See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/692/changes>
Changes: [mes] Changed node and edge indices from ints to longs so that now indices have the same value as the SUID. [mes] added ignore ------------------------------------------ [...truncated 4234 lines...] [INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] [INFO] Command Executor [INFO] org.cytoscape.equations-impl [INFO] model-impl-parent [INFO] org.cytoscape.model-impl [INFO] viewmodel-impl-parent [INFO] org.cytoscape.viewmodel-impl [INFO] Ding Implementation Parent Pom [INFO] org.cytoscape.util-intr [INFO] org.cytoscape.spacial [INFO] org.cytoscape.graph-render [INFO] org.cytoscape.ding-presentation-impl [INFO] org.cytoscape.core-task-impl [INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] [INFO] org.cytoscape.ding-customgraphics-manager-impl [INFO] org.cytoscape.group-impl [org.cytoscape.group.internal] [INFO] io-impl-parent [INFO] org.cytoscape.io-impl [org.cytoscape.io.internal] [INFO] event-impl-parent [INFO] org.cytoscape.event-impl [INFO] org.cytoscape.layout-impl [INFO] org.cytoscape.ding-impl-performance-debug [INFO] org.cytoscape.editor-impl [INFO] org.cytoscape.equations-functions-impl [INFO] org.cytoscape.event-impl-it [INFO] org.cytoscape.filter-impl [org.cytoscape.filter.internal] [INFO] GraphML Reader and Writer for Cytoscape 3 [INFO] org.cytoscape.group-data-impl [org.cytoscape.group.data.internal] [INFO] org.cytoscape.group-view-impl [org.cytoscape.group.view.internal] [INFO] org.cytoscape.io-impl-performance [INFO] org.cytoscape.layout-cytoscape-impl [csapps.layout] [INFO] org.cytoscape.layout-jgraph-impl [csapps.layout] [INFO] org.cytoscape.layout-prefuse-impl [org.cytoscape.prefuse.layouts.internal] [INFO] org.cytoscape.linkout-impl [org.cytoscape.linkout.internal] [INFO] org.cytoscape.log-swing-impl [org.cytoscape.log.internal] [INFO] Manual Layout [INFO] org.cytoscape.model-impl-performance-debug [INFO] NetworkAnalyzer [INFO] CyMerge [INFO] org.cytoscape.app-impl [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation.internal] [INFO] org.cytoscape.property.internal [INFO] psi-mi-impl-parent [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi.internal] [INFO] org.cytoscape.psi-mi-impl-performance [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml.internal] [INFO] org.cytoscape.search-impl [org.cytoscape.search.internal] [INFO] org.cytoscape.session-impl [INFO] Cytoscape Swing Application Impl [INFO] Cytoscape Table Browser Implementation [INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport.internal] [INFO] org.cytoscape.vizmap-gui-impl [INFO] vizmap-impl-parent [INFO] org.cytoscape.view.vizmap-impl [INFO] org.cytoscape.io.webservice-biomart-client-impl [org.cytoscape.io.webservice.biomart] [INFO] org.cytoscape.webservice-impl [org.cytoscape.webservice.internal] [INFO] org.cytoscape.webservice-ncbi-client-impl [org.cytoscape.webservice.ncbi] [INFO] work-swing-impl-parent [INFO] org.cytoscape.work-swing-impl [INFO] org.cytoscape.application-impl [INFO] org.cytoscape.webservice-psicquic-client-impl [org.cytoscape.webservice.psicquic] [INFO] datasource-impl [INFO] datasource-biogrid-impl [INFO] org.cytoscape.welcome-impl [org.cytoscape.welcome.internal] [INFO] org.cytoscape.gui-cmdline-parser-impl [org.cytoscape.cmdline.gui.internal] [INFO] edge-bundler [INFO] org.cytoscape.scripting-impl [org.cytoscape.scripting.internal] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Implementation Parent Project POM 3.0.0-alpha8-SNAPSHOT [INFO] ------------------------------------------------------------------------ ignoring exception during new ExecutedMojo null log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter). log4j:WARN Please initialize the log4j system properly. [INFO] [INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ impl-parent --- [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ impl-parent --- [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> to /opt/tomcat-home/.m2/repository/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-SNAPSHOT.pom [INFO] [INFO] --- maven-deploy-plugin:2.5:deploy (default-deploy) @ impl-parent --- Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 6.6 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20120403.200333-833.pom Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-20120403.200333-833.pom (11 KB at 81.2 KB/sec) Downloading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Downloaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (405 B at 5.7 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml (619 B at 8.2 KB/sec) Uploading: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml Uploaded: http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/impl-parent/maven-metadata.xml (405 B at 4.8 KB/sec) [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$impl-parent/builds/2012-04-03_15-03-23/archive/org.cytoscape/impl-parent/3.0.0-alpha8-SNAPSHOT/impl-parent-3.0.0-alpha8-SNAPSHOT.pom [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.biopax-impl [org.cytoscape.biopax] 3.0.0-alpha8-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ biopax-impl --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 13 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ biopax-impl --- [INFO] Compiling 28 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/target/classes> [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java>:[36,-1] cannot access org.cytoscape.service.util.AbstractCyActivator bad class file: org/cytoscape/service/util/AbstractCyActivator.class(org/cytoscape/service/util:AbstractCyActivator.class) unable to access file: corrupted zip file [INFO] 1 error [INFO] ------------------------------------------------------------- [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$biopax-impl/builds/2012-04-03_15-03-23/archive/org.cytoscape/biopax-impl/3.0.0-alpha8-SNAPSHOT/biopax-impl-3.0.0-alpha8-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [4.311s] [INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] .. FAILURE [3.756s] [INFO] Command Executor .................................. SKIPPED [INFO] org.cytoscape.equations-impl ...................... SKIPPED [INFO] model-impl-parent ................................. SKIPPED [INFO] org.cytoscape.model-impl .......................... SKIPPED [INFO] viewmodel-impl-parent ............................. SKIPPED [INFO] org.cytoscape.viewmodel-impl ...................... SKIPPED [INFO] Ding Implementation Parent Pom .................... SKIPPED [INFO] org.cytoscape.util-intr ........................... SKIPPED [INFO] org.cytoscape.spacial ............................. SKIPPED [INFO] org.cytoscape.graph-render ........................ SKIPPED [INFO] org.cytoscape.ding-presentation-impl .............. SKIPPED [INFO] org.cytoscape.core-task-impl ...................... SKIPPED [INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] .. SKIPPED [INFO] org.cytoscape.ding-customgraphics-manager-impl .... SKIPPED [INFO] org.cytoscape.group-impl [org.cytoscape.group.internal] SKIPPED [INFO] io-impl-parent .................................... SKIPPED [INFO] org.cytoscape.io-impl [org.cytoscape.io.internal] . SKIPPED [INFO] event-impl-parent ................................. SKIPPED [INFO] org.cytoscape.event-impl .......................... SKIPPED [INFO] org.cytoscape.layout-impl ......................... SKIPPED [INFO] org.cytoscape.ding-impl-performance-debug ......... SKIPPED [INFO] org.cytoscape.editor-impl ......................... SKIPPED [INFO] org.cytoscape.equations-functions-impl ............ SKIPPED [INFO] org.cytoscape.event-impl-it ....................... SKIPPED [INFO] org.cytoscape.filter-impl [org.cytoscape.filter.internal] SKIPPED [INFO] GraphML Reader and Writer for Cytoscape 3 ......... SKIPPED [INFO] org.cytoscape.group-data-impl [org.cytoscape.group.data.internal] SKIPPED [INFO] org.cytoscape.group-view-impl [org.cytoscape.group.view.internal] SKIPPED [INFO] org.cytoscape.io-impl-performance ................. SKIPPED [INFO] org.cytoscape.layout-cytoscape-impl [csapps.layout] SKIPPED [INFO] org.cytoscape.layout-jgraph-impl [csapps.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.internal] SKIPPED [INFO] Manual Layout ..................................... SKIPPED [INFO] org.cytoscape.model-impl-performance-debug ........ SKIPPED [INFO] NetworkAnalyzer ................................... SKIPPED [INFO] CyMerge ........................................... SKIPPED [INFO] org.cytoscape.app-impl ............................ SKIPPED [INFO] org.cytoscape.presentation-impl [org.cytoscape.view.presentation.internal] SKIPPED [INFO] org.cytoscape.property.internal ................... SKIPPED [INFO] psi-mi-impl-parent ................................ SKIPPED [INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi.internal] SKIPPED [INFO] org.cytoscape.psi-mi-impl-performance ............. SKIPPED [INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml.internal] SKIPPED [INFO] org.cytoscape.search-impl [org.cytoscape.search.internal] 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.internal] 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] org.cytoscape.webservice-psicquic-client-impl [org.cytoscape.webservice.psicquic] SKIPPED [INFO] datasource-impl ................................... SKIPPED [INFO] datasource-biogrid-impl ........................... SKIPPED [INFO] org.cytoscape.welcome-impl [org.cytoscape.welcome.internal] SKIPPED [INFO] org.cytoscape.gui-cmdline-parser-impl [org.cytoscape.cmdline.gui.internal] SKIPPED [INFO] edge-bundler ...................................... SKIPPED [INFO] org.cytoscape.scripting-impl [org.cytoscape.scripting.internal] SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11.315s [INFO] Finished at: Tue Apr 03 15:03:38 GMT-05:00 2012 [INFO] Final Memory: 21M/50M [INFO] ------------------------------------------------------------------------ Waiting for Jenkins to finish collecting data mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project biopax-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java>:[36,-1] cannot access org.cytoscape.service.util.AbstractCyActivator bad class file: org/cytoscape/service/util/AbstractCyActivator.class(org/cytoscape/service/util:AbstractCyActivator.class) unable to access file: corrupted zip file cause : Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java>:[36,-1] cannot access org.cytoscape.service.util.AbstractCyActivator bad class file: org/cytoscape/service/util/AbstractCyActivator.class(org/cytoscape/service/util:AbstractCyActivator.class) unable to access file: corrupted zip file Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project biopax-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java>:[36,-1] cannot access org.cytoscape.service.util.AbstractCyActivator bad class file: org/cytoscape/service/util/AbstractCyActivator.class(org/cytoscape/service/util:AbstractCyActivator.class) unable to access file: corrupted zip file 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: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.CompilationFailureException: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java>:[36,-1] cannot access org.cytoscape.service.util.AbstractCyActivator bad class file: org/cytoscape/service/util/AbstractCyActivator.class(org/cytoscape/service/util:AbstractCyActivator.class) unable to access file: corrupted zip file at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:656) at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:128) 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 -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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