See <https://builds.apache.org/job/ctakes-trunk-compiletest/906/changes>
Changes: [tmill] Add category to cluster relation. [tmill] Update to allow for coref evaluation given gold standard markables. [tmill] Factory methods for grabbing partial or complete coref pipelines. ------------------------------------------ [...truncated 3631 lines...] A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf A ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf A 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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 A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2 A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedWithin.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAllAssertionModels.txt AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyPathRegexpFeatureExtractor.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/XMIReader.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/SharpCorpusSplit.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityDomainAdaptationTests.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/ReadAndPreprocessForAttributeModels.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TrainAttributeModels.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TestAttributeModels.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityDomainAdaptationTrain.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/ReadPreprocessTrainTestJudge.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/JustJudgeStep.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/SemanticClasses.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationManualDepContextAnalyzer.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionTreeUtils.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java U . At revision 1772920 ERROR: Processing failed due to a bug in the code. 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hudson.maven.MavenModule@2284ec66[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-dictionary-lookup2-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-dictionary-lookup2-res][relativePath:ctakes-dictionary-lookup2-res], hudson.maven.MavenModule@42f95610[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-distribution][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-distribution][relativePath:ctakes-distribution], hudson.maven.MavenModule@450550f9[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-drug-ner][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-drug-ner][relativePath:ctakes-drug-ner], hudson.maven.MavenModule@252fb4f5[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-drug-ner-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-drug-ner-res][relativePath:ctakes-drug-ner-res], hudson.maven.MavenModule@204d8bea[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-examples][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-examples][relativePath:ctakes-examples], hudson.maven.MavenModule@288c0025[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-examples-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-examples-res][relativePath:ctakes-examples-res], hudson.maven.MavenModule@47611f55[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg][relativePath:ctakes-lvg], hudson.maven.MavenModule@1fb18350[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg-res][relativePath:ctakes-lvg-res], hudson.maven.MavenModule@536f4997[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts][relativePath:ctakes-ne-contexts], hudson.maven.MavenModule@1baaf6f7[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts-res][relativePath:ctakes-ne-contexts-res], hudson.maven.MavenModule@3f650dfd[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@547ec960[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@47467bbc[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][relativePath:ctakes-preprocessor], hudson.maven.MavenModule@6ecca132[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@221def52[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@a17b8[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@74e5179e[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@7fabed01[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@3201ead9[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@62e68cf6[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@661e3d71[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@3ee33ed3[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][relativePath:ctakes-temporal], hudson.maven.MavenModule@1e801feb[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@23ea79c0[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@753dd077[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][relativePath:ctakes-utils], hudson.maven.MavenModule@520f7da5[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][relativePath:ctakes-ytex], hudson.maven.MavenModule@4cee5f48[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@3c3a0b6c[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@279fcaf4[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@fd3dd91[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-2fc(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)
