See
<https://builds.apache.org/job/ctakes-trunk-Java-1.9/6/display/redirect?page=changes>
Changes:
[seanfinan] ConstituencyParser add dot logging since initialization can take
several seconds
TreeUtils added getTerminals(..) that accepts BaseTokens
MaxEntParserWrapper use uimafit index map instead of double select for speed
MarkableSalienceAnnotator added start, finish logging
MentionCluster.. added start, finish logging; still waiting on
notYetProcess(jCas)
------------------------------------------
[...truncated 990.56 KB...]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ...................................... SUCCESS [ 6.455 s]
[INFO] ctakes-gui-res ..................................... SUCCESS [ 4.619 s]
[INFO] Apache cTAKES Resources core ....................... SUCCESS [ 2.799 s]
[INFO] Apache cTAKES common type system ................... SUCCESS [ 10.926 s]
[INFO] Apache cTAKES utils ................................ SUCCESS [ 5.222 s]
[INFO] Apache cTAKES core ................................. SUCCESS [ 27.574 s]
[INFO] ctakes-gui ......................................... SUCCESS [ 5.304 s]
[INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [ 3.213 s]
[INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [ 6.301 s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [ 3.270 s]
[INFO] Apache cTAKES chunker .............................. SUCCESS [ 4.206 s]
[INFO] Apache cTAKES document preprocessor ................ SUCCESS [ 4.031 s]
[INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 11.593 s]
[INFO] Apache cTAKES dictionary lookup .................... SUCCESS [ 4.669 s]
[INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [ 5.262 s]
[INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 20.410 s]
[INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [ 5.219 s]
[INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [ 2.461 s]
[INFO] Apache cTAKES named entity contexts ................ SUCCESS [ 5.216 s]
[INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [ 4.973 s]
[INFO] Apache cTAKES Constituency Parser .................. SUCCESS [ 3.901 s]
[INFO] Apache cTAKES Resources coreference ................ SUCCESS [ 6.744 s]
[INFO] Apache cTAKES Resources temporal ................... SUCCESS [ 3.650 s]
[INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [ 2.854 s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [ 3.590 s]
[INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [ 3.636 s]
[INFO] Apache cTAKES Resources assertion .................. SUCCESS [ 4.118 s]
[INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 20.031 s]
[INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 40.678 s]
[INFO] Apache cTAKES Assertion ............................ SUCCESS [ 7.168 s]
[INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [ 3.123 s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [ 7.474 s]
[INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 12.043 s]
[INFO] Apache cTAKES Temporal Information Extraction ...... SUCCESS [01:47 min]
[INFO] Apache cTAKES CoReference Resolver ................. SUCCESS [ 11.648 s]
[INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [ 2.758 s]
[INFO] Apache cTAKES Drug NER ............................. SUCCESS [ 7.973 s]
[INFO] Apache cTAKES Resources side-effect ................ SUCCESS [ 2.763 s]
[INFO] Apache cTAKES Side Effects ......................... SUCCESS [ 7.063 s]
[INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [ 3.046 s]
[INFO] Apache cTAKES Smoking Status ....................... SUCCESS [ 7.386 s]
[INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [ 2.920 s]
[INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [ 3.410 s]
[INFO] ctakes-examples-res ................................ SUCCESS [ 3.012 s]
[INFO] ctakes-examples .................................... SUCCESS [ 10.369 s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [ 2.614 s]
[INFO] Apache cTAKES YTEX ................................. FAILURE [ 2.462 s]
[INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED
[INFO] Apache cTAKES YTEX Web ............................. SKIPPED
[INFO] Apache cTAKES Distribution ......................... SKIPPED
[INFO] Apache cTAKES Regression-test ...................... SKIPPED
[INFO] Apache cTAKES template filler ...................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 09:00 min
[INFO] Finished at: 2017-10-02T21:19:02Z
[INFO] Final Memory: 73M/256M
[INFO] ------------------------------------------------------------------------
java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at jenkins.maven3.agent.Maven35Main.launch(Maven35Main.java:176)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:139)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:70)
at hudson.remoting.UserRequest.perform(UserRequest.java:181)
at hudson.remoting.UserRequest.perform(UserRequest.java:52)
at hudson.remoting.Request$2.run(Request.java:336)
at
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
at
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)
at java.base/java.lang.Thread.run(Thread.java:844)
Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.<init>(BGMBuilder.java:147)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.build(BGMBuilder.java:117)
at com.sun.tools.xjc.ModelLoader.annotateXMLSchema(ModelLoader.java:425)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:174)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:119)
at com.sun.tools.xjc.Driver.run(Driver.java:333)
at
org.codehaus.mojo.jaxb2.AbstractXjcMojo.execute(AbstractXjcMojo.java:316)
at
org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:154)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:146)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
at
org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at
org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:309)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:194)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:107)
at
org.jvnet.hudson.maven3.launcher.Maven35Launcher.main(Maven35Launcher.java:130)
... 21 more
Caused by: java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 40 more
Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BindingComponent.getClassSelector(BindingComponent.java:65)
at
com.sun.tools.xjc.reader.xmlschema.ColorBinder.<init>(ColorBinder.java:62)
at
com.sun.tools.xjc.reader.xmlschema.BindGreen.<init>(BindGreen.java:63)
... 45 more
Caused by: java.lang.reflect.InvocationTargetException
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at
java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at
java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 48 more
Caused by: java.lang.NoClassDefFoundError:
javax/activation/MimeTypeParseException
at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
at
java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3110)
at java.base/java.lang.Class.getConstructor0(Class.java:3315)
at java.base/java.lang.Class.getDeclaredConstructor(Class.java:2510)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:100)
at
com.sun.tools.xjc.reader.xmlschema.DefaultClassBinder.<init>(DefaultClassBinder.java:98)
at
com.sun.tools.xjc.reader.xmlschema.ClassSelector.<init>(ClassSelector.java:214)
... 53 more
Caused by: java.lang.ClassNotFoundException:
javax.activation.MimeTypeParseException
at
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 60 more
ERROR: Failed to parse POMs
java.io.IOException: java.lang.reflect.InvocationTargetException
at hudson.maven.Maven3Builder.call(Maven3Builder.java:179)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:70)
at hudson.remoting.UserRequest.perform(UserRequest.java:181)
at hudson.remoting.UserRequest.perform(UserRequest.java:52)
at hudson.remoting.Request$2.run(Request.java:336)
at
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
at java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)
at java.lang.Thread.run(Thread.java:844)
at ......remote call to Channel to Maven
[/home/jenkins/tools/java/latest1.9/bin/java, -Xmx4g, -Xms256m,
-Dmaven.test.failure.ignore=false, -cp,
/home/jenkins/jenkins-slave/maven35-agent.jar:/home/jenkins/tools/maven/apache-maven-3.5.0/boot/plexus-classworlds-2.5.2.jar:/home/jenkins/tools/maven/apache-maven-3.5.0/conf/logging,
jenkins.maven3.agent.Maven35Main,
/home/jenkins/tools/maven/apache-maven-3.5.0,
/home/jenkins/jenkins-slave/slave.jar,
/home/jenkins/jenkins-slave/maven35-interceptor.jar,
/home/jenkins/jenkins-slave/maven3-interceptor-commons.jar, 36347](Native
Method)
at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1554)
at hudson.remoting.UserResponse.retrieve(UserRequest.java:281)
at hudson.remoting.Channel.call(Channel.java:839)
at hudson.maven.ProcessCache$MavenProcess.call(ProcessCache.java:161)
at
hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:879)
at
hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:496)
at hudson.model.Run.execute(Run.java:1737)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:543)
at hudson.model.ResourceController.execute(ResourceController.java:97)
at hudson.model.Executor.run(Executor.java:419)
Caused by: java.lang.reflect.InvocationTargetException
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:564)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:139)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:70)
at hudson.remoting.UserRequest.perform(UserRequest.java:181)
at hudson.remoting.UserRequest.perform(UserRequest.java:52)
at hudson.remoting.Request$2.run(Request.java:336)
at
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
at java.util.concurrent.FutureTask.run(FutureTask.java:264)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)
at java.lang.Thread.run(Thread.java:844)
Caused by: java.lang.Exception: java.lang.reflect.InvocationTargetException
at jenkins.maven3.agent.Maven35Main.launch(Maven35Main.java:179)
... 14 more
Caused by: java.lang.reflect.InvocationTargetException
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:564)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at jenkins.maven3.agent.Maven35Main.launch(Maven35Main.java:176)
... 14 more
Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.<init>(BGMBuilder.java:147)
at
com.sun.tools.xjc.reader.xmlschema.BGMBuilder.build(BGMBuilder.java:117)
at com.sun.tools.xjc.ModelLoader.annotateXMLSchema(ModelLoader.java:425)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:174)
at com.sun.tools.xjc.ModelLoader.load(ModelLoader.java:119)
at com.sun.tools.xjc.Driver.run(Driver.java:333)
at
org.codehaus.mojo.jaxb2.AbstractXjcMojo.execute(AbstractXjcMojo.java:316)
at
org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:154)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:146)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
at
org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at
org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:309)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:194)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:107)
at
org.jvnet.hudson.maven3.launcher.Maven35Launcher.main(Maven35Launcher.java:130)
... 21 more
Caused by: java.lang.reflect.InvocationTargetException
at
jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 40 more
Caused by: java.lang.Error: java.lang.reflect.InvocationTargetException
at com.sun.tools.xjc.reader.Ring.get(Ring.java:113)
at
com.sun.tools.xjc.reader.xmlschema.BindingComponent.getClassSelector(BindingComponent.java:65)
at
com.sun.tools.xjc.reader.xmlschema.ColorBinder.<init>(ColorBinder.java:62)
at
com.sun.tools.xjc.reader.xmlschema.BindGreen.<init>(BindGreen.java:63)
... 45 more
Caused by: java.lang.reflect.InvocationTargetException
at
jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:102)
... 48 more
Caused by: java.lang.NoClassDefFoundError:
javax/activation/MimeTypeParseException
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:3110)
at java.lang.Class.getConstructor0(Class.java:3315)
at java.lang.Class.getDeclaredConstructor(Class.java:2510)
at com.sun.tools.xjc.reader.Ring.get(Ring.java:100)
at
com.sun.tools.xjc.reader.xmlschema.DefaultClassBinder.<init>(DefaultClassBinder.java:98)
at
com.sun.tools.xjc.reader.xmlschema.ClassSelector.<init>(ClassSelector.java:214)
... 53 more
Caused by: java.lang.ClassNotFoundException:
javax.activation.MimeTypeParseException
at
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 60 more
channel stopped
