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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #200
Date Fri, 08 Mar 2013 22:08:50 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/200/changes>

Changes:

[chenpei] CTAKES-84 - Add a MAX Timeout setting in the tests just in case the async cpe processing
doesn't come back in a reasonable time and surefire's process doesn't kill this automatically.

[chenpei] CTAKES-84 - During the XMLDiff in XMLUnit, ignore the attribute values for now.
 This is because the xcas could have the same Type and offset, but have different _id, and
id attribute values that will cause it to fail.

------------------------------------------
[...truncated 4919 lines...]
08 Mar 2013 21:52:50  INFO MipacqSvmChainCreator - Done classifying document: doc2_07543210_sample_current.txt
08 Mar 2013 21:52:50  INFO CasConsumer - Started
08 Mar 2013 21:52:50  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:52:50  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:52:50  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:52:50  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:52:50  INFO POSTagger - process(JCas)
08 Mar 2013 21:52:50  INFO Chunker -  process(JCas)
08 Mar 2013 21:52:50  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:52:50  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:52:50  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:52:50  INFO MaxentParserWrapper - Started processing: doc1_07543210_sample_current.txt
   ....ended with 0 vectors.
08 Mar 2013 21:52:51  INFO MipacqSvmChainCreator - Classifying coreference in document: doc1_07543210_sample_current.txt
08 Mar 2013 21:52:51  INFO MipacqSvmChainCreator - Done classifying document: doc1_07543210_sample_current.txt
08 Mar 2013 21:52:51  INFO CasConsumer - Started
08 Mar 2013 21:52:51  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:52:51  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:52:51  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:52:51  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:52:51  INFO POSTagger - process(JCas)
08 Mar 2013 21:52:51  INFO Chunker -  process(JCas)
08 Mar 2013 21:52:51  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:52:51  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:52:51  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:52:51  INFO MaxentParserWrapper - Started processing: doc1_07543210_sample_past_smoker.txt
   ....ended with 1 vectors.
08 Mar 2013 21:52:52  INFO MipacqSvmChainCreator - Classifying coreference in document: doc1_07543210_sample_past_smoker.txt
08 Mar 2013 21:52:52  INFO MipacqSvmChainCreator - Done classifying document: doc1_07543210_sample_past_smoker.txt
08 Mar 2013 21:52:52  INFO CasConsumer - Started
08 Mar 2013 21:52:52  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:52:52  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:52:52  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:52:52  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:52:52  INFO POSTagger - process(JCas)
08 Mar 2013 21:52:52  INFO Chunker -  process(JCas)
08 Mar 2013 21:52:52  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:52:52  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:52:52  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:52:52  INFO MaxentParserWrapper - Started processing: doc2_07543210_sample_past_smoker.txt
   ....ended with 0 vectors.
08 Mar 2013 21:52:53  INFO MipacqSvmChainCreator - Classifying coreference in document: doc2_07543210_sample_past_smoker.txt
08 Mar 2013 21:52:53  INFO MipacqSvmChainCreator - Done classifying document: doc2_07543210_sample_past_smoker.txt
08 Mar 2013 21:52:53  INFO CasConsumer - Started
08 Mar 2013 21:52:53  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:52:53  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:52:53  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:52:53  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:52:53  INFO POSTagger - process(JCas)
08 Mar 2013 21:52:53  INFO Chunker -  process(JCas)
08 Mar 2013 21:52:53  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:52:53  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:52:53  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:52:53  INFO MaxentParserWrapper - Started processing: testpatient_plaintext_2.txt
   ....ended with 0 vectors.
08 Mar 2013 21:52:53  INFO MipacqSvmChainCreator - Classifying coreference in document: testpatient_plaintext_2.txt
08 Mar 2013 21:52:53  INFO MipacqSvmChainCreator - Done classifying document: testpatient_plaintext_2.txt
08 Mar 2013 21:52:53  INFO CasConsumer - Started
08 Mar 2013 21:52:53  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:52:53  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:52:53  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:52:54  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:52:54  INFO POSTagger - process(JCas)
08 Mar 2013 21:52:54  INFO Chunker -  process(JCas)
08 Mar 2013 21:52:54  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:52:54  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:52:54  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:52:54  INFO MaxentParserWrapper - Started processing: SampleInputRadiologyNotes.txt
   ....ended with 2 vectors.
08 Mar 2013 21:53:01  INFO MipacqSvmChainCreator - Classifying coreference in document: SampleInputRadiologyNotes.txt
08 Mar 2013 21:53:01  INFO MipacqSvmChainCreator - Done classifying document: SampleInputRadiologyNotes.txt
08 Mar 2013 21:53:01  INFO CasConsumer - Started
08 Mar 2013 21:53:01  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:53:01  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:53:01  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:53:01  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:53:01  INFO POSTagger - process(JCas)
08 Mar 2013 21:53:01  INFO Chunker -  process(JCas)
08 Mar 2013 21:53:01  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:53:01  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:53:01  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:53:01  INFO MaxentParserWrapper - Started processing: testfakenote.txt
   ....ended with 5 vectors.
08 Mar 2013 21:53:02  INFO MipacqSvmChainCreator - Classifying coreference in document: testfakenote.txt
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Done classifying document: testfakenote.txt
08 Mar 2013 21:53:03  INFO CasConsumer - Started
08 Mar 2013 21:53:03  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:53:03  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:53:03  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO POSTagger - process(JCas)
08 Mar 2013 21:53:03  INFO Chunker -  process(JCas)
08 Mar 2013 21:53:03  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO MaxentParserWrapper - Started processing: sample_note_plaintext
   ....ended with 2 vectors.
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Classifying coreference in document: sample_note_plaintext
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Done classifying document: sample_note_plaintext
08 Mar 2013 21:53:03  INFO CasConsumer - Started
08 Mar 2013 21:53:03  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:53:03  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:53:03  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO POSTagger - process(JCas)
08 Mar 2013 21:53:03  INFO Chunker -  process(JCas)
08 Mar 2013 21:53:03  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO MaxentParserWrapper - Started processing: text1.txt
   ....ended with 0 vectors.
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Classifying coreference in document: text1.txt
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Done classifying document: text1.txt
08 Mar 2013 21:53:03  INFO CasConsumer - Started
08 Mar 2013 21:53:03  INFO SentenceDetector - Starting processing.
08 Mar 2013 21:53:03  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Mar 2013 21:53:03  INFO LvgAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO POSTagger - process(JCas)
08 Mar 2013 21:53:03  INFO Chunker -  process(JCas)
08 Mar 2013 21:53:03  INFO CopyAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO OverlapAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO DictionaryLookupAnnotator - process(JCas)
08 Mar 2013 21:53:03  INFO MaxentParserWrapper - Started processing: sample_note
   ....ended with 0 vectors.
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Classifying coreference in document: sample_note
08 Mar 2013 21:53:03  INFO MipacqSvmChainCreator - Done classifying document: sample_note
08 Mar 2013 21:53:03  INFO CasConsumer - Started
08 Mar 2013 21:53:03  INFO RegressionPipelineTest - Completed 12 documents
08 Mar 2013 21:53:03  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 '51289' - 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:149)
	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 [3.888s]
[INFO] Apache cTAKES common type system .................. SUCCESS [9.988s]
[INFO] Apache cTAKES utils ............................... SUCCESS [2.134s]
[INFO] Apache cTAKES core ................................ SUCCESS [6.639s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [2.279s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [1.125s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.485s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [8.941s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [0.880s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [0.871s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [1.828s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [1.087s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [7.038s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [6.068s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [2.566s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [2.226s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [2.609s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [2.558s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [2.290s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [0.954s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [6.788s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [6.788s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [2.559s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [0.641s]
[INFO] Apache cTAKES Regression-test ..................... FAILURE [15:02.519s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 16:28.879s
[INFO] Finished at: Fri Mar 08 22:07:01 UTC 2013
[INFO] Final Memory: 36M/169M
[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$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	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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