See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/1148/changes>
Changes: [kono] First version using row-oriented view model. This is a big change and still need some bug fixes. You can start Cytoscape Desktop, but may not be able to create/load networks. ------------------------------------------ [...truncated 2 lines...] Checking out http://chianti.ucsd.edu/svn/core3/default-mappingcalculators/trunk A osgi.bnd A src A src/main A src/main/java A src/main/java/org A src/main/java/org/cytoscape A src/main/java/org/cytoscape/view A src/main/java/org/cytoscape/view/vizmap A src/main/java/org/cytoscape/view/vizmap/mappings A src/main/java/org/cytoscape/view/vizmap/mappings/BoundaryRangeValues.java A src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java AU src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java A src/main/java/org/cytoscape/view/vizmap/mappings/AbstractMappingFunction.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/Interpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberToNumberInterpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberInterpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberToColorInterpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/FlatInterpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/NumberInterpolator.java A src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMappingPoint.java A src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java A src/main/resources A src/main/resources/META-INF A src/main/resources/META-INF/spring A src/main/resources/META-INF/spring/bundle-context-osgi.xml A src/main/resources/META-INF/spring/bundle-context.xml A pom.xml U . At revision 21343 No emails were triggered. Parsing POMs [trunk] $ java -cp /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-agent-1.369.jar:/R1/tools/maven/apache-maven-2.1.0/boot/classworlds-1.1.jar hudson.maven.agent.Main /R1/tools/maven/apache-maven-2.1.0 /R1/resources/webservers/tomcat_2/webapps/hudson/WEB-INF/lib/remoting-1.369.jar /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-interceptor-1.369.jar 44115 /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven2.1-interceptor-1.2.jar <===[HUDSON REMOTING CAPACITY]===> channel started Executing Maven: -B -f <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 2 resources [INFO] [pax:compile] [INFO] Compiling 12 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/classes> [INFO] [recovering meta-data] [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 Default Mapping Calculators/modules/org.cytoscape$default-mappings/builds/2010-08-11_20-44-26/archive/org.cytoscape/default-mappings/1.0-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java>:[71,7] org.cytoscape.view.vizmap.mappings.ContinuousMapping is not abstract and does not override abstract method <G>apply(org.cytoscape.view.model.ViewColumn<V>,java.util.List<? extends org.cytoscape.view.model.View<G>>) in org.cytoscape.view.vizmap.VisualMappingFunction <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java>:[60,7] org.cytoscape.view.vizmap.mappings.DiscreteMapping is not abstract and does not override abstract method <G>apply(org.cytoscape.view.model.ViewColumn<V>,java.util.List<? extends org.cytoscape.view.model.View<G>>) in org.cytoscape.view.vizmap.VisualMappingFunction <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java>:[47,7] org.cytoscape.view.vizmap.mappings.PassthroughMapping is not abstract and does not override abstract method <G>apply(org.cytoscape.view.model.ViewColumn<V>,java.util.List<? extends org.cytoscape.view.model.View<G>>) in org.cytoscape.view.vizmap.VisualMappingFunction [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 5 seconds [INFO] Finished at: Wed Aug 11 20:44:33 EDT 2010 [INFO] Final Memory: 47M/494M [INFO] ------------------------------------------------------------------------ Waiting for Hudson to finish collecting data 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://10.20.1.18:3306/sonar -Dsonar.host.url=http://localhost:8021/sonar/ -Dsonar.skipInstall=true [INFO] Scanning for projects... WAGON_VERSION: 1.0-beta-2 [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [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://10.20.1.18:3306/sonar [INFO] Sonar JDBC login: sonar [INFO] Sonar JDBC driver: com.mysql.jdbc.Driver [INFO] Sonar branch: [INFO] org.cytoscape.view.vizmap.mappings Selected quality profile : Cytoscape, language=java [INFO] org.cytoscape.view.vizmap.mappings Executing org.codehaus.mojo:findbugs-maven-plugin:[findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:1.2:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [resources:resources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 2 resources [INFO] [pax:compile] [INFO] Compiling 8 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/classes> [INFO] Setting property: classpath.resource.loader.class => 'org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader'. [INFO] Setting property: velocimacro.messages.on => 'false'. [INFO] Setting property: resource.loader => 'classpath'. [INFO] Setting property: resource.manager.logwhenfound => 'false'. [INFO] ************************************************************** [INFO] Starting Jakarta Velocity v1.4 [INFO] RuntimeInstance initializing. [INFO] Default Properties File: org/apache/velocity/runtime/defaults/velocity.properties [INFO] Default ResourceManager initializing. (class org.apache.velocity.runtime.resource.ResourceManagerImpl) [INFO] Resource Loader Instantiated: org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader [INFO] ClasspathResourceLoader : initialization starting. [INFO] ClasspathResourceLoader : initialization complete. [INFO] ResourceCache : initialized. (class org.apache.velocity.runtime.resource.ResourceCacheImpl) [INFO] Default ResourceManager initialization complete. [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Literal [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Macro [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Parse [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Include [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Foreach [INFO] Created: 20 parsers. [INFO] Velocimacro : initialization starting. [INFO] Velocimacro : adding VMs from VM library template : VM_global_library.vm [ERROR] ResourceManager : unable to find resource 'VM_global_library.vm' in any resource loader. [INFO] Velocimacro : error using VM library template VM_global_library.vm : org.apache.velocity.exception.ResourceNotFoundException: Unable to find resource 'VM_global_library.vm' [INFO] Velocimacro : VM library template macro registration complete. [INFO] Velocimacro : allowInline = true : VMs can be defined inline in templates [INFO] Velocimacro : allowInlineToOverride = false : VMs defined inline may NOT replace previous VM definitions [INFO] Velocimacro : allowInlineLocal = false : VMs defined inline will be global in scope if allowed. [INFO] Velocimacro : initialization complete. [INFO] Velocity successfully started. [INFO] [findbugs:findbugs] [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using FindBugs Version: 1.3.2 [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Using the xdoc format [INFO] Using maximum effort. [INFO] Using low threshold. [INFO] Using low threshold. [INFO] Debugging is Off [INFO] Using bug include filter <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/sonar/findbugs-include.xml> [INFO] No bug exclude filter. [INFO] Printing Errors [INFO] Printing Missing classes [INFO] Printing Source Roots [INFO] org.cytoscape.view.vizmap.mappings Executing org.apache.maven.plugins:maven-checkstyle-plugin:[checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [org.apache.maven.plugins:maven-checkstyle-plugin:2.2:checkstyle] [INFO] ------------------------------------------------------------------------ [INFO] Setting property: classpath.resource.loader.class => 'org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader'. [INFO] Setting property: velocimacro.messages.on => 'false'. [INFO] Setting property: resource.loader => 'classpath'. [INFO] Setting property: resource.manager.logwhenfound => 'false'. [INFO] ************************************************************** [INFO] Starting Jakarta Velocity v1.4 [INFO] RuntimeInstance initializing. [INFO] Default Properties File: org/apache/velocity/runtime/defaults/velocity.properties [INFO] Default ResourceManager initializing. (class org.apache.velocity.runtime.resource.ResourceManagerImpl) [INFO] Resource Loader Instantiated: org.codehaus.plexus.velocity.ContextClassLoaderResourceLoader [INFO] ClasspathResourceLoader : initialization starting. [INFO] ClasspathResourceLoader : initialization complete. [INFO] ResourceCache : initialized. (class org.apache.velocity.runtime.resource.ResourceCacheImpl) [INFO] Default ResourceManager initialization complete. [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Literal [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Macro [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Parse [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Include [INFO] Loaded System Directive: org.apache.velocity.runtime.directive.Foreach [INFO] Created: 20 parsers. [INFO] Velocimacro : initialization starting. [INFO] Velocimacro : adding VMs from VM library template : VM_global_library.vm [ERROR] ResourceManager : unable to find resource 'VM_global_library.vm' in any resource loader. [INFO] Velocimacro : error using VM library template VM_global_library.vm : org.apache.velocity.exception.ResourceNotFoundException: Unable to find resource 'VM_global_library.vm' [INFO] Velocimacro : VM library template macro registration complete. [INFO] Velocimacro : allowInline = true : VMs can be defined inline in templates [INFO] Velocimacro : allowInlineToOverride = false : VMs defined inline may NOT replace previous VM definitions [INFO] Velocimacro : allowInlineLocal = false : VMs defined inline will be global in scope if allowed. [INFO] Velocimacro : initialization complete. [INFO] Velocity successfully started. [INFO] [checkstyle:checkstyle] [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent! [INFO] There are 2 checkstyle errors. [INFO] org.cytoscape.view.vizmap.mappings Executing org.apache.maven.plugins:maven-pmd-plugin:[pmd] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [org.apache.maven.plugins:maven-pmd-plugin:2.4:pmd] [INFO] ------------------------------------------------------------------------ [INFO] [pmd:pmd] [INFO] org.cytoscape.view.vizmap.mappings Executing org.codehaus.mojo:javancss-maven-plugin:[report] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [org.codehaus.mojo:javancss-maven-plugin:2.0-beta-2:report] [INFO] ------------------------------------------------------------------------ [INFO] [javancss:report] [INFO] org.cytoscape.view.vizmap.mappings Executing org.codehaus.mojo:cobertura-maven-plugin:[cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.view.vizmap.mappings [INFO] task-segment: [org.codehaus.mojo:cobertura-maven-plugin:2.2:cobertura] [INFO] ------------------------------------------------------------------------ [INFO] Preparing cobertura:cobertura [INFO] [resources:resources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 2 resources [INFO] [pax:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [cobertura:instrument] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Instrumenting 12 files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/generated-classes/cobertura> Cobertura: Saved information on 12 classes. Instrument time: 592ms [INFO] Instrumentation was successful. [INFO] [resources:testResources] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/src/test/resources> [INFO] [pax:testCompile] [INFO] No sources to compile [INFO] [surefire:test] [INFO] No tests to run. [INFO] [cobertura:cobertura] [INFO] Cobertura 1.9 - GNU GPL License (NO WARRANTY) - See COPYRIGHT file Cobertura: Loaded information on 12 classes. Report time: 273ms [INFO] Cobertura Report generation was successful. [INFO] org.cytoscape.view.vizmap.mappings Executing org.apache.maven.plugins:maven-surefire-plugin:[] [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.findbugs.FindbugsMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.cpd.CpdMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings Collecting duplications... [INFO] org.cytoscape.view.vizmap.mappings File suffixes : java [INFO] org.cytoscape.view.vizmap.mappings Exclusions : {} [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.checkstyle.CheckstyleMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.pmd.PmdMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.core.SaveProfileMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.core.sources.ImportJavaSourcesMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.core.SaveProjectLinksFromPom] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.javancss.JavaNcssMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.cobertura.CoberturaMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/site/cobertura/coverage.xml> [INFO] org.cytoscape.view.vizmap.mappings [class org.sonar.plugins.surefire.SurefireMavenCollector] executing [INFO] org.cytoscape.view.vizmap.mappings parsing <http://cytoscape.wodaklab.org/hudson/job/Cy3%20Default%20Mapping%20Calculators/ws/trunk/target/surefire-reports> [INFO] Trigger server [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 43 seconds [INFO] Finished at: Wed Aug 11 20:45:58 EDT 2010 [INFO] Final Memory: 92M/782M [INFO] ------------------------------------------------------------------------ -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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