See <https://builds.apache.org/job/ctakes-trunk-compiletest/872/changes>
Changes: [seanfinan] Simple cli to run clinical pipeline on a directory of files, writing xmis if desired [seanfinan] EntityCollector better Entity for Collection [seanfinan] Adding Clinical-Pipeline-res Adding getReader, getAeNames to PipelineBuilder named simple pipeline configuration files ".piper" Adding piper file runner for easy cli refactoring ------------------------------------------ [...truncated 3568 lines...] AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XMLReader.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XmiCollectionReaderCtakes.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/RelationInfo.java A 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ctakes-assertion/pom.xml A ctakes-assertion/resources A ctakes-assertion/resources/launch AU ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_test.launch A ctakes-assertion/resources/launch/ctakes_assertion_evaluation_on_output.launch AU ctakes-assertion/resources/launch/ctakes_assertion_crossvalidation.launch AU ctakes-assertion/resources/launch/ctakes__assertion_eval.launch AU ctakes-assertion/resources/launch/ctakes_assertion_read_gold_and_preprocess.launch AU ctakes-assertion/resources/launch/UIMA_CVD--assertion.launch AU ctakes-assertion/resources/launch/ctakes__assertion_eval_preprocess.launch A ctakes-pos-tagger A ctakes-pos-tagger/scripts A ctakes-pos-tagger/scripts/java A ctakes-pos-tagger/scripts/java/data A ctakes-pos-tagger/scripts/java/data/pos A ctakes-pos-tagger/scripts/java/data/pos/training A ctakes-pos-tagger/scripts/java/data/pos/training/GeniaPosTrainingDataExtractor.java A 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At revision 1764824 ERROR: Processing failed due to a bug in the code. 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hudson.maven.MavenModule@4fb7f167[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-lvg-res][relativePath:ctakes-lvg-res], hudson.maven.MavenModule@42ec9dbb[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts][relativePath:ctakes-ne-contexts], hudson.maven.MavenModule@94cbc16[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ne-contexts-res][relativePath:ctakes-ne-contexts-res], hudson.maven.MavenModule@7a0fd2ed[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger][relativePath:ctakes-pos-tagger], hudson.maven.MavenModule@3f9e598f[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-pos-tagger-res][relativePath:ctakes-pos-tagger-res], hudson.maven.MavenModule@4b68c1be[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-preprocessor][relativePath:ctakes-preprocessor], hudson.maven.MavenModule@4dc1fdfe[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-regression-test][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-regression-test][relativePath:ctakes-regression-test], hudson.maven.MavenModule@599cd36c[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor][relativePath:ctakes-relation-extractor], hudson.maven.MavenModule@9e3a3e7[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-relation-extractor-res][relativePath:ctakes-relation-extractor-res], hudson.maven.MavenModule@2f5f7024[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect][relativePath:ctakes-side-effect], hudson.maven.MavenModule@65ebf70e[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-side-effect-res][relativePath:ctakes-side-effect-res], hudson.maven.MavenModule@1642a026[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status][relativePath:ctakes-smoking-status], hudson.maven.MavenModule@3c763bcd[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-smoking-status-res][relativePath:ctakes-smoking-status-res], hudson.maven.MavenModule@53051bbf[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-template-filler][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-template-filler][relativePath:ctakes-template-filler], hudson.maven.MavenModule@3837c4bf[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal][relativePath:ctakes-temporal], hudson.maven.MavenModule@17215c77[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-temporal-res][relativePath:ctakes-temporal-res], hudson.maven.MavenModule@2e2966ba[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-type-system][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-type-system][relativePath:ctakes-type-system], hudson.maven.MavenModule@1c6547ca[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-utils][relativePath:ctakes-utils], hudson.maven.MavenModule@51238cae[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex][relativePath:ctakes-ytex], hudson.maven.MavenModule@4dc70c80[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-res][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-res][relativePath:ctakes-ytex-res], hudson.maven.MavenModule@6ad1f6d2[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-uima][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-uima][relativePath:ctakes-ytex-uima], hudson.maven.MavenModule@7bf11325[ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-web][ctakes-trunk-compiletest/org.apache.ctakes:ctakes-ytex-web][relativePath:ctakes-ytex-web]] project.getRootModule()=hudson.maven.MavenModule@31ac69ac[ctakes-trunk-compiletest/org.apache.ctakes:ctakes][ctakes-trunk-compiletest/org.apache.ctakes:ctakes][relativePath:] FATAL: /home/jenkins/tools/maven/apache-maven-3.0.5 doesn't have a 'lib' subdirectory - thus cannot be a valid maven installation! java.lang.IllegalArgumentException: /home/jenkins/tools/maven/apache-maven-3.0.5 doesn't have a 'lib' subdirectory - thus cannot be a valid maven installation! at hudson.maven.MavenEmbedderUtils.buildClassRealm(MavenEmbedderUtils.java:83) at hudson.maven.MavenEmbedderUtils.getMavenVersion(MavenEmbedderUtils.java:188) at hudson.maven.MavenVersionCallable.call(MavenVersionCallable.java:70) at hudson.maven.MavenVersionCallable.call(MavenVersionCallable.java:42) at hudson.remoting.UserRequest.perform(UserRequest.java:153) at hudson.remoting.UserRequest.perform(UserRequest.java:50) at hudson.remoting.Request$2.run(Request.java:332) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) at ......remote call to jenkins-test-81c(Native Method) at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416) at hudson.remoting.UserResponse.retrieve(UserRequest.java:253) at hudson.remoting.Channel.call(Channel.java:781) at hudson.FilePath.act(FilePath.java:1102) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:629) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534) at hudson.model.Run.execute(Run.java:1741) at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:531) at hudson.model.ResourceController.execute(ResourceController.java:98) at hudson.model.Executor.run(Executor.java:410)
