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 ------------------------------------------ [...truncated 13114 lines...] 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 [JENKINS] Recording test results [JENKINS] Archiving disabled [INFO] ------------------------------------------------------------------------ [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] ------------------------------------------------------------------------ [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-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 Sending e-mails to: notifications@ctakes.apache.org c...@yelp.com channel stopped
