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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk-Java-1.8 #15
Date Tue, 24 Oct 2017 20:52:24 GMT
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/15/display/redirect?page=changes>

Changes:

[seanfinan] Set document count in patient note store

[seanfinan] patient store, etc. use total doc count instead of previous/next

------------------------------------------
[...truncated 780.80 KB...]
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
24 Oct 2017 20:17:37  INFO LvgAnnotator - URL for lvg.properties =file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:17:39  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:17:39  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:17:39  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file
= jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:17:39  INFO LvgCmdApiResourceImpl -   config file absolute path = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:17:39  INFO LvgCmdApiResourceImpl - cwd = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:17:39  INFO LvgCmdApiResourceImpl - cd jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
24 Oct 2017 20:17:39  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:17:39  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
24 Oct 2017 20:17:39  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:17:58  INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser,
using lemmatizer: true
24 Oct 2017 20:18:00  INFO SentenceDetector - Starting processing.
24 Oct 2017 20:18:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:00  INFO LvgAnnotator - process(JCas)
24 Oct 2017 20:18:00  INFO ContextDependentTokenizerAnnotator - process(JCas)
24 Oct 2017 20:18:00  INFO POSTagger - process(JCas)
24 Oct 2017 20:18:00  INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:main
24 Oct 2017 20:18:00  INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:main
24 Oct 2017 20:18:01  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: "DATE"
   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: 26.761 sec
Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest
24 Oct 2017 20:18:01  INFO LvgAnnotator - URL for lvg.properties =file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:02  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:18:02  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:02  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file
= jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:02  INFO LvgCmdApiResourceImpl -   config file absolute path = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:02  INFO LvgCmdApiResourceImpl - cwd = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:02  INFO LvgCmdApiResourceImpl - cd jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
24 Oct 2017 20:18:02  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:02  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
24 Oct 2017 20:18:02  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:18:16  INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser,
using lemmatizer: true
24 Oct 2017 20:18:19  INFO SentenceDetector - Starting processing.
24 Oct 2017 20:18:19  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:19  INFO LvgAnnotator - process(JCas)
24 Oct 2017 20:18:19  INFO ContextDependentTokenizerAnnotator - process(JCas)
24 Oct 2017 20:18:19  INFO POSTagger - process(JCas)
24 Oct 2017 20:18:19  INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:main
24 Oct 2017 20:18:19  INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:main
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.495 sec
Running org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest
24 Oct 2017 20:18:19  INFO LvgAnnotator - URL for lvg.properties =file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:21  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
24 Oct 2017 20:18:21  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
24 Oct 2017 20:18:21  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file
= jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:21  INFO LvgCmdApiResourceImpl -   config file absolute path = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/jar>:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
24 Oct 2017 20:18:21  INFO LvgCmdApiResourceImpl - cwd = <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:21  INFO LvgCmdApiResourceImpl - cd jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
** Configuration Error: jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
(No such file or directory)
** Error: problem of opening/reading config file: 'jar:file:/home/jenkins/jenkins-slave/maven-repositories/0/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties'.
Use -x option to specify the config file path.
24 Oct 2017 20:18:21  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal>
24 Oct 2017 20:18:21  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
24 Oct 2017 20:18:21  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
24 Oct 2017 20:24:01  INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser,
using lemmatizer: true

Results :

Tests run: 2, Failures: 0, Errors: 0, Skipped: 0

ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: ubuntu-us1 is offline; cannot locate JDK 1.8 (latest)
ERROR: ubuntu-us1 is offline; cannot locate Maven 3.5.0
ERROR: Failed to parse POMs
java.io.IOException: Backing channel 'ubuntu-us1' is disconnected.
	at hudson.remoting.RemoteInvocationHandler.channelOrFail(RemoteInvocationHandler.java:192)
	at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:257)
	at com.sun.proxy.$Proxy129.isAlive(Unknown Source)
	at hudson.Launcher$RemoteLauncher$ProcImpl.isAlive(Launcher.java:1138)
	at hudson.maven.ProcessCache$MavenProcess.call(ProcessCache.java:166)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:879)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:496)
	at hudson.model.Run.execute(Run.java:1737)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:419)
Caused by: hudson.remoting.Channel$OrderlyShutdown
	at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1138)
	at hudson.remoting.Channel$1.handle(Channel.java:535)
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:83)
Caused by: Command close created at
	at hudson.remoting.Command.<init>(Command.java:60)
	at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1132)
	at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1130)
	at hudson.remoting.Channel.close(Channel.java:1290)
	at hudson.remoting.Channel.close(Channel.java:1272)
	at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1137)
	... 2 more
FATAL: channel is already closed
Command close created at
	at hudson.remoting.Command.<init>(Command.java:60)
	at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1132)
	at hudson.remoting.Channel$CloseCommand.<init>(Channel.java:1130)
	at hudson.remoting.Channel.close(Channel.java:1290)
	at hudson.remoting.Channel.close(Channel.java:1272)
	at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1137)
Caused: hudson.remoting.Channel$OrderlyShutdown
	at hudson.remoting.Channel$CloseCommand.execute(Channel.java:1138)
	at hudson.remoting.Channel$1.handle(Channel.java:535)
	at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:83)
Caused: hudson.remoting.ChannelClosedException: channel is already closed
	at hudson.remoting.Channel.send(Channel.java:613)
	at hudson.remoting.Request.call(Request.java:130)
	at hudson.remoting.Channel.call(Channel.java:838)
	at hudson.Launcher$RemoteLauncher.kill(Launcher.java:1079)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:502)
	at hudson.model.Run.execute(Run.java:1737)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:419)

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