See <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/805/changes>
Changes: [clopes] Removed group-api dependency from io-impl: 2.x groups (XGMML) parsed as regular network pointers; will have to recreate groups in group-impl, on session-loaded events. XGMML writer/reader: removed "cy:networkPointer" attribute; network pointers saved as nested graph elements. Added some unit tests for XGMMLWriter. ------------------------------------------ [...truncated 5669 lines...] [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/DiscreteMappingEntry.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/Edge.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/Network.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/Node.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/ObjectFactory.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/PassthroughMapping.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/VisualProperty.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/VisualStyle.java [INFO] XJC writing: org/cytoscape/io/internal/util/vizmap/model/Vizmap.java [INFO] Finished execution. [INFO] [INFO] Started execution. [INFO] JAXB API is loaded from the [jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!]. [INFO] Detected JAXB API version [2.1]. [INFO] pluginArtifacts:[org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.4:, org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.4:compile, org.codehaus.plexus:plexus-utils:jar:1.1:compile, junit:junit:jar:4.8.1:compile, org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1:compile, org.sonatype.plexus:plexus-build-api:jar:0.0.6:compile, com.sun.xml.bind:jaxb-impl:jar:2.1.13:compile, javax.xml.bind:jaxb-api:jar:2.1:compile, javax.xml.stream:stax-api:jar:1.0-2:compile, javax.activation:activation:jar:1.1:compile, org.jvnet.jaxb2_commons:jaxb2-basics-jaxb-xjc:jar:2.1.13.MR2:compile, com.sun.codemodel:codemodel:jar:2.3:compile, com.sun.xml.dtd-parser:dtd-parser:jar:1.1:compile, com.sun.istack:istack-commons-tools:jar:2.2.MR1:compile, org.apache.ant:ant:jar:1.7.0:compile, org.apache.ant:ant-launcher:jar:1.7.0:compile, relaxngDatatype:relaxngDatatype:jar:20020414:compile, com.sun.org.apache.xml.internal:resolver:jar:20050927:compile, org.kohsuke.rngom:rngom:jar:20100718:compile, com.sun.xsom:xsom:jar:20100725:compile, sun.jdk:tools:jar:1.5.0:system] [INFO] schemaLanguage:null [INFO] schemaDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/main/resources/xsd> [INFO] schemaIncludes:[Ljava.lang.String;@5f76f5 [INFO] schemaExcludes:null [INFO] bindingDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/main/resources/xsd> [INFO] bindingIncludes:[Ljava.lang.String;@17aefd7 [INFO] bindingExcludes:null [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:com.sun.org.apache.xml.internal.resolver.tools.CatalogResolver [INFO] generatePackage:org.cytoscape.io.internal.util.session.model [INFO] generateDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/generated-sources/xjc> [INFO] readOnly:false [INFO] extension:false [INFO] strict:true [INFO] writeCode:true [INFO] verbose:true [INFO] debug:false [INFO] args:[] [INFO] forceRegenerate:true [INFO] removeOldOutput:false [INFO] produces:[**/*.*, **/*.java, **/bgm.ser, **/jaxb.properties] [INFO] otherDepends:null [INFO] episodeFile:<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/generated-sources/xjc/META-INF/sun-jaxb.episode> [INFO] episode:true [INFO] classpathElements:[<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/classes]> [INFO] plugins:null [INFO] episodes:null [INFO] xjcPlugins:null [INFO] episodes:null [INFO] specVersion:2.1 [INFO] schemaFiles (calculated):[<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/main/resources/xsd/cysession.xsd]> [INFO] bindingFiles (calculated):[] [INFO] xjcPluginArtifacts (resolved):[] [INFO] xjcPluginFiles (resolved):[] [INFO] xjcPluginURLs (resolved):[] [INFO] episodeArtifacts (resolved):[] [INFO] episodeFiles (resolved):[] [INFO] The schemaLanguage setting was not defined, assuming 'AUTODETECT'. Using java.util.ServiceLoader [INFO] Parsing input schema(s)... [INFO] --- maven-jaxb2-plugin:0.7.4:generate (session) @ io-impl --- [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/generated-sources/xjc].> [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Child.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Cysession.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Cytopanel.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Cytopanels.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Desktop.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/DesktopSize.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Edge.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/HiddenEdges.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/HiddenNodes.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Network.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/NetworkFrame.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/NetworkFrames.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/NetworkTree.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Node.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/ObjectFactory.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Ontology.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/OntologyServer.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Panel.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Panels.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Parent.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Plugin.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Plugins.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/SelectedEdges.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/SelectedNodes.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/Server.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/SessionState.java [INFO] XJC writing: org/cytoscape/io/internal/util/session/model/ViewableNodes.java [INFO] Finished execution. [INFO] [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ io-impl --- [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ io-impl --- [INFO] Compiling 192 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/classes> [INFO] [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ io-impl --- [INFO] Copying 13 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ io-impl --- [INFO] Compiling 16 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/target/test-classes> [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriterTest.java>:[71,34] cannot find symbol symbol : method getNetworkManager() location: class org.cytoscape.ding.NetworkViewTestSupport [INFO] 1 error [INFO] ------------------------------------------------------------- [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape 3 Implementation/modules/org.cytoscape$io-impl/builds/2012-04-23_18-03-47/archive/org.cytoscape/io-impl/3.0.0-alpha8-SNAPSHOT/io-impl-3.0.0-alpha8-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [5.704s] [INFO] Cytoscape BioPAX Impl (biopax-impl) ............... SUCCESS [17.600s] [INFO] Cytoscape Command Executor Impl (command-executor-impl) SUCCESS [5.140s] [INFO] Cytoscape Equations Impl (equations-impl) ......... SUCCESS [12.173s] [INFO] Cytoscape Model Impl Parent (model-impl-parent) ... SUCCESS [0.700s] [INFO] Cytoscape Model Impl (model-impl) ................. SUCCESS [13.893s] [INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) SUCCESS [0.725s] [INFO] Cytoscape View Model Impl (viewmodel-impl) ........ SUCCESS [8.301s] [INFO] Cytoscape Ding Impl Parent (ding-impl) ............ SUCCESS [0.709s] [INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) SUCCESS [5:21.260s] [INFO] Cytoscape Core Task Impl (core-task-impl) ......... SUCCESS [22.820s] [INFO] Cytoscape CPath2 Impl (cpath2-impl) ............... SUCCESS [12.408s] [INFO] Cytoscape IO Impl Parent (io-impl-parent) ......... SUCCESS [0.590s] [INFO] Cytoscape IO Impl (io-impl) ....................... FAILURE [4.788s] [INFO] Cytoscape Event Impl Parent (event-impl-parent) ... SKIPPED [INFO] Cytoscape Event Impl (event-impl) ................. SKIPPED [INFO] Cytoscape Layout Impl (layout-impl) ............... SKIPPED [INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) SKIPPED [INFO] Cytoscape Editor Impl (editor-impl) ............... SKIPPED [INFO] Cytoscape Equation Functions Impl (equations-functions-impl) SKIPPED [INFO] Cytoscape Event Impl IT (event-impl-it) ........... SKIPPED [INFO] Cytoscape Filters Impl (filter-impl) .............. SKIPPED [INFO] Cytoscape GraphML Impl (graphml-impl) ............. SKIPPED [INFO] Cytoscape Groups Impl (group-impl) ................ SKIPPED [INFO] Cytoscape Group Data Impl (group-data-impl) ....... SKIPPED [INFO] Cytoscape Group View Impl (group-view-impl) ....... SKIPPED [INFO] Cytoscape IO Impl Performance (io-impl-performance) SKIPPED [INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) SKIPPED [INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) . SKIPPED [INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl) SKIPPED [INFO] Cytoscape Linkout Impl (linkout-impl) ............. SKIPPED [INFO] Cytoscape Log Swing Impl (log-swing-impl) ......... SKIPPED [INFO] Cytoscape Manual Layout Impl (manual-layout-impl) . SKIPPED [INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) SKIPPED [INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) SKIPPED [INFO] Cytoscape NetworkAnalyzer Impl (network-analyzer-impl) SKIPPED [INFO] Cytoscape Merge Impl (network-merge-impl) ......... SKIPPED [INFO] Cytoscape App Impl (app-impl) ..................... SKIPPED [INFO] Cytoscape Presentation Impl (presentation-impl) ... SKIPPED [INFO] Cytoscape Property Impl (property-impl) ........... SKIPPED [INFO] Cytoscape PSI-MI Impl Parent (psi-mi-impl-parent) . SKIPPED [INFO] Cytoscape PSI-MI Impl (psi-mi-impl) ............... SKIPPED [INFO] Cytoscape PSI-MI Impl Performance (psi-mi-impl-performance) SKIPPED [INFO] Cytoscape SBML Impl (sbml-impl) ................... SKIPPED [INFO] Cytoscape Search Impl (search-impl) ............... SKIPPED [INFO] Cytoscape Session Impl (session-impl) ............. SKIPPED [INFO] Cytoscape Swing Application Impl (swing-application-impl) SKIPPED [INFO] Cytoscape Table Browser Impl (table-browser-impl) . SKIPPED [INFO] Cytoscape Table Import Impl (table-import-impl) ... SKIPPED [INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) ....... SKIPPED [INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) . SKIPPED [INFO] Cytoscape VizMap Impl (vizmap-impl) ............... SKIPPED [INFO] Cytoscape Biomart Webservice Impl (webservice-biomart-client-impl) SKIPPED [INFO] Cytoscape Webservice Impl (webservice-impl) ....... SKIPPED [INFO] Cytoscape NCBI Webservice Impl (webservice-ncbi-client-impl) SKIPPED [INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) SKIPPED [INFO] Cytoscape Work Swing Impl (work-swing-impl) ....... SKIPPED [INFO] Cytoscape Application Impl (application-impl) ..... SKIPPED [INFO] Cytoscape PSIQUIC Webservice Impl (webservice-psicquic-client-impl) SKIPPED [INFO] Cytoscape Datasource Impl (datasource-impl) ....... SKIPPED [INFO] Cytoscape BioGrid Datasource Impl (datasource-biogrid-impl) SKIPPED [INFO] Cytoscape Welcome Screen Impl (welcome-impl) ...... SKIPPED [INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) SKIPPED [INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) ... SKIPPED [INFO] Cytoscape Scripting Impl (scripting-impl) ......... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7:15.902s [INFO] Finished at: Mon Apr 23 18:11:08 GMT-05:00 2012 [INFO] Final Memory: 48M/120M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:testCompile (default-testCompile) on project io-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriterTest.java>:[71,34] cannot find symbol symbol : method getNetworkManager() location: class org.cytoscape.ding.NetworkViewTestSupport cause : Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriterTest.java>:[71,34] cannot find symbol symbol : method getNetworkManager() location: class org.cytoscape.ding.NetworkViewTestSupport Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:testCompile (default-testCompile) on project io-impl: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriterTest.java>:[71,34] cannot find symbol symbol : method getNetworkManager() location: class org.cytoscape.ding.NetworkViewTestSupport 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/io-impl/impl/src/test/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriterTest.java>:[71,34] cannot find symbol symbol : method getNetworkManager() location: class org.cytoscape.ding.NetworkViewTestSupport at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:656) at org.apache.maven.plugin.TestCompilerMojo.execute(TestCompilerMojo.java:161) 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 bad build status FAILURE -- 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.
