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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #1119
Date Wed, 08 Nov 2017 16:35:47 GMT
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] -------------------------------------------------------------
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[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] ------------------------------------------------------------------------
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[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: notifications@ctakes.apache.org timothy.miller@childrens.harvard.edu
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