See <https://builds.apache.org/job/ctakes-trunk-package/142/changes>
Changes: [swu] some extra stuff for feature selection grid search and evaluations in general [james-masanz] CTAKES-183 Update reference to resource that was moved to ctakes-core-res [james-masanz] CTAKES-218 Have FileLocator also try the second method to resolve the file path if the first returns null (in addition to if the first throws an exception) [clin] Make a Yate's parameter for Chi2 feature selection. So people may turn on or off the Yate's correction for Chi2 value calculation. If Yate's correction is on (boolean Yates = true), small difference between observed value and expected value (<0.5) will be ignored. More features will be trimmed. Else, small difference will be kept. Users have the freedom to keep all features. ------------------------------------------ Started by an SCM change Building remotely on ubuntu2 in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/> Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2013-07-20T00:45:54.041 +0000' U ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java U ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java U ctakes-assertion-zoner/pom.xml D ctakes-assertion/lib 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/MutualInformationFeatureSelection.java 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 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/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/medfacts/cleartk/GenericCleartkAnalysisEngine.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/eval/AssertionEvaluation.java AU ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/TestFeatureSelection.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java 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/util/NegationDepRegex.java U ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java U ctakes-distribution/src/main/assembly/bin.xml U KEYS U ctakes-clinical-pipeline/pom.xml U ctakes-temporal/pom.xml U ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java 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/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 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 A ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java U ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RouteFSM.java At revision 1505071 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@32401cae:ubuntu2 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
