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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #96
Date Tue, 30 Apr 2013 07:58:36 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/96/changes>

Changes:

[tmill] ctakes-159: modified package dictionary.lookup to use generics. (fixed a few other
minor things causing warnings).

[tmill] Cue word files for generating lucene index of cue words.

[tmill] Two new features for temporal relation extraction.

[tmill] ctakes-159: modified DirectPassThroughImpl to use generics, removed all warnings.

[dligach] use configuration parameters instead of hard-coded values

[tmill] cTAKES-193: Fix bug with text that openNLP tokenizes differently than cTAKES - directly
use openNLP api rather than static parseLine method.

------------------------------------------
[...truncated 3299 lines...]
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[716,27]
[unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<?
extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>)
as a member of the raw type org.cleartk.eval.AnnotationStatistics
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[726,23]
[unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<?
extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>)
as a member of the raw type org.cleartk.eval.AnnotationStatistics
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[736,23]
[unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<?
extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>)
as a member of the raw type org.cleartk.eval.AnnotationStatistics
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[747,23]
[unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<?
extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>)
as a member of the raw type org.cleartk.eval.AnnotationStatistics
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java>:[33,90]
[deprecation] org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory in org.cleartk.classifier.opennlp
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java>:[74,21]
[unchecked] unchecked cast
found   : org.apache.uima.jcas.tcas.Annotation
required: T
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java>:[59,49]
[deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java>:[62,8]
[deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java>:[93,35]
[unchecked] unchecked conversion
found   : java.util.List
required: java.util.List<java.io.File>
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XmiCollectionReaderCtakes.java>:[81,18]
[unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java>:[58,49]
[deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java>:[61,8]
[deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java>:[292,72]
[deprecation] org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory in org.cleartk.classifier.opennlp
has been deprecated
[debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/test/resources>

[INFO] Copying 3 resources
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-assertion
---
[INFO] [INFO] No sources to compile

[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-assertion
---
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-assertion ---[INFO] Tests
are skipped.

[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-assertion ---
[INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target/ctakes-assertion-3.1.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-assertion
---
[INFO] [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target/ctakes-assertion-3.1.0-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-assertion/3.1.0-SNAPSHOT/ctakes-assertion-3.1.0-SNAPSHOT.jar

[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-assertion ---
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-assertion/3.1.0-SNAPSHOT/ctakes-assertion-3.1.0-SNAPSHOT.pom
[INFO]                                                                         
[INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target>
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Resources temporal 3.1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-temporal-res ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-temporal-res ---
[debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.

[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-temporal-res
---
[INFO] Copying 1 resource
[INFO] Copying 3 resources
[INFO] [INFO] No sources to compile

[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-temporal-res ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-temporal-res
---
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/src/test/resources>
[INFO] Copying 3 resources
[INFO] [INFO] No sources to compile

[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-temporal-res
---
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-temporal-res ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-temporal-res ---
[INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target/ctakes-temporal-res-3.1.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-temporal-res
---
[INFO] [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target/ctakes-temporal-res-3.1.0-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-temporal-res/3.1.0-SNAPSHOT/ctakes-temporal-res-3.1.0-SNAPSHOT.jar

[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-temporal-res ---
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-temporal-res/3.1.0-SNAPSHOT/ctakes-temporal-res-3.1.0-SNAPSHOT.pom
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Temporal Information Extraction 3.1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target>
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-temporal ---
[INFO] 
[INFO] --- maven-dependency-plugin:2.6:unpack (unpack) @ ctakes-temporal ---
[INFO] Configured Artifact: net.sourceforge.ctakesresources:ctakes-resources-umls2011ab:3.1.0:jar
[INFO] Unpacking /home/jenkins/jenkins-slave/maven-repositories/1/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar
to <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target/unpacked>
with includes "" and excludes ""
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-temporal ---
[debug] execute contextualize
[INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/resources>
[INFO] Copying 3 resources

[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-temporal ---
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-temporal ---
[INFO] Compiling 45 source files to <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target/classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22]
moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [6.264s]
[INFO] Apache cTAKES common type system .................. SUCCESS [7.809s]
[INFO] Apache cTAKES utils ............................... SUCCESS [1.937s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [0.657s]
[INFO] Apache cTAKES core ................................ SUCCESS [3.377s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [0.683s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [1.371s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [0.657s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [1.018s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.690s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [0.917s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [12.502s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [0.949s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [0.788s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [1.186s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [0.562s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [1.023s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [0.793s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [1.094s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [1.378s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [0.617s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [1.727s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [1.520s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [4.005s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [2.678s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [0.820s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [2.561s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.845s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [2.106s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [2.493s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [2.037s]
[INFO] Apache cTAKES Resources pad-term-spotter-res ...... SUCCESS [1.663s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [2.223s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [1.055s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [0.804s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.019s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [8.212s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [0.606s]
[INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [6.964s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
[INFO] Apache cTAKES Distribution ........................ SKIPPED
[INFO] Apache cTAKES Regression-test ..................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:33.403s
[INFO] Finished at: Tue Apr 30 07:50:32 UTC 2013
[INFO] Final Memory: 42M/141M
[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-compiler-plugin:2.4:compile
(default-compile) on project ctakes-temporal: Compilation failure
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22]
moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor

cause : Compilation failure
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22]
moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor

Stack trace : 
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile
(default-compile) on project ctakes-temporal: Compilation failure
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22]
moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor

	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
	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.CompilationFailureException: Compilation failure
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22]
moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor

	at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:678)
	at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:128)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
	... 27 more
Sending e-mails to: ctakes-notifications@incubator.apache.org dmitriy.dligach@childrens.harvard.edu
timothy.miller@childrens.harvard.edu
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