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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #221
Date Mon, 28 Apr 2014 16:44:39 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/221/changes>

Changes:

[tmill] Fixed bug in dictionary lookup introduced by Java 7 changes.

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[tmill] Fixed reference to non-official model, and switched lvg to not post lemmas.

[tmill] CTAKES-297: First pass at some default pipelines. Full dictionary pipeline still WIP
but basics are set up.

[tmill] CTAKES-197: Update Dictionary module to java 7 (and java 5 and 6 while I was at it).

[tmill] CTAKES-297: Standardized Lvg static factory method by catching URI exception.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for ChunkAdjuster.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for Chunker.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for POSTagger.

[tmill] CTAKES-297: Added method for getting default descriptor for ContextDependentTokenizerAnnotator.

[tmill] CTAKES-297: Added method for getting descriptor for LvgAnnotator. Added unit test.
Made some parameters optional with sane defaults.

[tmill] CTAKES-297: Added method for getting descriptor for TokenizerAnnotatorPTB

[tmill] CTAKES-16: Fix TokenizerAnnotatorPTB to use UIMAFit select instead of iterator.

[tmill] CTAKES-297: Added methods for getting descriptors for SentenceDetector.

[tmill] CTAKES-297: Added methods for getting descriptors for SimpleSegmentAnnotator.

[tmill] CTAKES-16: Fix to use UIMAFit select instead of iterator.

[dligach] added note name to the output

[chenpei] CTAKES-286 - Remove no longer used pad term spotter and related resources.
Full Thread here: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201402.mbox/%3C924DE05C19409B438EB81DE683A942D91066CE4B%40CHEXMBX1A.CHBOSTON.ORG%3E

[chenpei] CTAKES-294
Wrong PROJECT_ATTR in ctakes-core/resources/launch/UIMA_CVD--core.launch
Thanks  iglewski for identifying the issue.

[dligach] got rid of the loop and replaced it with an iterator

[dligach] now using cumulative probability as a feature

[tmill] CTAKES-295: Update CopyAnnotator to use UimaFit-style configuration.

[tmill] CTAKES-295: Update ChunkAdjuster to use UimaFit-style configuration parameters.

[tmill] CTAKES-197: Used java 7 style generics w/o unnecessary type specifications to remove
warnings.

[tmill] Minor cleanup -- added comment to undocumented empty method.

[tmill] CTAKES-295: Updated to use uima-fit configuration parameters.

[tmill] CTAKES-295: Update pos tagger to use uimafit configuratino parameters, some other
minor java 7 updates.

[tmill] CTAKES-295: Update ContextDependentTokenizerAnnotator to UIMAFit-style methods and
Java >=6 overrides.

[tmill] CTAKES-295: Update LVG to use UIMAFit style configuration parameters and resources
-- changes some arguments to being optional with sane default values.

[dligach] added event-time relations where arg1=event and arg2=time

[clin] fix a typo in CheckSpecialWordRelatinExtractor, which is used for event-time relation
discovery.

[clin] added three more feature extractors for event-time relation discovery.

[dligach] added event-time relations

[dligach] Added a class to display duration information for event arguments of event-event
relations. Did some refactoring for EventTimeDurationStatistics related to this.

[dligach] output durations in days (instead of normalized seconds)

[clin] fix a dependency error. added dependency distance as a feature

[clin] add transitive closure for event-time relation discovery. Closure was added for both
training and testing, and both gold relations and system predictions.

[dligach] only print contexts of up to 80 characters

[tmill] CTAKES-197: Java 7 updates (mainly type/generic stuff, some try-with-resources) to
LVG Annotator.

[dligach] now including relation context too

[tmill] Fixed order of annotators in TokensAndSentencesTAE descriptor.

[dligach] dump duration of event and time arguments of time-event relations  to a file

[tmill] CTAKES-295: Updated TokenizerAnnotatorPTB to use UIMAFit configuration.

[tmill] CTAKES-295: Updated CDA segmenter to use uimafit configurations.

[tmill] CTAKES-197: Updates for java 7 to remove warnings.

[tmill] CTAKES-295: Updates SentenceDetector to use UimaFit-style configuration.

[tmill] CTAKES-70: Adds unit test for sentence detector.

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 U        .
At revision 1590699
Parsing POMs
Discovered a new module org.apache.ctakes:ctakes-ytex-res Apache cTAKES Resources ctakes-ytex-res
Discovered a new module org.apache.ctakes:ctakes-ytex Apache cTAKES YTEX
Discovered a new module org.apache.ctakes:ctakes-ytex-uima Apache cTAKES YTEX UIMA
Discovered a new module org.apache.ctakes:ctakes-ytex-web Apache cTAKES YTEX Web
Modules changed, recalculating dependency graph
maven3-agent.jar already up to date
maven3-interceptor.jar already up to date
maven3-interceptor-commons.jar already up to date
[ctakes-trunk-package] $ /home/hudson/tools/java/latest1.7/bin/java -cp /home/jenkins/jenkins-slave/maven3-agent.jar:/home/hudson/tools/maven/apache-maven-3.0.4/boot/plexus-classworlds-2.4.jar
org.jvnet.hudson.maven3.agent.Maven3Main /home/hudson/tools/maven/apache-maven-3.0.4 /home/jenkins/jenkins-slave/slave.jar
/home/jenkins/jenkins-slave/maven3-interceptor.jar /home/jenkins/jenkins-slave/maven3-interceptor-commons.jar
46666
<===[JENKINS REMOTING CAPACITY]===>channel started
   log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
Executing Maven:  -B -f <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml>
-Dmaven.repo.local=/home/jenkins/jenkins-slave/maven-repositories/1 clean install -DskipTests=true
-pl ctakes-utils,ctakes-core,ctakes-type-system,ctakes-pos-tagger,ctakes-chunker,ctakes-preprocessor,ctakes-dictionary-lookup,ctakes-context-tokenizer,ctakes-lvg,ctakes-ne-contexts,ctakes-constituency-parser,ctakes-coreference,ctakes-drug-ner,ctakes-side-effect,ctakes-smoking-status,ctakes-dependency-parser,ctakes-relation-extractor,ctakes-pad-term-spotter,ctakes-assertion,ctakes-assertion-zoner,ctakes-temporal,ctakes-clinical-pipeline,ctakes-regression-test,ctakes-assertion-res,ctakes-chunker-res,ctakes-constituency-parser-res,ctakes-core-res,ctakes-coreference-res,ctakes-dependency-parser-res,ctakes-dictionary-lookup-res,ctakes-lvg-res,ctakes-pad-term-spotter-res,ctakes-pos-tagger-res,ctakes-relation-extractor-res,ctakes-side-effect-res,ctakes-smoking-status-res,ctakes-temporal-res,ctakes-assertion-zoner-res,ctakes-drug-ner-res,ctakes-ne-contexts-res,ctakes-template-filler,ctakes-examples
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT
[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] 
[WARNING] Some problems were encountered while building the effective model for org.apache.ctakes:ctakes-distribution:pom:3.1.2-SNAPSHOT
[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] 
[WARNING] Some problems were encountered while building the effective model for org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:jaxb2-maven-plugin is missing.
@ line 231, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability
of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed
projects.
[WARNING] 
[ERROR] Could not find the selected project in the reactor: ctakes-pad-term-spotter ->
[Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following
articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MavenExecutionException
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