See <https://builds.apache.org/job/ctakes-trunk-compiletest/884/changes>
Changes: [dligach] now using token-based training data generatoin [seanfinan] uimafit version of assertion, with minor change and refactoring ------------------------------------------ [...truncated 3607 lines...] A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDistSemExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterMentionFeaturesExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDistanceFeaturesExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDepHeadExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSemTypeDepPrefsFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterUMLSFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAttributeFeaturesExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSalienceFeaturesExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSectionFeaturesExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/AttributeFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/SalienceFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PersonChainAnnotator.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableHeadTreeCreator.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableExpander.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java AU ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Test.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanOffsetComparator.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java A ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfMarkableSalience.java A ctakes-coreference/src/main/resources A ctakes-coreference/src/main/resources/org A ctakes-coreference/src/main/resources/org/apache A ctakes-coreference/src/main/resources/org/apache/ctakes A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Properties.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/DiscoveryTechnique.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Relation.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CoreferenceRelation.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/RelationArgument.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BooleanLabeledFS.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BinaryRelation.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/PredicateArgRelation.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CollectionRelation.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Pair.xml A ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml A ctakes-coreference/data A ctakes-coreference/data/test A ctakes-coreference/data/test/output A ctakes-coreference/data/test/output/testfakenote.xml A ctakes-coreference/data/test/testfakenote.txt A ctakes-coreference/pom.xml A ctakes-coreference/resources A ctakes-coreference/resources/launch AU ctakes-coreference/resources/launch/UIMA_CPE--coref-resolver.launch AU ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch A ctakes-clinical-pipeline A ctakes-clinical-pipeline/src A ctakes-clinical-pipeline/src/test A ctakes-clinical-pipeline/src/test/data A ctakes-clinical-pipeline/src/test/data/plaintext A ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_1.txt A ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_2.txt A ctakes-clinical-pipeline/src/test/data/plaintext/sample_note_plaintext A ctakes-clinical-pipeline/src/test/data/output A ctakes-clinical-pipeline/src/test/data/output/NotesIIST_RTF.DTD A ctakes-clinical-pipeline/src/test/data/output/testpatient_cn_1.xml.included.xml A ctakes-clinical-pipeline/src/test/data/testpatient_cn_1.xml A ctakes-clinical-pipeline/src/test/data/testpatient_cn_2.xml A ctakes-clinical-pipeline/src/main A ctakes-clinical-pipeline/src/main/java A ctakes-clinical-pipeline/src/main/java/org A ctakes-clinical-pipeline/src/main/java/org/apache A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java AU ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime AU ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java AU ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae A ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java A ctakes-clinical-pipeline/data A ctakes-clinical-pipeline/data/input A ctakes-clinical-pipeline/data/output A ctakes-clinical-pipeline/pom.xml A ctakes-clinical-pipeline/resources A ctakes-clinical-pipeline/resources/launch AU ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch AU ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch A ctakes-clinical-pipeline/SystemArchitectureOverview.txt A ctakes-clinical-pipeline/README A ctakes-clinical-pipeline/desc A ctakes-clinical-pipeline/desc/analysis_engine A ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml A ctakes-clinical-pipeline/desc/analysis_engine/auto A ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml A ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml A ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml A ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml A ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaProcessor.xml AU ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml A ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaUMLSProcessor.xml A ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml A ctakes-clinical-pipeline/desc/analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml A ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml A ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml A ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps A ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml A ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml A ctakes-clinical-pipeline/desc/collection_processing_engine A ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml A ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps A ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml A ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml A ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml A ctakes-clinical-pipeline/LICENSE A ctakes-constituency-parser A ctakes-constituency-parser/conf A ctakes-constituency-parser/doc A ctakes-constituency-parser/scripts A ctakes-constituency-parser/scripts/groovy AU ctakes-constituency-parser/scripts/groovy/parser.groovy A ctakes-constituency-parser/src A ctakes-constituency-parser/src/main A ctakes-constituency-parser/src/main/java A ctakes-constituency-parser/src/main/java/org A ctakes-constituency-parser/src/main/java/org/apache A ctakes-constituency-parser/src/main/java/org/apache/ctakes A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co/ParserTreeWriterConsumer.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ParserWrapper.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/TreeUtils.java AU ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeExtractor.java A ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeKernel.java A ctakes-constituency-parser/src/main/resources A ctakes-constituency-parser/src/main/resources/org A ctakes-constituency-parser/src/main/resources/org/apache A ctakes-constituency-parser/src/main/resources/org/apache/ctakes A ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency A ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser A ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types A ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml A ctakes-constituency-parser/data A ctakes-constituency-parser/data/test A ctakes-constituency-parser/data/test/testfakenote.txt A ctakes-constituency-parser/data/test/output A ctakes-constituency-parser/data/test/output/testfakenote.xml A ctakes-constituency-parser/pom.xml A ctakes-constituency-parser/resources A ctakes-constituency-parser/resources/launch AU ctakes-constituency-parser/resources/launch/UIMA_CPE--Constituency Parser.launch AU ctakes-constituency-parser/resources/launch/UIMA_CVD--Constituency Parser.launch A ctakes-constituency-parser/README A ctakes-constituency-parser/desc A ctakes-constituency-parser/desc/analysis_engine A ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml A ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml A ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml A ctakes-constituency-parser/desc/collection_processing_engine A ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml A ctakes-constituency-parser/desc/cas_consumer A ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml A ctakes-constituency-parser/metadata A ctakes-constituency-parser/metadata/install.xml A ctakes-constituency-parser/LICENSE U . At revision 1765729 ERROR: Processing failed due to a bug in the code. 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hudson.maven.MavenModule@69a581aa[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger][relativePath:ctakes-pos-tagger], hudson.maven.MavenModule@1feb65a[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger-res][relativePath:ctakes-pos-tagger-res], hudson.maven.MavenModule@2920586f[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][relativePath:ctakes-preprocessor], hudson.maven.MavenModule@3359d561[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-regression-test][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-regression-test][relativePath:ctakes-regression-test], hudson.maven.MavenModule@76b4ba71[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor][relativePath:ctakes-relation-extractor], hudson.maven.MavenModule@28c8e9b[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor-res][relativePath:ctakes-relation-extractor-res], hudson.maven.MavenModule@29445d85[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect][relativePath:ctakes-side-effect], hudson.maven.MavenModule@54cb6711[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect-res][relativePath:ctakes-side-effect-res], hudson.maven.MavenModule@7ff28cb[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status][relativePath:ctakes-smoking-status], hudson.maven.MavenModule@61e196f9[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status-res][relativePath:ctakes-smoking-status-res], hudson.maven.MavenModule@149ebe11[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-template-filler][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-template-filler][relativePath:ctakes-template-filler], hudson.maven.MavenModule@6ac24735[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][relativePath:ctakes-temporal], hudson.maven.MavenModule@65be4693[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal-res][relativePath:ctakes-temporal-res], hudson.maven.MavenModule@1b79839f[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-type-system][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-type-system][relativePath:ctakes-type-system], hudson.maven.MavenModule@76428857[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][relativePath:ctakes-utils], hudson.maven.MavenModule@e419245[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][relativePath:ctakes-ytex], hudson.maven.MavenModule@195cd7c0[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-res][relativePath:ctakes-ytex-res], hudson.maven.MavenModule@4eeeca0f[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-uima][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-uima][relativePath:ctakes-ytex-uima], hudson.maven.MavenModule@2c8ce3b5[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-web][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-web][relativePath:ctakes-ytex-web]] project.getRootModule()=hudson.maven.MavenModule@6b2f6ad5[ctakes-trunk-compiletest/org.apache.ctakes:ctakes][ctakes-trunk-compiletest/org.apache.ctakes:ctakes][relativePath:] FATAL: /home/jenkins/tools/maven/apache-maven-3.0.5 doesn't have a 'lib' subdirectory - thus cannot be a valid maven installation! java.lang.IllegalArgumentException: /home/jenkins/tools/maven/apache-maven-3.0.5 doesn't have a 'lib' subdirectory - thus cannot be a valid maven installation! at hudson.maven.MavenEmbedderUtils.buildClassRealm(MavenEmbedderUtils.java:83) at hudson.maven.MavenEmbedderUtils.getMavenVersion(MavenEmbedderUtils.java:188) at hudson.maven.MavenVersionCallable.call(MavenVersionCallable.java:70) at hudson.maven.MavenVersionCallable.call(MavenVersionCallable.java:42) at hudson.remoting.UserRequest.perform(UserRequest.java:153) at hudson.remoting.UserRequest.perform(UserRequest.java:50) at hudson.remoting.Request$2.run(Request.java:332) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) at ......remote call to jenkins-test-5b8(Native Method) at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416) at hudson.remoting.UserResponse.retrieve(UserRequest.java:253) at hudson.remoting.Channel.call(Channel.java:781) at hudson.FilePath.act(FilePath.java:1102) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:629) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534) at hudson.model.Run.execute(Run.java:1741) at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:531) at hudson.model.ResourceController.execute(ResourceController.java:98) at hudson.model.Executor.run(Executor.java:410)
