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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #498
Date Wed, 18 Jun 2014 18:01:00 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/498/changes>

Changes:

[chenpei] CTAKES-300 - Integrate improved dictionary lookup (ctakes-dictionary-lookup2)
Renamed to *-fast.  This is only temporary... this will eventually just replace the existing
dictionary lookup (next minor release?).

[chenpei] CTAKES-263 - Removed duplicate/redundant launch scripts.  It's confusing since there
is already a UIMA_CVD/CPE--clinical_documents_pipeline.launch in the same directory.

[chenpei] CTAKES-263 - OpenJDK6: Out of memory error on CVD default example
Made the max heap consistent to 3g across the pipelines launch startup scripts.  
Not sure why we actually need so many different eclipse launch scripts, but that is a separate
issue.

------------------------------------------
Started by an SCM change
Building remotely on ubuntu6 (Ubuntu ubuntu) in workspace <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/>
Cleaning up <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/.>
Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-constituency-parser/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-side-effect/target>
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Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-dictionary-lookup2/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-drug-ner-res/target>
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Deleting <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-assertion/target>
Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2014-06-18T17:58:37.133
+0000'
D         ctakes-dictionary-lookup2-res
D         ctakes-dictionary-lookup2
U         ctakes-coreference/resources/launch/UIMA_CPE--coref-resolver.launch
U         ctakes-coreference/resources/launch/UIMA_CVD--coref-resolver.launch
U         ctakes-constituency-parser/resources/launch/UIMA_CVD--Constituency Parser.launch
U         ctakes-constituency-parser/resources/launch/UIMA_CPE--Constituency Parser.launch
D         ctakes-clinical-pipeline/resources/launch/CPE cTAKES.launch
D         ctakes-clinical-pipeline/resources/launch/CVD cTAKES.launch
U         ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch
U         ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
U         ctakes-drug-ner/resources/launch/UIMA_CVD--Drug NER.launch
U         ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch
U         ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch
U         ctakes-core/resources/launch/CoreTests.launch
U         ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking.launch
U         ctakes-core/resources/launch/SentenceDetector_annotator.launch
U         ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch
U         ctakes-core/resources/launch/UIMA_CVD--core.launch
U         ctakes-core/resources/launch/Test--HyphenTextModifierImpl.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_0.launch
U         ctakes-core/resources/launch/Test--HyphenTextModifierImpl_with_sample_hyphenated_file.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_1.launch
U         ctakes-core/resources/launch/Tokenizer_annotator.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_3.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_2a.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_2b.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_4.launch
U         ctakes-core/resources/launch/Test--SentenceDetector--argument_checking_test_5.launch
A         ctakes-dictionary-lookup-fast-res
AU        ctakes-dictionary-lookup-fast-res/LICENSE
A         ctakes-dictionary-lookup-fast-res/src
A         ctakes-dictionary-lookup-fast-res/src/main
A         ctakes-dictionary-lookup-fast-res/src/main/resources
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/Snomed2011ab_ctakesTui/cTakesSnomed.xml
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionary.bsv
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/CustomBsvDictionaryTui.bsv
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/bsv/RareWord_BSV.xml
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/RareWord_SNOMED_BSV.xml
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multiresource/CustomBsvDictionary.bsv
A         ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable
AU        ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup2/example/multitable/RareWordTermsUMLS.xml
AU        ctakes-dictionary-lookup-fast-res/pom.xml
U         ctakes-utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation (for Apache UIMA
and cTAKES).launch
A         ctakes-dictionary-lookup-fast
AU        ctakes-dictionary-lookup-fast/LICENSE
A         ctakes-dictionary-lookup-fast/doc
AU        ctakes-dictionary-lookup-fast/doc/dantesgate.txt
AU        ctakes-dictionary-lookup-fast/doc/DictionaryLookupHelp.docx
A         ctakes-dictionary-lookup-fast/doc/DictionaryLookupHelp.txt
AU        ctakes-dictionary-lookup-fast/doc/DictionaryLookupStats.docx
A         ctakes-dictionary-lookup-fast/src
A         ctakes-dictionary-lookup-fast/src/main
A         ctakes-dictionary-lookup-fast/src/main/java
A         ctakes-dictionary-lookup-fast/src/main/java/org
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term/RareWordTerm.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term/SpannedRareWordTerm.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/PrecisionTermConsumer.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/WsdTermConsumer.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/TermConsumer.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/AbstractTermConsumer.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/TokenMatchUtil.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/DictionarySpec.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/LookupUtil.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/FastLookupToken.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/JCasTermAnnotator.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/WindowProcessor.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/MemRareWordDictionary.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionary.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryFactory.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/AbstractRareWordDictionary.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java
A         ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/TextSpan.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/DefaultTextSpan.java
AU        ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/MultiTextSpan.java
AU        ctakes-dictionary-lookup-fast/pom.xml
A         ctakes-dictionary-lookup-fast/example
A         ctakes-dictionary-lookup-fast/example/desc
A         ctakes-dictionary-lookup-fast/example/desc/analysis_engine
A         ctakes-dictionary-lookup-fast/example/desc/analysis_engine/ctakes-dictionary-lookup2
AU        ctakes-dictionary-lookup-fast/example/desc/analysis_engine/ctakes-dictionary-lookup2/CustomLookupAnnotatorBSV.xml
AU        ctakes-dictionary-lookup-fast/example/desc/analysis_engine/ctakes-dictionary-lookup2/CustomLookupAnnotatorJDBC.xml
AU        ctakes-dictionary-lookup-fast/README
A         ctakes-dictionary-lookup-fast/desc
A         ctakes-dictionary-lookup-fast/desc/analysis_engine
AU        ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml
AU        ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml
U         ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch
U         ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_output.launch
U         ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch
U         ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch
U         ctakes-assertion/resources/launch/UIMA_CVD--assertion.launch
U         ctakes-assertion/build.xml
U         ctakes-pos-tagger/resources/launch/UIMA_CPE_GUI--POS_tagger.launch
U         ctakes-pos-tagger/resources/launch/UIMA_CVD--POS_tagger.launch
U         ctakes-side-effect/conf/UIMA Run CPE (SideEffect).launch
U         ctakes-distribution/src/main/assembly/bin.xml
U         ctakes-distribution/src/main/bin/runctakesCPE.sh
U         ctakes-distribution/src/main/bin/runctakesCVD.sh
U         pom.xml
U         ctakes-relation-extractor/resources/launch/UIMA_CPE--relation-extractor.launch
U         ctakes-relation-extractor/resources/launch/UIMA_CVD--relation-extractor.launch
U         ctakes-preprocessor/resources/launch/UIMA_CPE_GUI--document_preprocessor.launch
U         ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
U         ctakes-smoking-status/launch/UIMA CPE GUI (SmokingStatus).launch
U         ctakes-lvg/resources/launch/UIMA_CVD--LVG.launch
U         ctakes-chunker/resources/launch/UIMA_CPE_GUI--chunker.launch
At revision 1603552
Parsing POMs
ERROR: Failed to parse POMs
java.io.IOException: remote file operation failed: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/>
at hudson.remoting.Channel@402c750c:ubuntu6
	at hudson.FilePath.act(FilePath.java:910)
	at hudson.FilePath.act(FilePath.java:887)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:953)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:681)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:585)
	at hudson.model.Run.execute(Run.java:1676)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:529)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:231)
Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: junit:junit:jar
-> duplicate declaration of version (?) @ line 154, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
will be unresolvable by dependent projects @ line 197, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar
will be unresolvable by dependent projects @ line 204, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
should not point at files within the project directory, ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 211, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar should
not point at files within the project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 218, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar
-> duplicate declaration of version (?) @ line 99, column 15
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:jaxb2-maven-plugin is missing.
@ line 231, column 12
[ERROR] 'dependencies.dependency.version' for org.apache.ctakes:ctakes-dictionary-lookup2-res:jar
is missing. @ line 32, column 19

	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1357)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1091)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2462)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:328)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
Caused by: hudson.remoting.ProxyException: org.apache.maven.project.ProjectBuildingException:
Some problems were encountered while processing the POMs:
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: junit:junit:jar
-> duplicate declaration of version (?) @ line 154, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
will be unresolvable by dependent projects @ line 197, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar should
not point at files within the project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar
will be unresolvable by dependent projects @ line 204, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar
should not point at files within the project directory, ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 211, column 16
[WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar should
not point at files within the project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @ line 218, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar
-> duplicate declaration of version (?) @ line 99, column 15
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:jaxb2-maven-plugin is missing.
@ line 231, column 12
[ERROR] 'dependencies.dependency.version' for org.apache.ctakes:ctakes-dictionary-lookup2-res:jar
is missing. @ line 32, column 19

	at org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:364)
	at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361)
	at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1294)
	... 10 more

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