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/> Cleaning up <https://builds.apache.org/job/ctakes-trunk-package/ws/.> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-uima/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-preprocessor/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-web/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-type-system/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-utils/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-context-tokenizer/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core-res/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status/target> Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target> 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
