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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #279
Date Wed, 05 Jun 2013 23:50:36 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/279/changes>

Changes:

[tmill] Completed method for event argument extraction.

------------------------------------------
[...truncated 6559 lines...]
05 Jun 2013 23:36:15  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO MaxentParserWrapper - Started processing: doc2_07543210_sample_past_smoker.txt
   ....ended with 0 vectors.
05 Jun 2013 23:36:15  INFO MipacqSvmChainCreator - Classifying coreference in document: doc2_07543210_sample_past_smoker.txt
05 Jun 2013 23:36:15  INFO MipacqSvmChainCreator - Done classifying document: doc2_07543210_sample_past_smoker.txt
05 Jun 2013 23:36:15  INFO CasConsumer - Started
05 Jun 2013 23:36:15  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:15  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:15  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:15  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:15  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:15  INFO MaxentParserWrapper - Started processing: testpatient_plaintext_2.txt
   ....ended with 0 vectors.
05 Jun 2013 23:36:16  INFO MipacqSvmChainCreator - Classifying coreference in document: testpatient_plaintext_2.txt
05 Jun 2013 23:36:16  INFO MipacqSvmChainCreator - Done classifying document: testpatient_plaintext_2.txt
05 Jun 2013 23:36:16  INFO CasConsumer - Started
05 Jun 2013 23:36:16  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:16  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:16  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:16  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:16  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:16  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:16  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:16  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:16  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:17  INFO MaxentParserWrapper - Started processing: SampleInputRadiologyNotes.txt
   ....ended with 2 vectors.
05 Jun 2013 23:36:19  INFO MipacqSvmChainCreator - Classifying coreference in document: SampleInputRadiologyNotes.txt
05 Jun 2013 23:36:19  INFO MipacqSvmChainCreator - Done classifying document: SampleInputRadiologyNotes.txt
05 Jun 2013 23:36:19  INFO CasConsumer - Started
05 Jun 2013 23:36:19  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:19  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:20  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:20  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:20  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:20  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:20  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:20  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:20  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:20  INFO MaxentParserWrapper - Started processing: testfakenote.txt
   ....ended with 5 vectors.
05 Jun 2013 23:36:20  INFO MipacqSvmChainCreator - Classifying coreference in document: testfakenote.txt
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Done classifying document: testfakenote.txt
05 Jun 2013 23:36:21  INFO CasConsumer - Started
05 Jun 2013 23:36:21  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:21  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:21  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:21  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:21  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO MaxentParserWrapper - Started processing: sample_note_plaintext
   ....ended with 2 vectors.
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Classifying coreference in document: sample_note_plaintext
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Done classifying document: sample_note_plaintext
05 Jun 2013 23:36:21  INFO CasConsumer - Started
05 Jun 2013 23:36:21  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:21  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:21  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:21  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:21  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO MaxentParserWrapper - Started processing: text1.txt
   ....ended with 1 vectors.
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Classifying coreference in document: text1.txt
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Done classifying document: text1.txt
05 Jun 2013 23:36:21  INFO CasConsumer - Started
05 Jun 2013 23:36:21  INFO SentenceDetector - Starting processing.
05 Jun 2013 23:36:21  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
05 Jun 2013 23:36:21  INFO LvgAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO ContextDependentTokenizerAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO POSTagger - process(JCas)
05 Jun 2013 23:36:21  INFO Chunker -  process(JCas)
05 Jun 2013 23:36:21  INFO CopyAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO OverlapAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO DictionaryLookupAnnotator - process(JCas)
05 Jun 2013 23:36:21  INFO MaxentParserWrapper - Started processing: sample_note
   ....ended with 2 vectors.
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Classifying coreference in document: sample_note
05 Jun 2013 23:36:21  INFO MipacqSvmChainCreator - Done classifying document: sample_note
05 Jun 2013 23:36:21  INFO CasConsumer - Started
05 Jun 2013 23:36:21  INFO RegressionPipelineTest - Completed 12 documents
05 Jun 2013 23:36:21  INFO RegressionPipelineTest - Verifying Test Output: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-regression-test/testdata/expectedoutput/CoreferenceCPETest/doc1_07543210_sample_unknown.txt.xml>
Exception in thread "BaseCPMImpl-Thread" junit.framework.AssertionFailedError: Verifying Test
Output: doc1_07543210_sample_unknown.txt.xmlorg.custommonkey.xmlunit.Diff
[different] Expected number of child nodes '51269' but was '51173' - comparing <CAS...>
at /CAS[1] to <CAS...> at /CAS[1]

	at junit.framework.Assert.fail(Assert.java:50)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at org.apache.ctakes.regression.test.RegressionPipelineTest.compareXMLOutput(RegressionPipelineTest.java:148)
	at org.apache.ctakes.regression.test.RegressionPipelineTest$StatusCallbackListenerImpl.collectionProcessComplete(RegressionPipelineTest.java:201)
	at org.apache.uima.collection.impl.cpm.BaseCPMImpl.run(BaseCPMImpl.java:538)
	at java.lang.Thread.run(Thread.java:662)

Results :

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

[JENKINS] Recording test results
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [4.358s]
[INFO] Apache cTAKES common type system .................. SUCCESS [9.796s]
[INFO] Apache cTAKES utils ............................... SUCCESS [2.043s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [0.738s]
[INFO] Apache cTAKES core ................................ SUCCESS [7.492s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [0.972s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [3.259s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [0.837s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [1.612s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.841s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [0.870s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [15.663s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [1.004s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [0.748s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [1.725s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [0.685s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [2.601s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [1.026s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [1.403s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [1.027s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [0.695s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [2.090s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [27.228s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [11.117s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [3.551s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [0.886s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [4.427s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.034s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [4.506s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [1.147s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [3.856s]
[INFO] Apache cTAKES Resources pad-term-spotter-res ...... SUCCESS [1.057s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [4.567s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [1.791s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [1.199s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.803s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [4.374s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [0.664s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [13.320s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [2.628s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [0.866s]
[INFO] Apache cTAKES Regression-test ..................... FAILURE [15:02.533s]
[INFO] Apache cTAKES template filler ..................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 17:38.272s
[INFO] Finished at: Wed Jun 05 23:50:27 UTC 2013
[INFO] Final Memory: 37M/249M
[INFO] ------------------------------------------------------------------------
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Waiting for Jenkins to finish collecting data
mavenExecutionResult exceptions not empty
message : Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12:test
(default-test) on project ctakes-regression-test: Failure or timeout
cause : Failure or timeout
Stack trace : 
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12:test
(default-test) on project ctakes-regression-test: Failure or timeout
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
	at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239)
	at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:100)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:66)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:662)
Caused by: org.apache.maven.plugin.MojoExecutionException: Failure or timeout
	at org.apache.maven.plugin.surefire.SurefirePlugin.assertNoFailureOrTimeout(SurefirePlugin.java:665)
	at org.apache.maven.plugin.surefire.SurefirePlugin.handleSummary(SurefirePlugin.java:646)
	at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:137)
	at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:98)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
	... 27 more
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