ctakes-notifications mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #141
Date Fri, 19 Jul 2013 01:37:56 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/141/changes>

Changes:

[mattcoarr] temporarily reverting library changes so I don't break the build

[mattcoarr] removed jcarafe-ext as it's not needed and it was causing depdency problems

CTAKES-76 and CTAKES-108

[mattcoarr] removed system dependencies (for the assertion module) from the two profiles for
running CPE and CVD


as per Steve Bethard's comments on CTAKES-76

[chenpei] CTAKES-76 using maven central now- deleting the physical jars from /lib

[chenpei] CTAKES-76 using maven central now- no need to copy them from lib for packing
- ctakes-assertion is upated to point four dependencies at their location on maven central:
- jcarafe-core
- jcarafe-ext
- mastif-i2b2 (previously named med-facts-i2b2)
- mastif-zoner (previously named med-facts-zoner)

[mattcoarr] As per CTAKES-76, ctakes-assertion is upated to point four dependencies at their
location on maven central:
- jcarafe-core
- jcarafe-ext
- mastif-i2b2 (previously named med-facts-i2b2)
- mastif-zoner (previously named med-facts-zoner)

[clin] Added Feature Selection for TimeAnnotator. The Feature Selection can be turned off
by setting --featureSelectionThreshold 0.
Other positive value of --featureSelectionThreshold will enable the feature selection process.

[stevenbethard] CTAKES-217: Fixes bug where printing of deltas was repeating some of the inserted/deleted
lines

[stevenbethard] CTAKES-217: Revises CompareFeatureStructures to use java-diff-utils. The search
for FeatureStructure equality is the same, but now nested uses of DiffUtils produce what is
hopefully better output. In particular, there should now be more useful output for the case
where annotations have been inserted or deleted (not just changed).

------------------------------------------
Started by an SCM change
Building remotely on ubuntu4 in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/>
Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2013-07-19T01:36:57.871
+0000'
U         ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RouteFSM.java
A         ctakes-temporal/src/main/resources/org/apache/ctakes/temporal/timenorm.en.grammar
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java
U         ctakes-temporal/pom.xml
U         KEYS
U         ctakes-dependency-parser/.settings/org.eclipse.core.resources.prefs
U         ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyRegex.java
U         ctakes-distribution/src/main/assembly/bin.xml
AU        ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
U         ctakes-clinical-pipeline/pom.xml
U         ctakes-assertion-zoner/pom.xml
D         ctakes-assertion/lib
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TrainAttributeModels.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationManualDepContextAnalyzer.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java
A         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java
At revision 1504744
Parsing POMs
ERROR: Failed to parse POMs
hudson.util.IOException2: remote file operation failed: <https://builds.apache.org/job/ctakes-trunk-package/ws/>
at hudson.remoting.Channel@5f258d19:ubuntu4
	at hudson.FilePath.act(FilePath.java:861)
	at hudson.FilePath.act(FilePath.java:838)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:862)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:620)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:592)
	at hudson.model.Run.execute(Run.java:1568)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:477)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:236)
Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: junit:junit:jar
-> duplicate declaration of version (?) @ line 154, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
will be unresolvable by dependent projects @ line 192, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar
will be unresolvable by dependent projects @ line 199, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
should not point at files within the project directory, ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 206, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar should
not point at files within the project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 213, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar>
@ line 192, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-zoner-1.1.jar>
@ line 199, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar>
@ line 206, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar>
@ line 213, column 16
[ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @
line 36, column 15
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar
-> duplicate declaration of version (?) @ line 91, column 17
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar
-> duplicate declaration of version (?) @ line 95, column 21
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar
-> duplicate declaration of version (?) @ line 99, column 15

	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1229)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:997)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2348)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
	at java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:679)
Caused by: hudson.remoting.ProxyException: org.apache.maven.project.ProjectBuildingException:
Some problems were encountered while processing the POMs:
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: junit:junit:jar
-> duplicate declaration of version (?) @ line 154, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
will be unresolvable by dependent projects @ line 192, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar
will be unresolvable by dependent projects @ line 199, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
should not point at files within the project directory, ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 206, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar should
not point at files within the project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 213, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar>
@ line 192, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-zoner-1.1.jar>
@ line 199, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar>
@ line 206, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers
to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar>
@ line 213, column 16
[ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @
line 36, column 15
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar
-> duplicate declaration of version (?) @ line 91, column 17
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar
-> duplicate declaration of version (?) @ line 95, column 21
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar
-> duplicate declaration of version (?) @ line 99, column 15

	at org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:363)
	at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361)
	at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1179)
	... 11 more

Mime
View raw message