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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #99
Date Mon, 07 Jan 2013 23:53:44 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/99/changes>

Changes:

[tmill] ctakes-111: Adds tree-based features for use in tree-kernel svms.

[tmill] ctakes-117: Adds features for doing mention similarity using statistics from wiki
articles.
Additional features multiply other features together in meaningful ways:
(shared cui X entity type) e.g., two mentions of "liver" is probably the same because
a person only has one liver.  two mentions of "pain" are less likely to be the same.
This feature captures that intuition by having type-specific synonym features.

------------------------------------------
[...truncated 2322 lines...]
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-assertion
---
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)
mojoStarted org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[INFO] [INFO] Surefire report directory: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-assertion/target/surefire-reports>

[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-assertion ---

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

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

mojoSucceeded org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[JENKINS] Recording test results
projectSucceeded org.apache.ctakes:ctakes-assertion:3.1.0-incubating-SNAPSHOT
projectStarted org.apache.ctakes:ctakes-clinical-pipeline:3.1.0-incubating-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES ctakes-clinical-pipeline 3.1.0-incubating-SNAPSHOT
[INFO] ------------------------------------------------------------------------
mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)[INFO] Deleting
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/target>

[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-clinical-pipeline ---
mojoSucceeded org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)
mojoStarted org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)[debug]
execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/resources>
[INFO] Copying 3 resources

[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-clinical-pipeline
---
[INFO] Compiling 1 source file to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/target/classes>
[WARNING] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java>:[167,17]
[unchecked] unchecked call to add(E) as a member of the raw type java.util.Set
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
mojoStarted org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
[debug] execute contextualize
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)[INFO] Using
'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/main/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources

[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
[INFO] [INFO] Nothing to compile - all classes are up to date

[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
[debug] execute contextualize
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)[INFO]
Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/src/test/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources

[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-testResources)
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)[INFO]
No sources to compile

[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-clinical-pipeline
---
mojoSucceeded org.apache.maven.plugins:maven-compiler-plugin:2.4(default-testCompile)
mojoStarted org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[INFO] [INFO] Surefire report directory: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/target/surefire-reports>

[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-clinical-pipeline ---

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

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

mojoSucceeded org.apache.maven.plugins:maven-surefire-plugin:2.12(default-test)
[JENKINS] Recording test results
projectSucceeded org.apache.ctakes:ctakes-clinical-pipeline:3.1.0-incubating-SNAPSHOT
projectStarted org.apache.ctakes:ctakes-relation-extractor:3.1.0-incubating-SNAPSHOT
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Relation Extractor 3.1.0-incubating-SNAPSHOT
[INFO] ------------------------------------------------------------------------
mojoStarted org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)[INFO] Deleting
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/target>

[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-relation-extractor ---
mojoSucceeded org.apache.maven.plugins:maven-clean-plugin:2.4.1(default-clean)
mojoStarted org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-relation-extractor
---
mojoSucceeded org.apache.maven.plugins:maven-remote-resources-plugin:1.3(default)
[debug] execute contextualize
mojoStarted org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)[INFO] Using
'UTF-8' encoding to copy filtered resources.

[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-relation-extractor
---
[INFO] Copying 22 resources
[INFO] Copying 3 resources
mojoSucceeded org.apache.maven.plugins:maven-resources-plugin:2.5(default-resources)
mojoStarted org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-relation-extractor
---
[INFO] Compiling 45 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/target/classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java>:[26,40]
cannot find symbol
symbol  : method getCommonAncestor(org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TreebankNode)
location: class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
[INFO] 1 error
[INFO] -------------------------------------------------------------
mojoFailed org.apache.maven.plugins:maven-compiler-plugin:2.4(default-compile)
projectFailed org.apache.ctakes:ctakes-relation-extractor:3.1.0-incubating-SNAPSHOT
sessionEnded
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [4.507s]
[INFO] Apache cTAKES common type system .................. SUCCESS [7.922s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.306s]
[INFO] Apache cTAKES core ................................ SUCCESS [8.977s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [4.161s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [2.565s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [2.445s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [9.384s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [1.460s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [1.688s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [2.932s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [3.224s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [8.396s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [2.609s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [6.552s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [3.940s]
[INFO] Apache cTAKES Relation Extractor .................. FAILURE [3.152s]
[INFO] Apache cTAKES CoReference Resolver ................ SKIPPED
[INFO] Apache cTAKES Drug NER ............................ SKIPPED
[INFO] Apache cTAKES Side Effects ........................ SKIPPED
[INFO] Apache cTAKES Smoking Status ...................... SKIPPED
[INFO] Apache cTAKES Pad Term Spotter .................... SKIPPED
[INFO] Apache cTAKES Temporal Information Extraction ..... SKIPPED
[INFO] Apache cTAKES Distribution ........................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:19.094s
[INFO] Finished at: Mon Jan 07 23:52:24 UTC 2013
[INFO] Final Memory: 31M/135M
[INFO] ------------------------------------------------------------------------
Projects to build: [MavenProject: org.apache.ctakes:ctakes:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-type-system:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-type-system/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-utils:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-core:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-core/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-pos-tagger:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-pos-tagger/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-chunker:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-chunker/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-preprocessor:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-preprocessor/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-dictionary-lookup:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-dictionary-lookup/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-context-tokenizer:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-context-tokenizer/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-lvg:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-lvg/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-ne-contexts:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-ne-contexts/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-constituency-parser:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-constituency-parser/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-dependency-parser:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-dependency-parser/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-assertion-zoner:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-assertion-zoner/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-assertion:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-assertion/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-clinical-pipeline:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-clinical-pipeline/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-relation-extractor:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-coreference:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-coreference/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-drug-ner:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-drug-ner/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-side-effect:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-side-effect/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-smoking-status:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-smoking-status/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-pad-term-spotter:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-pad-term-spotter/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-temporal:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/pom.xml,>
MavenProject: org.apache.ctakes:ctakes-distribution:3.1.0-incubating-SNAPSHOT @ <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-distribution/pom.xml]>
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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-relation-extractor: Compilation failure
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java>:[26,40]
cannot find symbol
symbol  : method getCommonAncestor(org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TreebankNode)
location: class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

cause : Compilation failure
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java>:[26,40]
cannot find symbol
symbol  : method getCommonAncestor(org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TreebankNode)
location: class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

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-relation-extractor: Compilation failure
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java>:[26,40]
cannot find symbol
symbol  : method getCommonAncestor(org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TreebankNode)
location: class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

	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-compiletest/ws/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java>:[26,40]
cannot find symbol
symbol  : method getCommonAncestor(org.apache.ctakes.typesystem.type.syntax.TreebankNode,org.apache.ctakes.typesystem.type.syntax.TreebankNode)
location: class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

	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
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