See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/55/>
------------------------------------------ [...truncated 114 lines...] [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository spring-osgified-artifacts (http://maven.springframework.org/osgi) Downloading: http://repository.ops4j.org/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.pom [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository ops4j.releases (http://repository.ops4j.org/maven2/) Downloading: http://www.l2fprod.com/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.pom [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository l2fprod-maven-repo (http://www.l2fprod.com/maven2/) [INFO] [jaxb2:xjc {execution: mi1}] [INFO] Generating source... [INFO] parsing a schema... [INFO] compiling a schema... [INFO] org/cytoscape/psi_mi/internal/schema/mi1/AttributeListType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/AvailabilityType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/BaseLocationType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/BibrefType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/BioSourceType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/CvType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/DbReferenceType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/EntrySet.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/ExperimentType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/FeatureType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/FullNameType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/InteractionElementType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/IntervalType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/LabelType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/NamesType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/ObjectFactory.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/OpenCvType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/PositionType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/ProteinParticipantType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/RefType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/XrefType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi1/package-info.java [INFO] [jaxb2:xjc {execution: mi25}] [INFO] Generating source... [INFO] parsing a schema... [INFO] compiling a schema... [INFO] org/cytoscape/psi_mi/internal/schema/mi25/AttributeListType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/AvailabilityType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/BaseLocationType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/BibrefType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/BioSourceType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ConfidenceListType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ConfidenceType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/CvType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/DbReferenceType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/EntrySet.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ExperimentRefListType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ExperimentType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/FeatureElementType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/FullNameType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/InteractionElementType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/InteractorElementType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/IntervalType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/LabelType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/NamesType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ObjectFactory.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/OpenCvType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ParameterType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/ParticipantType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/PositionType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/XrefType.java [INFO] org/cytoscape/psi_mi/internal/schema/mi25/package-info.java [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [pax:compile] [INFO] Compiling 76 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/target/classes> [INFO] [recovering meta-data] [HUDSON] Archiving <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/pom.xml> to /R1/resources/webapps/cytoscape_build_sys/hudson_home/jobs/Cy3 PSI-MI impl/modules/org.cytoscape$psi-mi-impl/builds/2010-10-25_16-11-28/archive/org.cytoscape/psi-mi-impl/1.0-SNAPSHOT/pom.xml [INFO] ------------------------------------------------------------------------ [ERROR] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Compilation failure <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java>:[568,19] cannot find symbol symbol : method contains(java.lang.String,java.lang.Class<java.lang.String>) location: interface org.cytoscape.model.CyRow <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java>:[614,17] cannot find symbol symbol : method contains(java.lang.String,java.lang.Class<capture#839 of ? extends java.lang.Object>) location: interface org.cytoscape.model.CyRow <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkWriterFactory.java>:[11,7] org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkWriterFactory is not abstract and does not override abstract method getWriterTask() in org.cytoscape.io.write.CyWriterFactory <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkWriterFactory.java>:[29,1] method does not override or implement a method from a supertype <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilter.java>:[18,7] org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter is not abstract and does not override abstract method accepts(java.io.InputStream,org.cytoscape.io.DataCategory) in org.cytoscape.io.CyFileFilter <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilter.java>:[41,1] method does not override or implement a method from a supertype <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilter.java>:[71,1] method does not override or implement a method from a supertype [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 24 seconds [INFO] Finished at: Mon Oct 25 16:11:55 EDT 2010 [INFO] Final Memory: 55M/605M [INFO] ------------------------------------------------------------------------ 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://localhost: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.psi-mi-impl [org.cytoscape.psi_mi] [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: 2.2 Downloading: http://maven.springframework.org/osgi/org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.pom [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository spring-osgified-artifacts (http://maven.springframework.org/osgi) Downloading: http://repository.ops4j.org/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.pom [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository ops4j.releases (http://repository.ops4j.org/maven2/) Downloading: http://www.l2fprod.com/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.pom [INFO] Unable to find resource 'org.cytoscape:service-util:pom:1.0-SNAPSHOT' in repository l2fprod-maven-repo (http://www.l2fprod.com/maven2/) Downloading: http://maven.springframework.org/osgi/org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository spring-osgified-artifacts (http://maven.springframework.org/osgi) Downloading: http://repository.ops4j.org/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository ops4j.releases (http://repository.ops4j.org/maven2/) Downloading: http://www.l2fprod.com/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository l2fprod-maven-repo (http://www.l2fprod.com/maven2/) Downloading: http://maven.springframework.org/osgi/org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository spring-osgified-artifacts (http://maven.springframework.org/osgi) Downloading: http://repository.ops4j.org/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository ops4j.releases (http://repository.ops4j.org/maven2/) Downloading: http://www.l2fprod.com/maven2//org/cytoscape/service-util/1.0-SNAPSHOT/service-util-1.0-SNAPSHOT.jar [INFO] Unable to find resource 'org.cytoscape:service-util:jar:1.0-SNAPSHOT' in repository l2fprod-maven-repo (http://www.l2fprod.com/maven2/) [INFO] [sonar-core:internal] [INFO] Database dialect class org.sonar.api.database.dialect.MySql [INFO] ------------- Analyzing org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi] [INFO] Selected quality profile : Cytoscape, language=java [INFO] Configure maven plugins... [INFO] Sensor JavaSourceImporter... [INFO] Sensor JavaSourceImporter done: 626 ms [INFO] Sensor AsynchronousMeasuresSensor... [INFO] Sensor AsynchronousMeasuresSensor done: 51 ms [INFO] Sensor SquidSensor... [INFO] Java AST scan... [INFO] Java AST scan done: 1379 ms [INFO] Java bytecode scan... [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/SchemaVersion' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapFromCytoscape' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/util/ContentReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/util/AttributeUtil' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/GoVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkWriterFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapInteractionsToPsiTwoFive' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiTwoFiveToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiTwoFiveToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiOneToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiOneToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiOneToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/InteractorVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapperUtil' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiTwoFiveToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/InteractionVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiWriter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType$Organism' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType$Organism' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType$Organism' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ProteinInteractorType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ExperimentType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ExperimentType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ExperimentType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/schema/mi1/ExperimentType' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/SchemaVersion' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapFromCytoscape' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/util/ContentReader' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/util/AttributeUtil' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/GoVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkWriterFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiCyFileFilter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapInteractionsToPsiTwoFive' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiOneToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/InteractorVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/Interaction' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapperUtil' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/data_mapper/MapPsiTwoFiveToInteractions' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/model/vocab/InteractionVocab' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiWriter' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory' is not accessible through the ClassLoader. [WARN] Class 'org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape' is not accessible through the ClassLoader. [INFO] Java bytecode scan done: 223 ms [INFO] Squid extraction... [INFO] Package design analysis... [INFO] Package design analysis done: 15 ms [INFO] Squid extraction done: 636 ms [INFO] Sensor SquidSensor done: 2356 ms [INFO] Sensor ProfileSensor... [INFO] Sensor ProfileSensor done: 25 ms [INFO] Sensor ProjectLinksSensor... [INFO] Sensor ProjectLinksSensor done: 5 ms [INFO] Sensor VersionEventsSensor... [INFO] Sensor VersionEventsSensor done: 45 ms [INFO] Sensor Maven dependencies... [INFO] Sensor Maven dependencies done: 498 ms [INFO] Execute maven plugin findbugs-maven-plugin... [INFO] ------------------------------------------------------------------------ [INFO] Building org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi] [INFO] task-segment: [org.codehaus.mojo:findbugs-maven-plugin:2.3.1:findbugs] [INFO] ------------------------------------------------------------------------ [INFO] Preparing findbugs:findbugs [INFO] [jaxb2:xjc {execution: mi1}] [INFO] No changes detected in schema or binding files, skipping source generation. [INFO] [jaxb2:xjc {execution: mi25}] [INFO] No changes detected in schema or binding files, skipping source generation. [INFO] [resources:resources] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 3 resources [INFO] [pax:compile] [INFO] Compiling 26 source files to <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/ws/trunk/target/classes> [INFO] [recovering meta-data] [INFO] ------------------------------------------------------------------------ [ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Can not execute Sonar Embedded error: Unable to execute maven plugin Compilation failure [INFO] ------------------------------------------------------------------------ [INFO] For more information, run Maven with the -e switch [INFO] ------------------------------------------------------------------------ [INFO] Total time: 32 seconds [INFO] Finished at: Mon Oct 25 16:12:39 EDT 2010 [INFO] Final Memory: 76M/727M [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.
