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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #286
Date Tue, 11 Nov 2014 11:44:16 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/286/changes>

Changes:

[clin] add annotators and update evaluation code for i2b2 data.
add more system-generated events for candidate temporal relations.

------------------------------------------
Started by an SCM change
Building remotely on ubuntu-2 (docker Ubuntu ubuntu) in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/>
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Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2014-11-11T11:42:06.618
+0000'
AU        ctakes-core/desc/analysis_engine/SectionSegmentAnnotator.xml
U         ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java
U         ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
U         ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java
U         ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java
U         ctakes-ytex/pom.xml
U         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml
U         ctakes-dictionary-lookup-fast-res/pom.xml
D         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/MetaWsdTermConsumer.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java
U         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java
U         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/collection/DefaultCollectionMap.java
U         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
U         ctakes-distribution/pom.xml
U         ctakes-distribution/src/main/assembly/bin.xml
U         ctakes-distribution/src/main/bin/runctakesCPE.bat
U         ctakes-distribution/src/main/bin/runctakesCPE.sh
U         ctakes-distribution/src/main/bin/runctakesCVD.bat
U         ctakes-distribution/src/main/bin/runctakesCVD.sh
D         ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml
AU        ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
U         ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml
U         ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
U         ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
U         ctakes-clinical-pipeline/pom.xml
U         ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java
U         pom.xml
U         ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/SampleInputRadiologyNotes.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_past_smoker.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/text1.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/edge_cases_plaintext_1.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_unknown.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testfakenote.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_1.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/testpatient_plaintext_2.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_current.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc2_07543210_sample_current.txt.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/sample_note_plaintext.xml
U         ctakes-regression-test/testdata/expectedoutput/RegressionPipelineCPETest/doc1_07543210_sample_past_smoker.txt.xml
U         ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/generic
AU        ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/generic/model.jar
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/historyOf
AU        ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/historyOf/model.jar
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/subject
AU        ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/subject/model.jar
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/conditional
AU        ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/conditional/model.jar
U         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/polarity/sharpi2b2mipacqnegex/model.jar
U         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/models/uncertainty/model.jar
AU        ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml
AU        ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml
AU        ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml
AU        ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml
AU        ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml
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
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/medfacts/cleartk/GenericCleartkAnalysisEngine.java
A         ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventtime
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventtime/Event_Time_with_UMLS_filter.txt
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventtime/Event_Time_no_UMLS_filter.txt
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventtime/READEME.txt
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventtime/model.jar
A         ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventevent
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventevent/model.jar
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventevent/READEME.txt
AU        ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventevent/Event_Event_UMLS_doubleFilter_useSystemEvents.txt
U         ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
U         ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
AU        ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java
U         ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
AU        ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
AU        ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
D         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.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/EvaluationOfEventCoreference.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java
A         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
A         ctakes-temporal/src/main/resources/org/apache/ctakes/temporal/TimeLexicon.csv
At revision 1638068
Parsing POMs
Modules changed, recalculating dependency graph
maven3-agent.jar already up to date
maven3-interceptor.jar already up to date
maven3-interceptor-commons.jar already up to date
[ctakes-trunk-package] $ /home/jenkins/tools/java/latest1.7/bin/java -Xmx26 -Xms256m -XX:MaxPermSize=512m
-cp /home/jenkins/jenkins-slave/maven3-agent.jar:/home/jenkins/jenkins-slave/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.5/boot/plexus-classworlds-2.4.jar
org.jvnet.hudson.maven3.agent.Maven3Main /home/jenkins/jenkins-slave/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.5
/home/jenkins/jenkins-slave/slave.jar /home/jenkins/jenkins-slave/maven3-interceptor.jar /home/jenkins/jenkins-slave/maven3-interceptor-commons.jar
33041
Error occurred during initialization of VM
Incompatible minimum and maximum heap sizes specified
ERROR: Failed to launch Maven. Exit code = 1


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