See <https://builds.apache.org/job/ctakes-trunk-compiletest/1119/display/redirect?page=changes>
Changes: [tmill] New patient collector model working for coreference evaluation. ------------------------------------------ [...truncated 807.48 KB...] Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 08 Nov 2017 16:34:50 INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser, using lemmatizer: true 08 Nov 2017 16:34:50 INFO BackwardsTimeAnnotator - Initializing ... 08 Nov 2017 16:34:50 INFO BackwardsTimeAnnotator - Finished. 08 Nov 2017 16:34:53 INFO EventEventRelationAnnotator - Initializing ... . 08 Nov 2017 16:34:53 INFO EventEventRelationAnnotator - Finished. 08 Nov 2017 16:34:53 INFO SentenceDetector - Starting processing. 08 Nov 2017 16:34:53 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 08 Nov 2017 16:34:53 INFO LvgAnnotator - process(JCas) 08 Nov 2017 16:34:53 INFO ContextDependentTokenizerAnnotator - process(JCas) 08 Nov 2017 16:34:53 INFO POSTagger - process(JCas) 08 Nov 2017 16:34:53 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:main 08 Nov 2017 16:34:53 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:main Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.747 sec Results : Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [JENKINS] Recording test results [JENKINS] Archiving disabled [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Apache cTAKES CoReference Resolver 4.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-coreference --- [INFO] [INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-coreference --- [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-coreference --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 12 resources [INFO] Copying 3 resources [INFO] [INFO] --- jcasgen-maven-plugin:2.9.0:generate (default) @ ctakes-coreference --- [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/PredicateArgRelation.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CollectionRelation.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Pair.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BooleanLabeledFS.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Properties.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CoreferenceRelation.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/RelationArgument.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BinaryRelation.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Relation.xml'> [INFO] JCasGen: Found descriptor '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/DiscoveryTechnique.xml'> [INFO] JCasGen: Limiting generation to descriptors in '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference'> [INFO] JCasGen: Output going to '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/target/generated-sources/jcasgen'> [INFO] JCasGen: Reading the XML TAE descriptor, and creating types, for xml input file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/target/jcasgen/typesystem.xml'.> [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.AnaphoricityVecInstance'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.AnaphoricityVecInstance_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.BinaryRelation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.BinaryRelation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.BooleanLabeledFS'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.BooleanLabeledFS_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.CollectionRelation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.CollectionRelation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.CoreferenceRelation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.CoreferenceRelation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.DemMarkable'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.DemMarkable_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.DiscoveryTechnique'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.DiscoveryTechnique_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Markable'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Markable_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.MarkablePair'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.MarkablePair_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.MarkablePairSet'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.MarkablePairSet_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.NEMarkable'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.NEMarkable_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.NonCoreferenceRelation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.NonCoreferenceRelation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Pair'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Pair_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.PredicateArgRelation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.PredicateArgRelation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.PronounMarkable'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.PronounMarkable_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Properties'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Properties_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Relation'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.Relation_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.RelationArgument'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.RelationArgument_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.UnrelationArgument'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.UnrelationArgument_Type'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.VecInstance'. [INFO] JCasGen: Creating: 'org.apache.ctakes.coreference.type.VecInstance_Type'. [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-coreference --- [INFO] Compiling 134 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/target/classes> [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterUMLSFeatureExtractor.java>:[14,41] error: cannot find symbol [ERROR] symbol: class HashableMarkable location: package org.apache.ctakes.coreference.util <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[1030,53] error: cannot find symbol [ERROR] symbol: method getPreviousPatientName() location: variable notes of type PatientNoteStore <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[1076,53] error: cannot find symbol [INFO] 3 errors [INFO] ------------------------------------------------------------- [JENKINS] Archiving disabled [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Apache cTAKES ..................................... SUCCESS [4.509s] [INFO] ctakes-gui-res .................................... SUCCESS [3.822s] [INFO] Apache cTAKES Resources core ...................... SUCCESS [2.688s] [INFO] Apache cTAKES common type system .................. SUCCESS [40.156s] [INFO] Apache cTAKES utils ............................... SUCCESS [3.379s] [INFO] Apache cTAKES core ................................ SUCCESS [23.005s] [INFO] ctakes-gui ........................................ SUCCESS [4.524s] [INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [2.242s] [INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.378s] [INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [2.369s] [INFO] Apache cTAKES chunker ............................. SUCCESS [3.048s] [INFO] Apache cTAKES document preprocessor ............... SUCCESS [3.654s] [INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [54.828s] [INFO] Apache cTAKES dictionary lookup ................... SUCCESS [4.229s] [INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [4.562s] [INFO] Apache cTAKES Resources lvg ....................... SUCCESS [29.002s] [INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [7.835s] [INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [2.322s] [INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.168s] [INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [2.289s] [INFO] Apache cTAKES Constituency Parser ................. SUCCESS [2.949s] [INFO] Apache cTAKES Resources coreference ............... SUCCESS [2.223s] [INFO] Apache cTAKES Resources temporal .................. SUCCESS [2.288s] [INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [2.151s] [INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [3.185s] [INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [3.291s] [INFO] Apache cTAKES Resources assertion ................. SUCCESS [17.310s] [INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [2.540s] [INFO] Apache cTAKES Dependency Parser ................... SUCCESS [37.109s] [INFO] Apache cTAKES Assertion ........................... SUCCESS [4.943s] [INFO] ctakes-clinical-pipeline-res ...................... SUCCESS [2.765s] [INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [4.963s] [INFO] Apache cTAKES Relation Extractor .................. SUCCESS [8.675s] [INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [1:25.242s] [INFO] Apache cTAKES CoReference Resolver ................ FAILURE [4.804s] [INFO] Apache cTAKES Resources drug-ner .................. SKIPPED [INFO] Apache cTAKES Drug NER ............................ SKIPPED [INFO] Apache cTAKES Resources side-effect ............... SKIPPED [INFO] Apache cTAKES Side Effects ........................ SKIPPED [INFO] Apache cTAKES Resources smoking-status ............ SKIPPED [INFO] Apache cTAKES Smoking Status ...................... SKIPPED [INFO] Apache cTAKES Resources assertion-zoner ........... SKIPPED [INFO] Apache cTAKES Assertion's zoner ................... SKIPPED [INFO] ctakes-examples-res ............................... SKIPPED [INFO] ctakes-examples ................................... SKIPPED [INFO] Apache cTAKES Resources ctakes-ytex-res ........... SKIPPED [INFO] Apache cTAKES YTEX ................................ SKIPPED [INFO] Apache cTAKES YTEX UIMA ........................... SKIPPED [INFO] Apache cTAKES YTEX Web ............................ SKIPPED [INFO] Apache cTAKES Distribution ........................ SKIPPED [INFO] Apache cTAKES Regression-test ..................... SKIPPED [INFO] Apache cTAKES template filler ..................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7:16.896s [INFO] Finished at: Wed Nov 08 16:35:01 UTC 2017 [INFO] Final Memory: 73M/631M [INFO] ------------------------------------------------------------------------ [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled Waiting for Jenkins to finish collecting data [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile (default-compile) on project ctakes-coreference: Compilation failure: Compilation failure: [ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterUMLSFeatureExtractor.java>:[14,41] error: cannot find symbol [ERROR] symbol: class HashableMarkable [ERROR] location: package org.apache.ctakes.coreference.util [ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[1030,53] error: cannot find symbol [ERROR] symbol: method getPreviousPatientName() [ERROR] location: variable notes of type PatientNoteStore [ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[1076,53] error: cannot find symbol [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn <goals> -rf :ctakes-coreference Sending e-mails to: [email protected] [email protected] channel stopped
