytoscape.webservice-impl [org.cytoscape.webservice.internal] SKIPPED [INFO] org.cytoscape.webservice-ncbi-client-impl [org.cytoscape.webservice.ncbi] SKIPPED [INFO] work-swing-impl-parent ............................ SKIPPED [INFO] org.cytoscape.work-swing-impl ..................... SKIPPED [INFO] org.cytoscape.application-impl .................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 12:34.401s [INFO] Finished at: Mon Nov 21 18:19:35 GMT-05:00 2011 [INFO] Final Memory: 66M/158M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-assembly-plugin:2.2:attached (make-assembly) on project io-impl-performance: Failed to create assembly: Error creating assembly archive jar-with-dependencies: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar cause : Failed to create assembly: Error creating assembly archive jar-with-dependencies: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-assembly-plugin:2.2:attached (make-assembly) on project io-impl-performance: Failed to create assembly: Error creating assembly archive jar-with-dependencies: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217) 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:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) 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:158) at hudson.maven.Maven3Builder.call(Maven3Builder.java:112) at hudson.maven.Maven3Builder.call(Maven3Builder.java:70) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:287) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:636) Caused by: org.apache.maven.plugin.MojoExecutionException: Failed to create assembly: Error creating assembly archive jar-with-dependencies: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar at org.apache.maven.plugin.assembly.mojos.AbstractAssemblyMojo.execute(AbstractAssemblyMojo.java:468) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Caused by: org.apache.maven.plugin.assembly.archive.ArchiveCreationException: Error creating assembly archive jar-with-dependencies: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar at org.apache.maven.plugin.assembly.archive.DefaultAssemblyArchiver.createArchive(DefaultAssemblyArchiver.java:196) at org.apache.maven.plugin.assembly.mojos.AbstractAssemblyMojo.execute(AbstractAssemblyMojo.java:409) ... 29 more Caused by: org.codehaus.plexus.archiver.ArchiverException: Problem creating jar: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar at org.codehaus.plexus.archiver.AbstractArchiver.createArchive(AbstractArchiver.java:888) at org.apache.maven.plugin.assembly.archive.archiver.AssemblyProxyArchiver.createArchive(AssemblyProxyArchiver.java:512) at org.apache.maven.plugin.assembly.archive.DefaultAssemblyArchiver.createArchive(DefaultAssemblyArchiver.java:192) ... 30 more Caused by: java.io.FileNotFoundException: JAR entry META-INF/maven/org.cytoscape.wrappers/org.swinglabs.swingx/pom.properties not found in /opt/tomcat-home/.m2/repository/org/cytoscape/wrappers/org.swinglabs.swingx/1.6.1/org.swinglabs.swingx-1.6.1.jar at sun.net.www.protocol.jar.JarURLConnection.connect(JarURLConnection.java:140) at sun.net.www.protocol.jar.JarURLConnection.getInputStream(JarURLConnection.java:150) at java.net.URL.openStream(URL.java:1029) at org.codehaus.plexus.components.io.resources.PlexusIoURLResource.getContents(PlexusIoURLResource.java:30) at org.codehaus.plexus.archiver.ArchiveEntry.getInputStream(ArchiveEntry.java:104) at org.codehaus.plexus.archiver.zip.AbstractZipArchiver.zipFile(AbstractZipArchiver.java:590) at org.codehaus.plexus.archiver.zip.AbstractZipArchiver.addResources(AbstractZipArchiver.java:426) at org.codehaus.plexus.archiver.zip.AbstractZipArchiver.createArchiveMain(AbstractZipArchiver.java:349) at org.codehaus.plexus.archiver.zip.AbstractZipArchiver.execute(AbstractZipArchiver.java:250) at org.codehaus.plexus.archiver.AbstractArchiver.createArchive(AbstractArchiver.java:871) ... 32 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