See <http://cytoscape.wodaklab.org/hudson/job/Cy3%20PSI-MI%20impl/54/>
------------------------------------------
[...truncated 111 lines...]
[org.cytoscape.psi_mi]
[INFO] task-segment: [deploy]
[INFO] ------------------------------------------------------------------------
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/)
[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_14-16-08/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#876 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/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: 27 seconds
[INFO] Finished at: Mon Oct 25 14:16:38 EDT 2010
[INFO] Final Memory: 54M/480M
[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: 506 ms
[INFO] Sensor AsynchronousMeasuresSensor...
[INFO] Sensor AsynchronousMeasuresSensor done: 29 ms
[INFO] Sensor SquidSensor...
[INFO] Java AST scan...
[INFO] Java AST scan done: 641 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: 104 ms
[INFO] Squid extraction...
[INFO] Package design analysis...
[INFO] Package design analysis done: 16 ms
[INFO] Squid extraction done: 499 ms
[INFO] Sensor SquidSensor done: 1298 ms
[INFO] Sensor ProfileSensor...
[INFO] Sensor ProfileSensor done: 25 ms
[INFO] Sensor ProjectLinksSensor...
[INFO] Sensor ProjectLinksSensor done: 4 ms
[INFO] Sensor VersionEventsSensor...
[INFO] Sensor VersionEventsSensor done: 38 ms
[INFO] Sensor Maven dependencies...
[INFO] Sensor Maven dependencies done: 315 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: 29 seconds
[INFO] Finished at: Mon Oct 25 14:17:19 EDT 2010
[INFO] Final Memory: 76M/721M
[INFO] ------------------------------------------------------------------------
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