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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #1101
Date Wed, 27 Sep 2017 20:25:50 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/1101/display/redirect?page=changes>

Changes:

[seanfinan] DocumentIDAnnotationUtil can now fetch idPrefix, useful for patient id
NumberedSuffixComparator to compare text and number strings logically - "abc1" < "abc10"
Add patient package for multi-document patient handling
AbstractPatientConsumer processes when patients are complete
PatientNoteCollector AE sends patient document cas to a cache
PatientNoteStore caches documents into views in a common patient cas
PatientViewUtil utilities for fetching cas views and view names.  Could be named "CasViewUtil"
and moved
MentionClusterCoreferenceAnnotator added notYetProcess() for Tim to review
PatientMentionClusterCoreferencer extends AbstractPatientConsumer and delegates to MentionClusterCoreferenceAnnotator

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[...truncated 320.51 KB...]
A         ctakes-relation-extractor/src/test
A         ctakes-relation-extractor/src/test/java
A         ctakes-relation-extractor/src/test/java/org
A         ctakes-relation-extractor/src/test/java/org/apache
A         ctakes-relation-extractor/src/test/java/org/apache/ctakes
A         ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor
A         ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae
AU        ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotatorsTest.java
AU        ctakes-relation-extractor/src/test/java/org/apache/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java
A         ctakes-relation-extractor/docs
A         ctakes-relation-extractor/docs/knowtator.txt
A         ctakes-relation-extractor/docs/readme.txt
A         ctakes-relation-extractor/docs/todo.txt
A         ctakes-relation-extractor/pom.xml
A         ctakes-relation-extractor/resources
A         ctakes-relation-extractor/resources/launch
AU        ctakes-relation-extractor/resources/launch/UIMA_CVD--relation-extractor.launch
AU        ctakes-relation-extractor/resources/launch/UIMA_CPE--relation-extractor.launch
A         ctakes-relation-extractor/desc
A         ctakes-relation-extractor/desc/analysis_engine
A         ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml
A         ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml
A         ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml
AU        ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml
AU        ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml
A         ctakes-relation-extractor/desc/analysis_engine/RemoteDictionary.xml
A         ctakes-relation-extractor/metadata
A         ctakes-relation-extractor/metadata/install.xml
A         ctakes-preprocessor
A         ctakes-preprocessor/LICENSE
A         ctakes-preprocessor/src
A         ctakes-preprocessor/src/test
A         ctakes-preprocessor/src/test/data
A         ctakes-preprocessor/src/test/data/output
A         ctakes-preprocessor/src/test/data/output/testpatient_cn_1.xml.included.xml
A         ctakes-preprocessor/src/test/resources
A         ctakes-preprocessor/src/test/resources/testpatient_cn_1.xml
A         ctakes-preprocessor/src/test/resources/NotesIIST_RTF.DTD
A         ctakes-preprocessor/src/test/java
A         ctakes-preprocessor/src/test/java/org
A         ctakes-preprocessor/src/test/java/org/apache
A         ctakes-preprocessor/src/test/java/org/apache/ctakes
A         ctakes-preprocessor/src/test/java/org/apache/ctakes/preprocessor
A         ctakes-preprocessor/src/test/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessorTest.java
A         ctakes-preprocessor/src/main
A         ctakes-preprocessor/src/main/java
A         ctakes-preprocessor/src/main/java/edu
A         ctakes-preprocessor/src/main/java/edu/mayo
A         ctakes-preprocessor/src/main/java/edu/mayo/bmi
A         ctakes-preprocessor/src/main/java/edu/mayo/bmi/uima
A         ctakes-preprocessor/src/main/java/org
A         ctakes-preprocessor/src/main/java/org/apache
A         ctakes-preprocessor/src/main/java/org/apache/ctakes
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Annotation.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/IntegerRange.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DocumentMetaData.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/test
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/test/TestDriver.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DTDloader.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/SegmentMetaData.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Utility.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java
A         ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/PreProcessor.java
A         ctakes-preprocessor/src/main/resources
A         ctakes-preprocessor/src/main/resources/org
A         ctakes-preprocessor/src/main/resources/org/apache
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/cda
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/cda/NotesIIST_RTF.DTD
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer/hyphenated.txt
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer/hyphenated_sample.txt
A         ctakes-preprocessor/src/main/resources/org/apache/ctakes/preprocessor/tokenizer/hyphenated.README.mayo
A         ctakes-preprocessor/pom.xml
A         ctakes-preprocessor/resources
A         ctakes-preprocessor/resources/launch
AU        ctakes-preprocessor/resources/launch/document_preprocessor.launch
AU        ctakes-preprocessor/resources/launch/UIMA_CPE_GUI--document_preprocessor.launch
A         ctakes-preprocessor/README
A         ctakes-preprocessor/desc
A         ctakes-preprocessor/desc/CdaCasInitializer.xml
A         ctakes-preprocessor/desc/CPE_CdaCasInitializer.xml
A         ctakes-preprocessor/desc/AggregateAE.xml
A         ctakes-smoking-status
A         ctakes-smoking-status/desc
A         ctakes-smoking-status/desc/cas_consumer
AU        ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.xml
A         ctakes-smoking-status/desc/analysis_engine
AU        ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
AU        ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml
AU        ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml
AU        ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
AU        ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml
AU        ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml
AU        ctakes-smoking-status/desc/analysis_engine/Sentence.xml
AU        ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml
AU        ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml
AU        ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml
A         ctakes-smoking-status/desc/collection_processing_engine
AU        ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml
AU        ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_cda.xml
A         ctakes-smoking-status/metadata
AU        ctakes-smoking-status/metadata/PEAR.properties
AU        ctakes-smoking-status/metadata/setenv.txt
AU        ctakes-smoking-status/metadata/install.xml
AU        ctakes-smoking-status/LICENSE
A         ctakes-smoking-status/src
A         ctakes-smoking-status/src/main
A         ctakes-smoking-status/src/main/java
A         ctakes-smoking-status/src/main/java/org
A         ctakes-smoking-status/src/main/java/org/apache
A         ctakes-smoking-status/src/main/java/org/apache/ctakes
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/i2b2
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/machine/NegationFSM.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java
A         ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil
AU        ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java
A         ctakes-smoking-status/src/main/resources
A         ctakes-smoking-status/src/main/resources/org
A         ctakes-smoking-status/src/main/resources/org/apache
A         ctakes-smoking-status/src/main/resources/org/apache/ctakes
A         ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus
A         ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types
A         ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
A         ctakes-smoking-status/data
A         ctakes-smoking-status/data/test
A         ctakes-smoking-status/data/test/output
AU        ctakes-smoking-status/data/test/output/record_resolution.txt
AU        ctakes-smoking-status/data/test/doc1_07543210_sample_past_smoker.txt
AU        ctakes-smoking-status/data/test/doc2_07543210_sample_past_smoker.txt
A         ctakes-smoking-status/data/test/cda
A         ctakes-smoking-status/data/test/cda/testpatient_cn_1.xml
AU        ctakes-smoking-status/data/test/doc1_07543210_sample_unknown.txt
AU        ctakes-smoking-status/data/test/doc1_07543210_sample_current.txt
AU        ctakes-smoking-status/data/test/doc2_07543210_sample_current.txt
A         ctakes-smoking-status/launch
AU        ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
AU        ctakes-smoking-status/launch/UIMA CPE GUI (SmokingStatus).launch
AU        ctakes-smoking-status/launch/UIMA CAS Visual Debugger (Smoking Status).launch
A         ctakes-smoking-status/pom.xml
AU        ctakes-smoking-status/README
A         ctakes-assertion-zoner-res
A         ctakes-assertion-zoner-res/src
A         ctakes-assertion-zoner-res/src/test
A         ctakes-assertion-zoner-res/src/main
A         ctakes-assertion-zoner-res/src/main/resources
A         ctakes-assertion-zoner-res/src/main/resources/META-INF
A         ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit
A         ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/types.txt
A         ctakes-assertion-zoner-res/src/main/resources/org
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/mayo_sections.xml
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml.bak2
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.06162011.xml
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.xml
A         ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/section_regex.out.xml
A         ctakes-assertion-zoner-res/pom.xml
A         ctakes-assertion-zoner-res/LICENSE
 U        .
At revision 1809920

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@76e412b9:H27: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-scaleout>
of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does not exist
@ 

	at hudson.FilePath.act(FilePath.java:993)
	at hudson.FilePath.act(FilePath.java:975)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:985)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:690)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:490)
	at hudson.model.Run.execute(Run.java:1735)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:542)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:405)
Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-scaleout>
of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does not exist
@ 

	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1389)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1123)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2739)
	at hudson.remoting.UserRequest.perform(UserRequest.java:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	at hudson.remoting.Request$2.run(Request.java:336)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)
	at ......remote call to H27(Native Method)
	at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1545)
	at hudson.remoting.UserResponse.retrieve(UserRequest.java:253)
	at hudson.remoting.Channel.call(Channel.java:830)
	at hudson.FilePath.act(FilePath.java:986)
	... 8 more
Caused by: hudson.remoting.ProxyException: org.apache.maven.project.ProjectBuildingException:
Some problems were encountered while processing the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-scaleout>
of <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml> does not exist
@ 

	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$PomParser.invoke(MavenModuleSetBuild.java:1326)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1123)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2739)
	at hudson.remoting.UserRequest.perform(UserRequest.java:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	at hudson.remoting.Request$2.run(Request.java:336)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

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