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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #569
Date Thu, 30 Oct 2014 17:35:19 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/569/changes>

Changes:

[chenpei] CTAKES-94: Adding factory method to SubjectCleartkAnalysisEngine.java

[tmill] Added fast dictionary retriever plus reference to polarity and uncertainty and sample
text to test them.

------------------------------------------
[...truncated 6893 lines...]
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Predicate'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Predicate_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.List'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.List_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Paragraph'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Paragraph_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Segment'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Segment_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Sentence'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Sentence_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pair'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pair_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pairs'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pairs_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.Date'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.Date_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.DocKey'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.DocKey_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.KeyValuePair'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.ytex.uima.types.KeyValuePair_Type'.
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-ytex-uima ---
[INFO] Compiling 320 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-ytex-uima/target/classes>
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-ytex-uima
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-ytex-uima
---
[INFO] Compiling 11 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-ytex-uima/target/test-classes>
[WARNING] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java>:[89,15]
[unchecked] unchecked conversion
[INFO] 
[INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @ ctakes-ytex-uima ---
[INFO] Tests are skipped.
[JENKINS] Archiving disabled
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES ctakes-clinical-pipeline 3.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-clinical-pipeline ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-clinical-pipeline
---
Downloading: http://repo.maven.apache.org/maven2/jwnl/jwnl/1.3.3/jwnl-1.3.3.pom
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-clinical-pipeline
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/resources>
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-clinical-pipeline
---
[INFO] Compiling 5 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/target/classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[40,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[41,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[42,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java>:[92,55]
[unchecked] unchecked cast
[ERROR]   required: Class<T>
  found:    Type
  where T is a type-variable:
    T extends Annotation declared in class BagOfAnnotationsGenerator
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[82,64]
error: cannot find symbol
[ERROR]   symbol:   class DefaultJCasTermAnnotator
  location: class ClinicalPipelineFactory
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[83,10]
error: cannot find symbol
[ERROR]   symbol:   variable AbstractJCasTermAnnotator
  location: class ClinicalPipelineFactory
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[85,10]
error: cannot find symbol
[ERROR]   symbol:   variable JCasTermAnnotator
  location: class ClinicalPipelineFactory
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java>:[167,17]
[unchecked] unchecked call to add(E) as a member of the raw type Set
[INFO] 8 errors 
[INFO] -------------------------------------------------------------
[JENKINS] Archiving disabled
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [26.603s]
[INFO] Apache cTAKES common type system .................. SUCCESS [11.748s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.798s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [1.013s]
[INFO] Apache cTAKES core ................................ SUCCESS [18.115s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [2.701s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.586s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [2.773s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [3.480s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [6.103s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [11.797s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [6.391s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [4.715s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [2.781s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [5.288s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [2.801s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [5.192s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [2.878s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [4.956s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [2.776s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [2.806s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [3.019s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [32.782s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [9.615s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [8.318s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [2.791s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [8.258s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [3.080s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [6.576s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [2.864s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [6.202s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.927s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [8.937s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [2.976s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [4.967s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [2.736s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [2.552s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [11.300s]
[INFO] Apache cTAKES YTEX UIMA ........................... SUCCESS [14.800s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ FAILURE [3.059s]
[INFO] Apache cTAKES Temporal Information Extraction ..... 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] ctakes-examples ................................... SKIPPED
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res  SKIPPED
[INFO] Apache cTAKES dictionary lookup fast .............. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5:17.119s
[INFO] Finished at: Thu Oct 30 17:34:40 UTC 2014
[INFO] Final Memory: 77M/294M
[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-clinical-pipeline: Compilation failure: Compilation failure:
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[40,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[41,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[42,46]
error: package org.apache.ctakes.dictionary.lookup2.ae does not exist
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java>:[92,55]
[unchecked] unchecked cast
[ERROR] required: Class<T>
[ERROR] found:    Type
[ERROR] where T is a type-variable:
[ERROR] T extends Annotation declared in class BagOfAnnotationsGenerator
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[82,64]
error: cannot find symbol
[ERROR] symbol:   class DefaultJCasTermAnnotator
[ERROR] location: class ClinicalPipelineFactory
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[83,10]
error: cannot find symbol
[ERROR] symbol:   variable AbstractJCasTermAnnotator
[ERROR] location: class ClinicalPipelineFactory
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java>:[85,10]
error: cannot find symbol
[ERROR] symbol:   variable JCasTermAnnotator
[ERROR] location: class ClinicalPipelineFactory
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java>:[167,17]
[unchecked] unchecked call to add(E) as a member of the raw type Set
[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-clinical-pipeline
Sending e-mails to: notifications@ctakes.apache.org timothy.miller@childrens.harvard.edu
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