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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #821
Date Tue, 19 Jul 2016 19:45:18 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/821/changes>

Changes:

[clin] python scripts that are needed for running keras-based CNN

[clin] Enable Convolutional Neural Network for event-time classification. May need further
debug.

NeuralEventTimeRelationsEvaluation: will evaluate pre-trained embedding features.

NeuralEventTimeRelationsCNNEvaluation: will write sequece of tokens to feed in to the CNN.

Both above evals will evaluate the test instances within the cleartk framework.

[clin] add syntactic embedding features for classic event-event model

[clin] add syntactic features for classic event-time model

[clin] temporally remove confidence score from classification results for CNN implementation

[clin] modify the way to generate embedding features for CNN

[clin] relax the rule for removing non-contains relations

------------------------------------------
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Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/stopWords.data>
(No such file or directory)
** Error: problem of opening/reading stop words file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/stopWords.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/nonInfoWords.data>
(No such file or directory)
** Error: problem of opening/reading non-Info words file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/nonInfoWords.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/conjunctionWord.data>
(No such file or directory)
** Error: problem of opening/reading conjunction words file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/conjunctionWord.data'.>
** ERR: problem of opening/reading diacritics file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/diacriticMap.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/diacriticMap.data>
(No such file or directory)
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/ligatureMap.data>
(No such file or directory)
** Error: problem of opening/reading ligature file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/ligatureMap.data'.>
** Error: problem of opening/reading symbol synonym file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/synonymMap.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/synonymMap.data>
(No such file or directory)
**Error: problem of opening/reading file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/removeS.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/removeS.data>
(No such file or directory)
** Error: problem of opening/reading Unicode symbol file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/symbolMap.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/symbolMap.data>
(No such file or directory)
** Error: problem of opening/reading Unicode file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/unicodeMap.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/unicodeMap.data>
(No such file or directory)
** Error: problem of opening/reading nonStripMap file: '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/nonStripMap.data'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/nonStripMap.data>
(No such file or directory)
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/im.rul>
(No such file or directory)
**Error: problem of opening/reading file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/im.rul'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/im.rul>
(No such file or directory)
**Error: problem of opening/reading file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/im.rul'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/dm.rul>
(No such file or directory)
**Error: problem of opening/reading file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/dm.rul'.>
Exception: java.io.FileNotFoundException: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/dm.rul>
(No such file or directory)
**Error: problem of opening/reading file '<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/dm.rul'.>
19 Jul 2016 19:44:39  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
19 Jul 2016 19:44:39  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
19 Jul 2016 19:44:39  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
19 Jul 2016 19:44:39  INFO SentenceDetector - Starting processing.
19 Jul 2016 19:44:39  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
19 Jul 2016 19:44:39  INFO LvgAnnotator - process(JCas)
19 Jul 2016 19:44:39  INFO ContextDependentTokenizerAnnotator - process(JCas)
19 Jul 2016 19:44:39  INFO POSTagger - process(JCas)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
19 Jul 2016 19:44:39  INFO EventTimeRelationAnnotatorTest - Relation: RelationArgument
   id: 0
   argument: TimeMention
      sofa: _InitialView
      begin: 58
      end: 66
      id: 0
      ontologyConceptArr: <null>
      typeID: 0
      segmentID: <null>
      sentenceID: <null>
      discoveryTechnique: 0
      confidence: 0.0
      polarity: 0
      uncertainty: 0
      conditional: false
      generic: false
      subject: <null>
      historyOf: 0
      originalText: <null>
      date: <null>
      time: <null>
      timeClass: <null>
   role: "Arg1"
   participatesIn: <null>
 RelationArgument
   id: 0
   argument: EventMention
      sofa: _InitialView
      begin: 67
      end: 76
      id: 0
      ontologyConceptArr: <null>
      typeID: 0
      segmentID: <null>
      sentenceID: <null>
      discoveryTechnique: 0
      confidence: 1.3807402
      polarity: 0
      uncertainty: 0
      conditional: false
      generic: false
      subject: <null>
      historyOf: 0
      originalText: <null>
      event: Event
         id: 0
         ontologyConcept: <null>
         mentions: <null>
         discoveryTechnique: 0
         confidence: 0.0
         conditional: false
         generic: false
         subject: <null>
         polarity: 0
         uncertainty: 0
         historyOf: 0
         properties: EventProperties
            contextualModality: <null>
            contextualAspect: <null>
            permanence: <null>
            category: <null>
            aspect: <null>
            docTimeRel: <null>
            degree: <null>
            polarity: 0
   role: "Arg2"
   participatesIn: <null>
 Category: CONTAINS
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.504 sec
Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest
19 Jul 2016 19:44:42  INFO ClearNLPDependencyParserAE - using Morphy analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x0000000767580000,
409993216, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 409993216 bytes for committing reserved memory.
# An error report file with more information is saved as:
# <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/hs_err_pid4708.log>

Results :

Tests run: 3, Failures: 0, Errors: 0, Skipped: 0

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[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [15.949s]
[INFO] Apache cTAKES common type system .................. SUCCESS [15.958s]
[INFO] Apache cTAKES utils ............................... SUCCESS [9.692s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [1.421s]
[INFO] Apache cTAKES core ................................ SUCCESS [1:02.226s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [3.411s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [11.474s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [1.392s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [2.527s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [2.786s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [22.830s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [11.011s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [3.870s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [31.424s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [7.200s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [1.527s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.738s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [9.206s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [5.741s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [3.746s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [2.388s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [6.045s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [27.508s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [24.540s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [1.539s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [14.497s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [1.776s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res  SUCCESS [4.697s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [10.137s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [6.554s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [14.833s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [1.540s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [16.745s]
[INFO] Apache cTAKES YTEX UIMA ........................... SUCCESS [17.921s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [10.895s]
[INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [1:33.888s]
[INFO] Apache cTAKES CoReference Resolver ................ 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] 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] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8:57.170s
[INFO] Finished at: Tue Jul 19 19:44:48 UTC 2016
[INFO] Final Memory: 98M/588M
[INFO] ------------------------------------------------------------------------
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[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test
(default-test) on project ctakes-temporal: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test
failed: The forked VM terminated without saying properly goodbye. VM crash or System.exit
called ? -> [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/PluginExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :ctakes-temporal
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