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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #1082
Date Fri, 25 Aug 2017 20:34:21 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/1082/display/redirect?page=changes>

Changes:

[tmill] Changes to coreference for processing multiple notes per patient in a single cas.

------------------------------------------
[...truncated 813.40 KB...]
[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 130 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/eval/EvaluationOfEventCoreference.java>:[46,36]
error: cannot find symbol
[ERROR]   symbol:   class ThymePatientViewAnnotator
  location: package org.apache.ctakes.temporal.ae
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[280,37]
error: cannot find symbol
[ERROR]   symbol:   variable MAX_DOC_VIEWS
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[413,35]
error: cannot find symbol
[ERROR]   symbol:   variable MAX_DOC_VIEWS
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[477,35]
error: cannot find symbol
[ERROR]   symbol:   variable MAX_DOC_VIEWS
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[564,66]
error: cannot find symbol
[ERROR]   symbol:   class ThymePatientViewAnnotator
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[567,23]
error: cannot find symbol
[ERROR]   symbol:   variable MAX_DOC_VIEWS
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[573,21]
error: cannot find symbol
[ERROR]   symbol:   method getLinguisticProcessingDescription()
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[575,21]
error: cannot find symbol
[ERROR]   symbol:   method getGoldWritingAggregate(String)
  location: class EvaluationOfEventCoreference
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java>:[97,36]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java>:[169,30]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java>:[185,30]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java>:[53,50]
[deprecation] locateFile(String) in FileLocator has been deprecated
[INFO] 12 errors 
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[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [4.599s]
[INFO] ctakes-gui-res .................................... SUCCESS [3.966s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [2.474s]
[INFO] Apache cTAKES common type system .................. SUCCESS [7.379s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.484s]
[INFO] Apache cTAKES core ................................ SUCCESS [33.581s]
[INFO] ctakes-gui ........................................ SUCCESS [3.632s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [2.365s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [4.595s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [2.222s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [3.150s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [3.624s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [10.076s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [3.937s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [4.631s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [26.730s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [4.834s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [17.284s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.294s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [2.486s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [3.086s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [2.294s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [2.166s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [2.210s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res  SUCCESS [3.239s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [3.097s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.667s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [2.819s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [36.344s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [5.284s]
[INFO] ctakes-clinical-pipeline-res ...................... SUCCESS [2.536s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [19.297s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [8.065s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [1:28.087s]
[INFO] Apache cTAKES CoReference Resolver ................ FAILURE [4.593s]
[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: 6:18.820s
[INFO] Finished at: Fri Aug 25 20:33:30 UTC 2017
[INFO] Final Memory: 75M/479M
[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/eval/EvaluationOfEventCoreference.java>:[46,36]
error: cannot find symbol
[ERROR] symbol:   class ThymePatientViewAnnotator
[ERROR] location: package org.apache.ctakes.temporal.ae
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[280,37]
error: cannot find symbol
[ERROR] symbol:   variable MAX_DOC_VIEWS
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[413,35]
error: cannot find symbol
[ERROR] symbol:   variable MAX_DOC_VIEWS
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[477,35]
error: cannot find symbol
[ERROR] symbol:   variable MAX_DOC_VIEWS
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[564,66]
error: cannot find symbol
[ERROR] symbol:   class ThymePatientViewAnnotator
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[567,23]
error: cannot find symbol
[ERROR] symbol:   variable MAX_DOC_VIEWS
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[573,21]
error: cannot find symbol
[ERROR] symbol:   method getLinguisticProcessingDescription()
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java>:[575,21]
error: cannot find symbol
[ERROR] symbol:   method getGoldWritingAggregate(String)
[ERROR] location: class EvaluationOfEventCoreference
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java>:[97,36]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java>:[169,30]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java>:[185,30]
[deprecation] locateFile(String) in FileLocator has been deprecated
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java>:[53,50]
[deprecation] locateFile(String) in FileLocator has been deprecated
[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
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