See <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/35/changes>
Changes: [rodche] Much internally re-factored the biopax core plugin to make it (the code and result) more like it is already in Cytoscape 3 (incl. auto-converting BioPAX L1, L2 to BioPAX L3 before creating CyNetwork and arrtibutes.), and to make it easier to support both. ------------------------------------------ [...truncated 14337 lines...] [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_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc/META-INF/sun-jaxb.episode> [INFO] episode:true [INFO] classpathElements:[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/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_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd/SearchResponse.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 (SearchResponse) @ cpath2 --- [INFO] Compiling input schema(s)... [INFO] Writing output to [<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc].> [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/BasicRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/DataSourceType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ErrorType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ExtendedRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/ObjectFactory.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/OrganismType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/PathwayListType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/PathwayType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/SearchResponseType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/search_response/XRefType.java [INFO] Finished execution. [INFO] [INFO] Started execution. [INFO] JAXB API is loaded from the [jar:file:/opt/jdk1.6.0_32/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_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd> [INFO] schemaIncludes:[Ljava.lang.String;@1ff2338 [INFO] schemaExcludes:null [INFO] bindingDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd> [INFO] bindingIncludes:[Ljava.lang.String;@1615eaa [INFO] bindingExcludes:null [INFO] disableDefaultExcludes:false [INFO] catalog:null [INFO] catalogResolver:com.sun.org.apache.xml.internal.resolver.tools.CatalogResolver [INFO] generatePackage:org.cytoscape.coreplugin.cpath2.schemas.summary_response [INFO] generateDirectory:<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/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_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc/META-INF/sun-jaxb.episode> [INFO] episode:true [INFO] classpathElements:[<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/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_2.X_application/ws/trunk/coreplugins/cPath2/src/main/resources/xsd/SummaryResponse.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] Compiling input schema(s)... [INFO] Writing output to [<http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/generated-sources/xjc].> [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/BasicRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/DataSourceType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ErrorType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ExtendedRecordType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/ObjectFactory.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/OrganismType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/PathwayListType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/PathwayType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/SummaryResponseType.java [INFO] XJC writing: org/cytoscape/coreplugin/cpath2/schemas/summary_response/XRefType.java [INFO] Finished execution. [INFO] --- maven-jaxb2-plugin:0.7.4:generate (SummaryResponse) @ cpath2 --- [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 12 resources [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] --- maven-resources-plugin:2.4.3:resources (default-resources) @ cpath2 --- [INFO] [INFO] Compiling 83 source files to <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/target/classes> [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ cpath2 --- [INFO] ------------------------------------------------------------- [WARNING] COMPILATION WARNING : [INFO] ------------------------------------------------------------- [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[87,66] [deprecation] NODE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[86,42] [deprecation] DiscreteMapping(java.lang.Object,java.lang.String,byte) in cytoscape.visual.mappings.DiscreteMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[101,64] [deprecation] NODE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[100,42] [deprecation] DiscreteMapping(java.lang.Object,java.lang.String,byte) in cytoscape.visual.mappings.DiscreteMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[113,48] [deprecation] EDGE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[112,36] [deprecation] DiscreteMapping(java.lang.Object,java.lang.String,byte) in cytoscape.visual.mappings.DiscreteMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[139,48] [deprecation] EDGE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[138,36] [deprecation] DiscreteMapping(java.lang.Object,java.lang.String,byte) in cytoscape.visual.mappings.DiscreteMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[159,78] [deprecation] NODE_MAPPING in cytoscape.visual.mappings.ObjectMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[158,42] [deprecation] PassThroughMapping(java.lang.Object,byte) in cytoscape.visual.mappings.PassThroughMapping has been deprecated [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java>:[160,20] [deprecation] setControllingAttributeName(java.lang.String,cytoscape.CyNetwork,boolean) in cytoscape.visual.mappings.AbstractMapping has been deprecated [INFO] 11 warnings [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java>:[438,48] cannot find symbol symbol : method getObjects(org.biopax.paxtools.model.Model,java.lang.Class<org.biopax.paxtools.model.level2.physicalEntity>,java.lang.Class<org.biopax.paxtools.model.level3.PhysicalEntity>) location: class cytoscape.coreplugins.biopax.util.BioPaxUtil [INFO] 1 error [INFO] ------------------------------------------------------------- [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$cpath2/builds/2012-10-22_18-05-03/archive/cytoscape.coreplugins/cpath2/2.8.4-SNAPSHOT/cpath2-2.8.4-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Parent POM .............................. SUCCESS [3.731s] [INFO] Cytoscape Core Libraries Parent POM ............... SUCCESS [0.464s] [INFO] commons-cli-1-x-cytocape-custom ................... SUCCESS [7.144s] [INFO] equations ......................................... SUCCESS [6.052s] [INFO] util-intr ......................................... SUCCESS [4.247s] [INFO] geom-spacial ...................................... SUCCESS [1.975s] [INFO] geom-rtree ........................................ SUCCESS [2.599s] [INFO] GINY API .......................................... SUCCESS [3.694s] [INFO] graph-fixed ....................................... SUCCESS [5.581s] [INFO] graph-dynamic ..................................... SUCCESS [6.108s] [INFO] nerius-math-xform ................................. SUCCESS [2.279s] [INFO] obo ............................................... SUCCESS [2.867s] [INFO] phoebe-dnd ........................................ SUCCESS [4.069s] [INFO] render-immed ...................................... SUCCESS [37.346s] [INFO] render-export ..................................... SUCCESS [3.547s] [INFO] render-stateful ................................... SUCCESS [6.769s] [INFO] task .............................................. SUCCESS [5.503s] [INFO] undo-support ...................................... SUCCESS [5.785s] [INFO] fing .............................................. SUCCESS [4.738s] [INFO] ding .............................................. SUCCESS [4.995s] [INFO] Cytoscape Documentation ........................... SUCCESS [17.165s] [INFO] Cytoscape Application ............................. SUCCESS [2:02.906s] [INFO] Cytoscape Core Plugins Parent POM ................. SUCCESS [0.967s] [INFO] Advanced Network Merge ............................ SUCCESS [11.137s] [INFO] Automatic Layout .................................. SUCCESS [20.975s] [INFO] BioMart Client .................................... SUCCESS [7.419s] [INFO] BioPAX ............................................ SUCCESS [14.724s] [INFO] Editor ............................................ SUCCESS [8.164s] [INFO] Equation Functions ................................ SUCCESS [3.370s] [INFO] Manual Layout ..................................... SUCCESS [11.313s] [INFO] NCBI Client ....................................... SUCCESS [21.611s] [INFO] PSI-MI ............................................ SUCCESS [16.854s] [INFO] QuickFind ......................................... SUCCESS [13.489s] [INFO] RFilters .......................................... SUCCESS [12.028s] [INFO] SBML Reader ....................................... SUCCESS [5.038s] [INFO] Table Import ...................................... SUCCESS [18.161s] [INFO] Attribute Browser ................................. SUCCESS [12.704s] [INFO] cPath ............................................. SUCCESS [8.382s] [INFO] Pathway Commons plugin ............................ FAILURE [1.539s] [INFO] Filters ........................................... SKIPPED [INFO] Linkout ........................................... SKIPPED [INFO] Core Commands Plugin .............................. SKIPPED [INFO] NetworkAnalyzer ................................... SKIPPED [INFO] Cytoscape Distribution ............................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 8:15.018s [INFO] Finished at: Mon Oct 22 18:13:20 GMT-05:00 2012 [INFO] Final Memory: 156M/372M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project cpath2: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java>:[438,48] cannot find symbol symbol : method getObjects(org.biopax.paxtools.model.Model,java.lang.Class<org.biopax.paxtools.model.level2.physicalEntity>,java.lang.Class<org.biopax.paxtools.model.level3.PhysicalEntity>) location: class cytoscape.coreplugins.biopax.util.BioPaxUtil cause : Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java>:[438,48] cannot find symbol symbol : method getObjects(org.biopax.paxtools.model.Model,java.lang.Class<org.biopax.paxtools.model.level2.physicalEntity>,java.lang.Class<org.biopax.paxtools.model.level3.PhysicalEntity>) location: class cytoscape.coreplugins.biopax.util.BioPaxUtil 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 cpath2: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java>:[438,48] cannot find symbol symbol : method getObjects(org.biopax.paxtools.model.Model,java.lang.Class<org.biopax.paxtools.model.level2.physicalEntity>,java.lang.Class<org.biopax.paxtools.model.level3.PhysicalEntity>) location: class cytoscape.coreplugins.biopax.util.BioPaxUtil 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: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: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:662) Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/cPath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java>:[438,48] cannot find symbol symbol : method getObjects(org.biopax.paxtools.model.Model,java.lang.Class<org.biopax.paxtools.model.level2.physicalEntity>,java.lang.Class<org.biopax.paxtools.model.level3.PhysicalEntity>) location: class cytoscape.coreplugins.biopax.util.BioPaxUtil 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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