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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-Java-1.9 #2
Date Fri, 29 Sep 2017 18:17:53 GMT
See <https://builds.apache.org/job/ctakes-trunk-Java-1.9/2/display/redirect?page=changes>

Changes:

[seanfinan] Check of some things that I've been sitting on ...
todo in PipelineBuilder
StringUtil faster split
DefaultSectionRegex more regex
AbstractJCasTermAnnotator use JCasUtil.indexCovered(..) for speed
DictionaryLookupFactory deprecated
WindowProcessor use basetokens directly for speed
BsvConceptFactory use StringUtil in core for speed
DefaultConcept primitive loop replaces stream for speed
JdbcConceptFactory add deprecation tag
SemanticCleanupTermConsumer primitive loop replaces stream for speed
BsvRareWordDictionary use StringUtil in core for speed
RareWordTermMapCreator use StringUtil in core for consolidation
LookupUtil add deprecated tag

------------------------------------------
[...truncated 955.56 KB...]
[INFO] 
[INFO] Apache cTAKES ...................................... SUCCESS [  7.659 s]
[INFO] ctakes-gui-res ..................................... SUCCESS [  4.763 s]
[INFO] Apache cTAKES Resources core ....................... SUCCESS [  2.691 s]
[INFO] Apache cTAKES common type system ................... SUCCESS [ 10.017 s]
[INFO] Apache cTAKES utils ................................ SUCCESS [  4.943 s]
[INFO] Apache cTAKES core ................................. SUCCESS [ 27.904 s]
[INFO] ctakes-gui ......................................... SUCCESS [ 14.423 s]
[INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [  3.471 s]
[INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [  6.164 s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [  3.380 s]
[INFO] Apache cTAKES chunker .............................. SUCCESS [  4.052 s]
[INFO] Apache cTAKES document preprocessor ................ SUCCESS [  4.252 s]
[INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 16.811 s]
[INFO] Apache cTAKES dictionary lookup .................... SUCCESS [  5.089 s]
[INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [  5.457 s]
[INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 26.128 s]
[INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [  5.776 s]
[INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [  2.544 s]
[INFO] Apache cTAKES named entity contexts ................ SUCCESS [  5.318 s]
[INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [  4.745 s]
[INFO] Apache cTAKES Constituency Parser .................. SUCCESS [  3.578 s]
[INFO] Apache cTAKES Resources coreference ................ SUCCESS [  6.329 s]
[INFO] Apache cTAKES Resources temporal ................... SUCCESS [  3.053 s]
[INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [  2.677 s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [  3.869 s]
[INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [  3.629 s]
[INFO] Apache cTAKES Resources assertion .................. SUCCESS [  4.092 s]
[INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 19.441 s]
[INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 49.463 s]
[INFO] Apache cTAKES Assertion ............................ SUCCESS [  7.146 s]
[INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [  2.644 s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [  7.698 s]
[INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 12.493 s]
[INFO] Apache cTAKES Temporal Information Extraction ...... FAILURE [ 28.154 s]
[INFO] Apache cTAKES CoReference Resolver ................. SKIPPED
[INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [  2.662 s]
[INFO] Apache cTAKES Drug NER ............................. SUCCESS [  7.738 s]
[INFO] Apache cTAKES Resources side-effect ................ SUCCESS [  2.728 s]
[INFO] Apache cTAKES Side Effects ......................... SUCCESS [  7.364 s]
[INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [  2.613 s]
[INFO] Apache cTAKES Smoking Status ....................... SUCCESS [  7.133 s]
[INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [  2.618 s]
[INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [  3.209 s]
[INFO] ctakes-examples-res ................................ SUCCESS [  2.869 s]
[INFO] ctakes-examples .................................... SKIPPED
[INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [  2.556 s]
[INFO] Apache cTAKES YTEX ................................. FAILURE [  3.266 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: 07:41 min
[INFO] Finished at: 2017-09-29T18:17:45Z

[INFO] Final Memory: 71M/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:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	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
Sending e-mails to: notifications@ctakes.apache.org
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:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	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,
51428](Native Method)
	at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1545)
	at hudson.remoting.UserResponse.retrieve(UserRequest.java:253)
	at hudson.remoting.Channel.call(Channel.java:830)
	at hudson.maven.ProcessCache$MavenProcess.call(ProcessCache.java:161)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:878)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:490)
	at hudson.model.Run.execute(Run.java:1735)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:542)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:405)
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:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	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

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