See <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/1/>
------------------------------------------ [...truncated 1256 lines...] A QuickFind/src/main/java/prefuse/util A QuickFind/src/main/java/prefuse/util/TypeLib.java A QuickFind/src/main/java/prefuse/util/ui A QuickFind/src/main/java/prefuse/util/ui/JRangeSlider.java A QuickFind/src/main/java/prefuse/util/ui/ValuedRangeModel.java A QuickFind/src/main/resources A QuickFind/src/main/resources/csplugins A QuickFind/src/main/resources/csplugins/quickfind A QuickFind/src/main/resources/csplugins/quickfind/plugin A QuickFind/src/main/resources/csplugins/quickfind/plugin/plugin.props A QuickFind/src/main/resources/resources AU QuickFind/src/main/resources/resources/config.png A QuickFind/UI_Testing.txt A QuickFind/pom.xml A QuickFind/README.txt A EquationFunctions A EquationFunctions/src A EquationFunctions/src/main A EquationFunctions/src/main/java A EquationFunctions/src/main/java/org A EquationFunctions/src/main/java/org/cytoscape A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/InDegree.java A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/OutDegree.java A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/TargetID.java A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/Degree.java A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/functions/SourceID.java A EquationFunctions/src/main/java/org/cytoscape/EquationFunctions/EquationFunctionsPlugin.java A EquationFunctions/src/main/resources A EquationFunctions/src/main/resources/org A EquationFunctions/src/main/resources/org/cytoscape A EquationFunctions/src/main/resources/org/cytoscape/EquationFunctions A EquationFunctions/src/main/resources/org/cytoscape/EquationFunctions/plugin.props A EquationFunctions/pom.xml A EquationFunctions/classes At revision 21187 WARNING: clock of the subversion server appears to be out of sync. This can result in inconsistent check out behavior. No emails were triggered. Parsing POMs Discovered a new module cytoscape.coreplugins:parent Cytoscape Core Plugins Parent POM Discovered a new module cytoscape.coreplugins:advanced-network-merge Advanced Network Merge Discovered a new module cytoscape.coreplugins:automatic-layout Automatic Layout Discovered a new module cytoscape.coreplugins:biomart-client BioMart Client Discovered a new module cytoscape.coreplugins:biopax BioPAX Discovered a new module cytoscape.coreplugins:editor Editor Discovered a new module cytoscape.coreplugins:equation-functions Equation Functions Discovered a new module cytoscape.coreplugins:manual-layout Manual Layout Discovered a new module cytoscape.coreplugins:ncbi-client NCBI Client Discovered a new module cytoscape.coreplugins:psi-mi PSI-MI Discovered a new module cytoscape.coreplugins:quickfind QuickFind Discovered a new module cytoscape.coreplugins:rfilters RFilters Discovered a new module cytoscape.coreplugins:sbml-reader SBML Reader Discovered a new module cytoscape.coreplugins:table-import Table Import Discovered a new module cytoscape.coreplugins:attribute-browser Attribute Browser Discovered a new module cytoscape.coreplugins:cpath cPath Discovered a new module cytoscape.coreplugins:cpath2 cPath2 Discovered a new module cytoscape.coreplugins:filters Filters Discovered a new module cytoscape.coreplugins:linkout Linkout [trunk] $ java -cp /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-agent-1.354.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-1.354.jar /R1/resources/webapps/cytoscape_build_sys/hudson_home/plugins/maven-plugin/WEB-INF/lib/maven-interceptor-1.354.jar 47637 /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/Cytoscape%202.X%20coreplugins/ws/trunk/pom.xml> deploy [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] Cytoscape Core Plugins Parent POM [INFO] Advanced Network Merge [INFO] Automatic Layout [INFO] BioMart Client [INFO] BioPAX [INFO] Editor [INFO] Equation Functions [INFO] Manual Layout [INFO] NCBI Client [INFO] PSI-MI [INFO] QuickFind [INFO] RFilters [INFO] SBML Reader [INFO] Table Import [INFO] Attribute Browser [INFO] cPath [INFO] cPath2 [INFO] Filters [INFO] Linkout [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Core Plugins Parent POM [INFO] task-segment: [deploy] [INFO] ------------------------------------------------------------------------ [INFO] [site:attach-descriptor] [INFO] [install:install] [INFO] Installing <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/target/pom-transformed.xml> to /home/bturner/.m2/repository/cytoscape/coreplugins/parent/2.8.0-SNAPSHOT/parent-2.8.0-SNAPSHOT.pom [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cytoscape%202.X%20coreplugins/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cytoscape 2.X coreplugins/modules/cytoscape.coreplugins$parent/builds/2010-08-04_14-03-41/archive/cytoscape.coreplugins/parent/2.8.0-SNAPSHOT/pom.xml [HUDSON] Archiving /home/bturner/.m2/repository/cytoscape/coreplugins/parent/2.8.0-SNAPSHOT/parent-2.8.0-SNAPSHOT.pom to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cytoscape 2.X coreplugins/modules/cytoscape.coreplugins$parent/builds/2010-08-04_14-03-41/archive/cytoscape.coreplugins/parent/2.8.0-SNAPSHOT/parent-2.8.0-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Failed to configure plugin parameters for: org.apache.maven.plugins:maven-deploy-plugin:2.4 check that the following section of the pom.xml is present and correct: <distributionManagement> <!-- use the following if you're not using a snapshot version. --> <repository> <id>repo</id> <name>Repository Name</name> <url>scp://host/path/to/repo</url> </repository> <!-- use the following if you ARE using a snapshot version. --> <snapshotRepository> <id>repo</id> <name>Repository Name</name> <url>scp://host/path/to/repo</url> </snapshotRepository> </distributionManagement> Cause: Class 'org.apache.maven.artifact.repository.ArtifactRepository' cannot be instantiated [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 5 seconds [INFO] Finished at: Wed Aug 04 14:04:09 EDT 2010 [INFO] Final Memory: 24M/339M [INFO] ------------------------------------------------------------------------ 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://10.20.1.1:7070/sonar -Dsonar.host.url=http://localhost:8021/sonar/ -Dsonar.skipInstall=true [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] Cytoscape Core Plugins Parent POM [INFO] Advanced Network Merge [INFO] Automatic Layout [INFO] BioMart Client [INFO] BioPAX [INFO] Editor [INFO] Equation Functions [INFO] Manual Layout [INFO] NCBI Client [INFO] PSI-MI [INFO] QuickFind [INFO] RFilters [INFO] SBML Reader [INFO] Table Import [INFO] Attribute Browser [INFO] cPath [INFO] cPath2 [INFO] Filters [INFO] Linkout [INFO] ------------------------------------------------------------------------ [INFO] Building Cytoscape Core Plugins Parent POM [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://10.20.1.1:7070/sonar [INFO] Sonar JDBC login: sonar [INFO] Sonar JDBC driver: com.mysql.jdbc.Driver [INFO] Sonar branch: [INFO] ------------------------------------------------------------------------ [ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Can not execute Sonar Embedded error: can not autodetect the dialect Communications link failure due to underlying exception: ** BEGIN NESTED EXCEPTION ** java.net.ConnectException MESSAGE: Connection refused STACKTRACE: java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) at java.net.Socket.connect(Socket.java:529) at java.net.Socket.connect(Socket.java:478) at java.net.Socket.<init>(Socket.java:375) at java.net.Socket.<init>(Socket.java:218) at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256) at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:271) at com.mysql.jdbc.Connection.createNewIO(Connection.java:2771) at com.mysql.jdbc.Connection.<init>(Connection.java:1555) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:285) at java.sql.DriverManager.getConnection(DriverManager.java:582) at java.sql.DriverManager.getConnection(DriverManager.java:185) at org.sonar.commons.database.DriverDatabaseConnector.getConnection(DriverDatabaseConnector.java:90) at org.sonar.commons.database.AbstractDatabaseConnector.getDialect(AbstractDatabaseConnector.java:167) at org.sonar.commons.database.DriverDatabaseConnector.getEntityManagerFactory(DriverDatabaseConnector.java:111) at org.sonar.commons.database.DriverDatabaseConnector.createEntityManager(DriverDatabaseConnector.java:139) at org.sonar.commons.database.DatabaseSession.start(DatabaseSession.java:55) at org.sonar.commons.database.ThreadLocalDatabaseSessionFactory.getSession(ThreadLocalDatabaseSessionFactory.java:35) at org.sonar.commons.database.DatabaseSessionProvider.provide(DatabaseSessionProvider.java:28) 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.picocontainer.injectors.MethodInjector.invokeMethod(MethodInjector.java:137) at org.picocontainer.injectors.MethodInjector.access$000(MethodInjector.java:39) at org.picocontainer.injectors.MethodInjector$2.run(MethodInjector.java:123) at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:289) at org.picocontainer.injectors.MethodInjector.decorateComponentInstance(MethodInjector.java:130) at org.picocontainer.injectors.CompositeInjector.decorateComponentInstance(CompositeInjector.java:59) at org.picocontainer.injectors.Reinjector.reinject(Reinjector.java:99) at org.picocontainer.injectors.ProviderAdapter.getComponentInstance(ProviderAdapter.java:84) at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:573) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:534) at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:546) at org.sonar.mojo.MavenExtensionsContainer.stop(MavenExtensionsContainer.java:91) at org.sonar.mojo.InternalMojo.execute(InternalMojo.java:153) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:483) at org.sonar.mojo.bootstrap.Bootstraper.executeMojo(Bootstraper.java:76) at org.sonar.mojo.bootstrap.Bootstraper.start(Bootstraper.java:62) at org.sonar.mojo.bootstrap.SonarMojo.execute(SonarMojo.java:112) at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:483) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:678) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:553) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:523) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:371) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:268) at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:181) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:356) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:137) at org.apache.maven.cli.MavenCli.main(MavenCli.java:356) 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.classworlds.Launcher.launchEnhanced(Launcher.java:315) at org.codehaus.classworlds.Launcher.launch(Launcher.java:255) at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430) at org.codehaus.classworlds.Launcher.main(Launcher.java:375) ** END NESTED EXCEPTION ** Last packet sent to the server was 0 ms ago. [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3 seconds [INFO] Finished at: Wed Aug 04 14:04:14 EDT 2010 [INFO] Final Memory: 23M/338M [INFO] ------------------------------------------------------------------------ -- 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.
