See <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/21/>
------------------------------------------ [...truncated 11064 lines...] Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//package-frame.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//package-summary.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//package-tree.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//package-frame.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//package-summary.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//package-tree.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//package-frame.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//package-summary.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//package-tree.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/constant-values.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/serialized-form.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//class-use/BiomartStub.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//class-use/BiomartClient.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//class-use/BiomartClientPlugin.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//class-use/BiomartMainDialog.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//class-use/DatabaseSpecificUtils.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//class-use/BiomartAttrMappingPanel.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//class-use/QueryBuilderUtil.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//class-use/XMLQueryBuilder.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//class-use/Filter.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//class-use/Dataset.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//class-use/Attribute.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient//package-use.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/ui//package-use.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/edu/ucsd/bioeng/idekerlab/biomartclient/utils//package-use.html...> Building index for all the packages and classes... Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/overview-tree.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/index-all.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/deprecated-list.html...> Building index for all classes... Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/allclasses-frame.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/allclasses-noframe.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/index.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/overview-summary.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/help-doc.html...> Generating <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/apidocs/stylesheet.css...> 1 warning [WARNING] Javadoc Warnings [WARNING] <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/src/main/java/edu/ucsd/bioeng/idekerlab/biomartclient/BiomartClient.java>:130: warning - @throws tag has no arguments. [INFO] Building jar: <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-javadoc.jar> ignoring exception during new ExecutedMojo null [INFO] [INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ biomart-client --- [INFO] edu already added, skipping [INFO] edu/ucsd already added, skipping [INFO] edu/ucsd/bioeng already added, skipping [INFO] edu/ucsd/bioeng/idekerlab already added, skipping [INFO] edu/ucsd/bioeng/idekerlab/biomartclient already added, skipping [INFO] Building jar: <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-sources.jar> [INFO] edu already added, skipping [INFO] edu/ucsd already added, skipping [INFO] edu/ucsd/bioeng already added, skipping [INFO] edu/ucsd/bioeng/idekerlab already added, skipping [INFO] edu/ucsd/bioeng/idekerlab/biomartclient already added, skipping [INFO] [INFO] --- maven-assembly-plugin:2.2-beta-5:single (make-assembly) @ biomart-client --- [INFO] Building jar: <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-jar-with-dependencies.jar> [INFO] [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT.jar> to /opt/tomcat-home/.m2/repository/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT.jar [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/pom.xml> to /opt/tomcat-home/.m2/repository/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT.pom [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-javadoc.jar> to /opt/tomcat-home/.m2/repository/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT-javadoc.jar [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-sources.jar> to /opt/tomcat-home/.m2/repository/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT-sources.jar [INFO] Installing <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-jar-with-dependencies.jar> to /opt/tomcat-home/.m2/repository/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT-jar-with-dependencies.jar [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ biomart-client --- [INFO] [INFO] --- maven-deploy-plugin:2.5:deploy (default-deploy) @ biomart-client --- Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml Downloaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml (2 KB at 13.9 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164.jar Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164.jar (42 KB at 464.9 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164.pom Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164.pom (2 KB at 12.4 KB/sec) Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/maven-metadata.xml Downloaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/maven-metadata.xml (493 B at 6.8 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml (2 KB at 15.3 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/maven-metadata.xml (493 B at 3.5 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-javadoc.jar Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-javadoc.jar (98 KB at 971.9 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml (2 KB at 12.9 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-sources.jar Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-sources.jar (31 KB at 429.1 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml (2 KB at 29.6 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-jar-with-dependencies.jar Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-20121013.012102-164-jar-with-dependencies.jar (41 KB at 1009.2 KB/sec) Uploading: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml Uploaded: http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/cytoscape/coreplugins/biomart-client/2.8.4-SNAPSHOT/maven-metadata.xml (2 KB at 37.3 KB/sec) [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biomart-client/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biomart-client/2.8.4-SNAPSHOT/biomart-client-2.8.4-SNAPSHOT.pom [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biomart-client/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biomart-client/2.8.4-20121013.012102-164/biomart-client-2.8.4-20121013.012102-164.jar [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-javadoc.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biomart-client/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biomart-client/2.8.4-20121013.012102-164/biomart-client-2.8.4-20121013.012102-164-javadoc.jar [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-sources.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biomart-client/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biomart-client/2.8.4-20121013.012102-164/biomart-client-2.8.4-20121013.012102-164-sources.jar [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioMartClient/target/biomart-client-2.8.4-SNAPSHOT-jar-with-dependencies.jar> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biomart-client/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biomart-client/2.8.4-20121013.012102-164/biomart-client-2.8.4-20121013.012102-164-jar-with-dependencies.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building BioPAX 2.8.4-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/releases/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom Downloading: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom Downloading: http://repo1.maven.org/maven2/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom [JENKINS] Archiving <http://code.cytoscape.org/jenkins/job/Cytoscape_2.X_application/ws/trunk/coreplugins/BioPAX/pom.xml> to /opt/tomcat-home/jenkins/jobs/Cytoscape_2.X_application/modules/cytoscape.coreplugins$biopax/builds/2012-10-12_20-14-20/archive/cytoscape.coreplugins/biopax/2.8.4-SNAPSHOT/biopax-2.8.4-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Cytoscape Parent POM .............................. SUCCESS [5.255s] [INFO] Cytoscape Core Libraries Parent POM ............... SUCCESS [0.478s] [INFO] commons-cli-1-x-cytocape-custom ................... SUCCESS [11.287s] [INFO] equations ......................................... SUCCESS [9.555s] [INFO] util-intr ......................................... SUCCESS [5.887s] [INFO] geom-spacial ...................................... SUCCESS [5.853s] [INFO] geom-rtree ........................................ SUCCESS [3.281s] [INFO] GINY API .......................................... SUCCESS [7.328s] [INFO] graph-fixed ....................................... SUCCESS [3.848s] [INFO] graph-dynamic ..................................... SUCCESS [8.931s] [INFO] nerius-math-xform ................................. SUCCESS [4.216s] [INFO] obo ............................................... SUCCESS [5.697s] [INFO] phoebe-dnd ........................................ SUCCESS [4.433s] [INFO] render-immed ...................................... SUCCESS [43.512s] [INFO] render-export ..................................... SUCCESS [4.228s] [INFO] render-stateful ................................... SUCCESS [8.019s] [INFO] task .............................................. SUCCESS [5.361s] [INFO] undo-support ...................................... SUCCESS [5.939s] [INFO] fing .............................................. SUCCESS [5.305s] [INFO] ding .............................................. SUCCESS [9.282s] [INFO] Cytoscape Documentation ........................... SUCCESS [24.196s] [INFO] Cytoscape Application ............................. SUCCESS [2:05.097s] [INFO] Cytoscape Core Plugins Parent POM ................. SUCCESS [1.414s] [INFO] Advanced Network Merge ............................ SUCCESS [11.517s] [INFO] Automatic Layout .................................. SUCCESS [26.372s] [INFO] BioMart Client .................................... SUCCESS [10.384s] [INFO] BioPAX ............................................ FAILURE [0.298s] [INFO] Editor ............................................ SKIPPED [INFO] Equation Functions ................................ SKIPPED [INFO] Manual Layout ..................................... SKIPPED [INFO] NCBI Client ....................................... SKIPPED [INFO] PSI-MI ............................................ SKIPPED [INFO] QuickFind ......................................... SKIPPED [INFO] RFilters .......................................... SKIPPED [INFO] SBML Reader ....................................... SKIPPED [INFO] Table Import ...................................... SKIPPED [INFO] Attribute Browser ................................. SKIPPED [INFO] cPath ............................................. SKIPPED [INFO] cPath2 ............................................ SKIPPED [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: 6:39.970s [INFO] Finished at: Fri Oct 12 20:21:04 GMT-05:00 2012 [INFO] Final Memory: 62M/292M [INFO] ------------------------------------------------------------------------ mavenExecutionResult exceptions not empty message : Failed to execute goal on project biopax: Could not resolve dependencies for project cytoscape.coreplugins:biopax:jar:2.8.4-SNAPSHOT: Failed to collect dependencies for [commons-lang:commons-lang:jar:2.4 (provided), net.sourceforge.collections:collections-generic:jar:4.01 (compile), org.biopax.paxtools:paxtools-core:jar:4.1.1 (compile), commons-logging:commons-logging:jar:1.1.1 (test), cytoscape:application:jar:2.8.4-SNAPSHOT (provided), junit:junit:jar:3.8.1 (test)] cause : Could not resolve dependencies for project cytoscape.coreplugins:biopax:jar:2.8.4-SNAPSHOT: Failed to collect dependencies for [commons-lang:commons-lang:jar:2.4 (provided), net.sourceforge.collections:collections-generic:jar:4.01 (compile), org.biopax.paxtools:paxtools-core:jar:4.1.1 (compile), commons-logging:commons-logging:jar:1.1.1 (test), cytoscape:application:jar:2.8.4-SNAPSHOT (provided), junit:junit:jar:3.8.1 (test)] Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project biopax: Could not resolve dependencies for project cytoscape.coreplugins:biopax:jar:2.8.4-SNAPSHOT: Failed to collect dependencies for [commons-lang:commons-lang:jar:2.4 (provided), net.sourceforge.collections:collections-generic:jar:4.01 (compile), org.biopax.paxtools:paxtools-core:jar:4.1.1 (compile), commons-logging:commons-logging:jar:1.1.1 (test), cytoscape:application:jar:2.8.4-SNAPSHOT (provided), junit:junit:jar:3.8.1 (test)] at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:196) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies(LifecycleDependencyResolver.java:108) at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved(MojoExecutor.java:258) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:201) 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.project.DependencyResolutionException: Could not resolve dependencies for project cytoscape.coreplugins:biopax:jar:2.8.4-SNAPSHOT: Failed to collect dependencies for [commons-lang:commons-lang:jar:2.4 (provided), net.sourceforge.collections:collections-generic:jar:4.01 (compile), org.biopax.paxtools:paxtools-core:jar:4.1.1 (compile), commons-logging:commons-logging:jar:1.1.1 (test), cytoscape:application:jar:2.8.4-SNAPSHOT (provided), junit:junit:jar:3.8.1 (test)] at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:139) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies(LifecycleDependencyResolver.java:171) ... 30 more Caused by: org.sonatype.aether.collection.DependencyCollectionException: Failed to collect dependencies for [commons-lang:commons-lang:jar:2.4 (provided), net.sourceforge.collections:collections-generic:jar:4.01 (compile), org.biopax.paxtools:paxtools-core:jar:4.1.1 (compile), commons-logging:commons-logging:jar:1.1.1 (test), cytoscape:application:jar:2.8.4-SNAPSHOT (provided), junit:junit:jar:3.8.1 (test)] at org.sonatype.aether.impl.internal.DefaultDependencyCollector.collectDependencies(DefaultDependencyCollector.java:262) at org.sonatype.aether.impl.internal.DefaultRepositorySystem.collectDependencies(DefaultRepositorySystem.java:345) at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve(DefaultProjectDependenciesResolver.java:131) ... 31 more Caused by: org.sonatype.aether.resolution.ArtifactDescriptorException: Failed to read artifact descriptor for org.biopax.paxtools:paxtools-core:jar:4.1.1 at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:282) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor(DefaultArtifactDescriptorReader.java:172) at org.sonatype.aether.impl.internal.DefaultDependencyCollector.process(DefaultDependencyCollector.java:419) at org.sonatype.aether.impl.internal.DefaultDependencyCollector.collectDependencies(DefaultDependencyCollector.java:243) ... 33 more Caused by: org.sonatype.aether.resolution.ArtifactResolutionException: Could not transfer artifact org.biopax.paxtools:paxtools-core:pom:4.1.1 from/to cytoscape_biopax_release (http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/): Error transferring file: Server returned HTTP response code: 500 for URL: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:541) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:220) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:197) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom(DefaultArtifactDescriptorReader.java:267) ... 36 more Caused by: org.sonatype.aether.transfer.ArtifactTransferException: Could not transfer artifact org.biopax.paxtools:paxtools-core:pom:4.1.1 from/to cytoscape_biopax_release (http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/): Error transferring file: Server returned HTTP response code: 500 for URL: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:949) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$4.wrap(WagonRepositoryConnector.java:940) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.flush(WagonRepositoryConnector.java:695) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.flush(WagonRepositoryConnector.java:689) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector.get(WagonRepositoryConnector.java:445) at org.sonatype.aether.impl.internal.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:460) ... 39 more Caused by: org.apache.maven.wagon.TransferFailedException: Error transferring file: Server returned HTTP response code: 500 for URL: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom at org.apache.maven.wagon.providers.http.LightweightHttpWagon.fillInputData(LightweightHttpWagon.java:143) at org.apache.maven.wagon.StreamWagon.getInputStream(StreamWagon.java:116) at org.apache.maven.wagon.StreamWagon.getIfNewer(StreamWagon.java:88) at org.apache.maven.wagon.StreamWagon.get(StreamWagon.java:61) at org.sonatype.aether.connector.wagon.WagonRepositoryConnector$GetTask.run(WagonRepositoryConnector.java:608) at org.sonatype.aether.util.concurrency.RunnableErrorForwarder$1.run(RunnableErrorForwarder.java:64) ... 3 more Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1491) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1485) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1139) at org.apache.maven.wagon.providers.http.LightweightHttpWagon.fillInputData(LightweightHttpWagon.java:122) ... 8 more Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://cytoscape.wodaklab.org/nexus/content/repositories/biopax-release/org/biopax/paxtools/paxtools-core/4.1.1/paxtools-core-4.1.1.pom at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1436) at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:379) at org.apache.maven.wagon.providers.http.LightweightHttpWagon.fillInputData(LightweightHttpWagon.java:115) ... 8 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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