Return-Path: X-Original-To: apmail-ctakes-notifications-archive@www.apache.org Delivered-To: apmail-ctakes-notifications-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 3A03C108EC for ; Sat, 20 Jul 2013 00:47:11 +0000 (UTC) Received: (qmail 13123 invoked by uid 500); 20 Jul 2013 00:47:11 -0000 Delivered-To: apmail-ctakes-notifications-archive@ctakes.apache.org Received: (qmail 13101 invoked by uid 500); 20 Jul 2013 00:47:11 -0000 Mailing-List: contact notifications-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list notifications@ctakes.apache.org Received: (qmail 13094 invoked by uid 99); 20 Jul 2013 00:47:11 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 20 Jul 2013 00:47:11 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.8] (HELO aegis.apache.org) (140.211.11.8) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 20 Jul 2013 00:47:07 +0000 Received: from aegis.apache.org (localhost [127.0.0.1]) by aegis.apache.org (Postfix) with ESMTP id DF019C02A3; Sat, 20 Jul 2013 00:46:45 +0000 (UTC) Date: Sat, 20 Jul 2013 00:46:42 +0000 (UTC) From: Apache Jenkins Server To: notifications@ctakes.apache.org, masanz.james@gmail.com, mattcoarr@gmail.com, steven.bethard@gmail.com, chen.lin@childrens.harvard.edu, wu.stephen@mayo.edu, peistation@gmail.com Message-ID: <386743100.849.1374281205900.JavaMail.hudson@aegis> In-Reply-To: <1829170479.545.1374197878763.JavaMail.hudson@aegis> References: <1829170479.545.1374197878763.JavaMail.hudson@aegis> Subject: Build failed in Jenkins: ctakes-trunk-package #142 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit X-Jenkins-Job: ctakes-trunk-package X-Jenkins-Result: FAILURE X-Virus-Checked: Checked by ClamAV on apache.org See 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 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: 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, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar will be unresolvable by dependent projects @ line 213, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers to a non-existing file @ line 192, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers to a non-existing file @ line 199, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar refers to a non-existing file @ line 206, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers to a non-existing file @ line 213, column 16 [ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @ line 36, column 15 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar -> duplicate declaration of version (?) @ line 91, column 17 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar -> duplicate declaration of version (?) @ line 95, column 21 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar -> duplicate declaration of version (?) @ line 99, column 15 at hudson.maven.MavenModuleSetBuild$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, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar will be unresolvable by dependent projects @ line 213, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-i2b2:jar refers to a non-existing file @ line 192, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.medfacts:medfacts-zoner:jar refers to a non-existing file @ line 199, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.core:jcarafe.core:jar refers to a non-existing file @ line 206, column 16 [WARNING] 'dependencies.dependency.systemPath' for org.mitre.jcarafe.ext:jcarafe.ext:jar refers to a non-existing file @ line 213, column 16 [ERROR] 'dependencies.dependency.version' for net.sf.mastif:mastif-zoner:jar is missing. @ line 36, column 15 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.jdom:jdom2:jar -> duplicate declaration of version (?) @ line 91, column 17 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.lexicalscope.jewelcli:jewelcli:jar -> duplicate declaration of version (?) @ line 95, column 21 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.ctakes:ctakes-ne-contexts:jar -> duplicate declaration of version (?) @ line 99, column 15 at org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:363) at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361) at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331) at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1179) ... 11 more