See <https://builds.apache.org/job/ctakes-trunk-package/141/changes>
Changes: [mattcoarr] temporarily reverting library changes so I don't break the build [mattcoarr] removed jcarafe-ext as it's not needed and it was causing depdency problems CTAKES-76 and CTAKES-108 [mattcoarr] removed system dependencies (for the assertion module) from the two profiles for running CPE and CVD as per Steve Bethard's comments on CTAKES-76 [chenpei] CTAKES-76 using maven central now- deleting the physical jars from /lib [chenpei] CTAKES-76 using maven central now- no need to copy them from lib for packing - ctakes-assertion is upated to point four dependencies at their location on maven central: - jcarafe-core - jcarafe-ext - mastif-i2b2 (previously named med-facts-i2b2) - mastif-zoner (previously named med-facts-zoner) [mattcoarr] As per CTAKES-76, ctakes-assertion is upated to point four dependencies at their location on maven central: - jcarafe-core - jcarafe-ext - mastif-i2b2 (previously named med-facts-i2b2) - mastif-zoner (previously named med-facts-zoner) [clin] Added Feature Selection for TimeAnnotator. The Feature Selection can be turned off by setting --featureSelectionThreshold 0. Other positive value of --featureSelectionThreshold will enable the feature selection process. [stevenbethard] CTAKES-217: Fixes bug where printing of deltas was repeating some of the inserted/deleted lines [stevenbethard] CTAKES-217: Revises CompareFeatureStructures to use java-diff-utils. The search for FeatureStructure equality is the same, but now nested uses of DiffUtils produce what is hopefully better output. In particular, there should now be more useful output for the case where annotations have been inserted or deleted (not just changed). ------------------------------------------ Started by an SCM change Building remotely on ubuntu4 in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/> Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2013-07-19T01:36:57.871 +0000' U ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RouteFSM.java A ctakes-temporal/src/main/resources/org/apache/ctakes/temporal/timenorm.en.grammar A ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java A ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java A ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java U ctakes-temporal/pom.xml U KEYS U ctakes-dependency-parser/.settings/org.eclipse.core.resources.prefs U ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyRegex.java U ctakes-distribution/src/main/assembly/bin.xml AU ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java U ctakes-clinical-pipeline/pom.xml U ctakes-assertion-zoner/pom.xml D ctakes-assertion/lib AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TrainAttributeModels.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationManualDepContextAnalyzer.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java A ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java At revision 1504744 Parsing POMs ERROR: Failed to parse POMs hudson.util.IOException2: remote file operation failed: <https://builds.apache.org/job/ctakes-trunk-package/ws/> at hudson.remoting.Channel@5f258d19:ubuntu4 at hudson.FilePath.act(FilePath.java:861) at hudson.FilePath.act(FilePath.java:838) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:862) at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:620) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:592) at hudson.model.Run.execute(Run.java:1568) at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:477) at hudson.model.ResourceController.execute(ResourceController.java:88) at hudson.model.Executor.run(Executor.java:236) Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [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 192, 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 199, 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 206, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar should not point at files within the project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar will be unresolvable by dependent projects @ line 213, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar> @ line 192, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-zoner-1.1.jar> @ line 199, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar> @ line 206, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar> @ line 213, column 16 [ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @ line 36, column 15 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar -> duplicate declaration of version (?) @ line 91, column 17 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar -> duplicate declaration of version (?) @ line 95, column 21 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar -> duplicate declaration of version (?) @ line 99, column 15 at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1229) at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:997) at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2348) 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:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:679) Caused by: hudson.remoting.ProxyException: org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing the POMs: [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 192, 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 199, 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 206, 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 213, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar> @ line 192, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/med-facts-zoner-1.1.jar> @ line 199, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar> @ line 206, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers to a non-existing file <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar> @ line 213, column 16 [ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @ line 36, column 15 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar -> duplicate declaration of version (?) @ line 91, column 17 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar -> duplicate declaration of version (?) @ line 95, column 21 [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 at org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:363) at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361) at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331) at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1179) ... 11 more
