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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #142
Date Sat, 20 Jul 2013 00:46:42 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/142/changes>

Changes:

[swu] some extra stuff for feature selection grid search and evaluations in general

[james-masanz] CTAKES-183 Update reference to resource that was moved to ctakes-core-res

[james-masanz] CTAKES-218 Have FileLocator also try the second method to resolve the file
path if the first returns null (in addition to if the first throws an exception)

[clin] Make a Yate's parameter for Chi2 feature selection. So people may turn on or off the
Yate's correction for Chi2 value calculation.
If Yate's correction is on (boolean Yates = true), small difference between observed value
and expected value (<0.5) will be ignored. More features will be trimmed.
Else, small difference will be kept. Users have the freedom to keep all features.

------------------------------------------
Started by an SCM change
Building remotely on ubuntu2 in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/>
Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2013-07-20T00:45:54.041
+0000'
U         ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java
U         ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java
U         ctakes-assertion-zoner/pom.xml
D         ctakes-assertion/lib
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/MutualInformationFeatureSelection.java
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
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/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/medfacts/cleartk/GenericCleartkAnalysisEngine.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/eval/AssertionEvaluation.java
AU        ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java
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/util/NegationDepRegex.java
U         ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java
U         ctakes-distribution/src/main/assembly/bin.xml
U         KEYS
U         ctakes-clinical-pipeline/pom.xml
U         ctakes-temporal/pom.xml
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
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/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
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
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
U         ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RouteFSM.java
At revision 1505071
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@32401cae:ubuntu2
	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

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