See <https://builds.apache.org/job/ctakes-trunk-package/96/changes>
Changes: [tmill] ctakes-159: modified package dictionary.lookup to use generics. (fixed a few other minor things causing warnings). [tmill] Cue word files for generating lucene index of cue words. [tmill] Two new features for temporal relation extraction. [tmill] ctakes-159: modified DirectPassThroughImpl to use generics, removed all warnings. [dligach] use configuration parameters instead of hard-coded values [tmill] cTAKES-193: Fix bug with text that openNLP tokenizes differently than cTAKES - directly use openNLP api rather than static parseLine method. ------------------------------------------ [...truncated 3299 lines...] [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[716,27] [unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<? extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>) as a member of the raw type org.cleartk.eval.AnnotationStatistics [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[726,23] [unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<? extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>) as a member of the raw type org.cleartk.eval.AnnotationStatistics [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[736,23] [unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<? extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>) as a member of the raw type org.cleartk.eval.AnnotationStatistics [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java>:[747,23] [unchecked] unchecked call to <ANNOTATION_TYPE,SPAN_TYPE>add(java.util.Collection<? extends ANNOTATION_TYPE>,java.util.Collection<? extends ANNOTATION_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,SPAN_TYPE>,com.google.common.base.Function<ANNOTATION_TYPE,OUTCOME_TYPE>) as a member of the raw type org.cleartk.eval.AnnotationStatistics [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java>:[33,90] [deprecation] org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory in org.cleartk.classifier.opennlp has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java>:[74,21] [unchecked] unchecked cast found : org.apache.uima.jcas.tcas.Annotation required: T [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java>:[59,49] [deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java>:[62,8] [deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java>:[93,35] [unchecked] unchecked conversion found : java.util.List required: java.util.List<java.io.File> [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XmiCollectionReaderCtakes.java>:[81,18] [unchecked] unchecked call to add(E) as a member of the raw type java.util.ArrayList [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java>:[58,49] [deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java>:[61,8] [deprecation] org.cleartk.classifier.feature.extractor.ContextExtractor in org.cleartk.classifier.feature.extractor has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java>:[292,72] [deprecation] org.cleartk.classifier.opennlp.DefaultMaxentDataWriterFactory in org.cleartk.classifier.opennlp has been deprecated [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/src/test/resources> [INFO] Copying 3 resources [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-assertion --- [INFO] [INFO] No sources to compile [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-assertion --- [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-assertion ---[INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-assertion --- [INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target/ctakes-assertion-3.1.0-SNAPSHOT.jar> [INFO] [INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-assertion --- [INFO] [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target/ctakes-assertion-3.1.0-SNAPSHOT.jar> to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-assertion/3.1.0-SNAPSHOT/ctakes-assertion-3.1.0-SNAPSHOT.jar [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-assertion --- [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/pom.xml> to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-assertion/3.1.0-SNAPSHOT/ctakes-assertion-3.1.0-SNAPSHOT.pom [INFO] [INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target> [INFO] ------------------------------------------------------------------------ [INFO] Building Apache cTAKES Resources temporal 3.1.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-temporal-res --- [INFO] [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-temporal-res --- [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-temporal-res --- [INFO] Copying 1 resource [INFO] Copying 3 resources [INFO] [INFO] No sources to compile [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-temporal-res --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-temporal-res --- [INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/src/test/resources> [INFO] Copying 3 resources [INFO] [INFO] No sources to compile [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-temporal-res --- [INFO] [INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-temporal-res --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-temporal-res --- [INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target/ctakes-temporal-res-3.1.0-SNAPSHOT.jar> [INFO] [INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-temporal-res --- [INFO] [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target/ctakes-temporal-res-3.1.0-SNAPSHOT.jar> to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-temporal-res/3.1.0-SNAPSHOT/ctakes-temporal-res-3.1.0-SNAPSHOT.jar [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-temporal-res --- [INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/pom.xml> to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-temporal-res/3.1.0-SNAPSHOT/ctakes-temporal-res-3.1.0-SNAPSHOT.pom [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Apache cTAKES Temporal Information Extraction 3.1.0-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target> [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-temporal --- [INFO] [INFO] --- maven-dependency-plugin:2.6:unpack (unpack) @ ctakes-temporal --- [INFO] Configured Artifact: net.sourceforge.ctakesresources:ctakes-resources-umls2011ab:3.1.0:jar [INFO] Unpacking /home/jenkins/jenkins-slave/maven-repositories/1/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target/unpacked> with includes "" and excludes "" [INFO] [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-temporal --- [debug] execute contextualize [INFO] [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/resources> [INFO] Copying 3 resources [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-temporal --- [INFO] [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-temporal --- [INFO] Compiling 45 source files to <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target/classes> [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22] moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor [INFO] 1 error [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Apache cTAKES ..................................... SUCCESS [6.264s] [INFO] Apache cTAKES common type system .................. SUCCESS [7.809s] [INFO] Apache cTAKES utils ............................... SUCCESS [1.937s] [INFO] Apache cTAKES Resources core ...................... SUCCESS [0.657s] [INFO] Apache cTAKES core ................................ SUCCESS [3.377s] [INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [0.683s] [INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [1.371s] [INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [0.657s] [INFO] Apache cTAKES chunker ............................. SUCCESS [1.018s] [INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.690s] [INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [0.917s] [INFO] Apache cTAKES dictionary lookup ................... SUCCESS [12.502s] [INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [0.949s] [INFO] Apache cTAKES Resources lvg ....................... SUCCESS [0.788s] [INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [1.186s] [INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [0.562s] [INFO] Apache cTAKES named entity contexts ............... SUCCESS [1.023s] [INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [0.793s] [INFO] Apache cTAKES Constituency Parser ................. SUCCESS [1.094s] [INFO] Apache cTAKES Resources coreference ............... SUCCESS [1.378s] [INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [0.617s] [INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [1.727s] [INFO] Apache cTAKES Dependency Parser ................... SUCCESS [1.520s] [INFO] Apache cTAKES Relation Extractor .................. SUCCESS [4.005s] [INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [2.678s] [INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [0.820s] [INFO] Apache cTAKES Drug NER ............................ SUCCESS [2.561s] [INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.845s] [INFO] Apache cTAKES Side Effects ........................ SUCCESS [2.106s] [INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [2.493s] [INFO] Apache cTAKES Smoking Status ...................... SUCCESS [2.037s] [INFO] Apache cTAKES Resources pad-term-spotter-res ...... SUCCESS [1.663s] [INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [2.223s] [INFO] Apache cTAKES Resources assertion ................. SUCCESS [1.055s] [INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [0.804s] [INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.019s] [INFO] Apache cTAKES Assertion ........................... SUCCESS [8.212s] [INFO] Apache cTAKES Resources temporal .................. SUCCESS [0.606s] [INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [6.964s] [INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED [INFO] Apache cTAKES Distribution ........................ SKIPPED [INFO] Apache cTAKES Regression-test ..................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1:33.403s [INFO] Finished at: Tue Apr 30 07:50:32 UTC 2013 [INFO] Final Memory: 42M/141M [INFO] ------------------------------------------------------------------------ [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] Archiving disabled [JENKINS] 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<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22] moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor cause : Compilation failure <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22] moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor 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-temporal: Compilation failure <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22] moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor 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-package/ws/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalFTExtractor.java>:[78,22] moveTimexDownToNP(org.apache.ctakes.utils.tree.SimpleTree) has private access in org.apache.ctakes.temporal.ae.feature.TemporalPETExtractor 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 Sending e-mails to: [email protected] [email protected] [email protected] channel stopped
