Hi Gandhi, Thank you for your reply. I installed the source code following the Developer's install guide. ( subversion + Git and then Rebase after svn checkin) https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
I should mention I have not worked with Java and Maven before. Is there any other working directory that you would recommend me to get the source code from. I have macOS Mojave. Thanks, Maral On Wed, Jul 17, 2019 at 8:25 PM gandhi rajan <gandhiraja...@gmail.com> wrote: > Hi Maral, > > I could see the following error in the stacktrace, > > java.lang.NoClassDefFoundError: > javax/activation/MimeTypeParseException > > Could be an issue related to missing jar or classpath. Between, from where > did you check out the source code from? > > On Thursday, July 18, 2019, Maral Amir <maraljav...@gmail.com> wrote: > > > Hi, > > > > I am building the cTAKES developer version using the following command. > > > > mvn --fail-at-end --errors --update-snapshots clean install sonar:sonar > > -DskipTests=false -Dsonar.scm.provider=svn -Dsonar.host.url= > > https://builds.apache.org/analysis > > > > I also tried the following command: > > > > > > mvn clean install > > > > > > For both I get the following error: > > > > > > > > [*INFO*] *-------------------< *org.apache.ctakes:ctakes-ytex* > > >--------------------* > > > > [*INFO*] *Building Apache cTAKES YTEX 4.0.1-SNAPSHOT > > [48/53]* > > > > [*INFO*] *--------------------------------[ jar > > ]---------------------------------* > > > > [*INFO*] > > > > [*INFO*] *--- *maven-clean-plugin:2.4.1:clean *(default-clean)* @ > > ctakes-ytex* ---* > > > > [*INFO*] Deleting /Users/mamir/projects/ctakes/trunk/ctakes-ytex/target > > > > [*INFO*] > > > > [*INFO*] *--- *jaxb2-maven-plugin:1.6:xjc *(default)* @ ctakes-ytex* ---* > > > > [*INFO*] Generating source... > > > > [*INFO*] parsing a schema... > > > > [*INFO*] > > > *------------------------------------------------------------------------* > > > > [*INFO*] *Reactor Summary for Apache cTAKES 4.0.1-SNAPSHOT:* > > > > [*INFO*] > > > > [*INFO*] Apache cTAKES ...................................... > > *SUCCESS* [ 0.870 > > s] > > > > [*INFO*] ctakes-gui-res ..................................... > > *SUCCESS* [ 0.862 > > s] > > > > [*INFO*] Apache cTAKES Resources coreference ................ > > *SUCCESS* [ 3.261 > > s] > > > > [*INFO*] Apache cTAKES Resources temporal ................... > > *SUCCESS* [ 0.584 > > s] > > > > [*INFO*] Apache cTAKES Resources relation-extractor ......... > > *SUCCESS* [ 0.267 > > s] > > > > [*INFO*] Apache cTAKES Resources dictionary-lookup-fast-res . > > *SUCCESS* [ 0.945 > > s] > > > > [*INFO*] Apache cTAKES Resources core ....................... > > *SUCCESS* [ 0.355 > > s] > > > > [*INFO*] Apache cTAKES common type system ................... > > *SUCCESS* [ 3.086 > > s] > > > > [*INFO*] Apache cTAKES utils ................................ > > *SUCCESS* [ 0.783 > > s] > > > > [*INFO*] Apache cTAKES core ................................. > > *SUCCESS* [ 5.913 > > s] > > > > [*INFO*] Apache cTAKES dictionary lookup fast ............... > > *SUCCESS* [ 0.890 > > s] > > > > [*INFO*] Apache cTAKES document preprocessor ................ > > *SUCCESS* [ 0.911 > > s] > > > > [*INFO*] Apache cTAKES Resources lvg ........................ *SUCCESS* [ > > 11.864 s] > > > > [*INFO*] Apache cTAKES LVG lexical tools .................... > > *SUCCESS* [ 0.719 > > s] > > > > [*INFO*] Apache cTAKES Resources ne-contexts ................ > > *SUCCESS* [ 0.226 > > s] > > > > [*INFO*] Apache cTAKES named entity contexts ................ > > *SUCCESS* [ 1.503 > > s] > > > > [*INFO*] Apache cTAKES Resources assertion .................. > > *SUCCESS* [ 1.482 > > s] > > > > [*INFO*] Apache cTAKES Resources constituency-parser ........ > > *SUCCESS* [ 1.999 > > s] > > > > [*INFO*] Apache cTAKES Constituency Parser .................. > > *SUCCESS* [ 0.769 > > s] > > > > [*INFO*] Apache cTAKES Resources dependency-parser .......... *SUCCESS* [ > > 14.499 s] > > > > [*INFO*] Apache cTAKES Resources pos-tagger ................. > > *SUCCESS* [ 0.878 > > s] > > > > [*INFO*] Apache cTAKES part-of-speech tagger ................ > > *SUCCESS* [ 1.723 > > s] > > > > [*INFO*] Apache cTAKES Dependency Parser .................... *SUCCESS* [ > > 17.419 s] > > > > [*INFO*] Apache cTAKES context dependent tokenizer .......... > > *SUCCESS* [ 1.547 > > s] > > > > [*INFO*] Apache cTAKES Resources ctakes-chunker-res ......... > > *SUCCESS* [ 0.822 > > s] > > > > [*INFO*] Apache cTAKES chunker .............................. > > *SUCCESS* [ 0.835 > > s] > > > > [*INFO*] Apache cTAKES Assertion ............................ > > *SUCCESS* [ 1.726 > > s] > > > > [*INFO*] ctakes-clinical-pipeline-res ....................... > > *SUCCESS* [ 0.200 > > s] > > > > [*INFO*] Apache cTAKES ctakes-clinical-pipeline ............. > > *SUCCESS* [ 1.046 > > s] > > > > [*INFO*] Apache cTAKES Relation Extractor ................... > > *SUCCESS* [ 3.062 > > s] > > > > [*INFO*] Apache cTAKES Temporal Information Extraction ...... *SUCCESS* [ > > 52.554 s] > > > > [*INFO*] Apache cTAKES CoReference Resolver ................. > > *SUCCESS* [ 2.403 > > s] > > > > [*INFO*] ctakes-gui ......................................... > > *SUCCESS* [ 1.531 > > s] > > > > [*INFO*] Apache cTAKES fhir support ......................... > > *SUCCESS* [ 0.759 > > s] > > > > [*INFO*] Apache cTAKES Resources dictionary-lookup .......... > > *SUCCESS* [ 7.312 > > s] > > > > [*INFO*] Apache cTAKES dictionary lookup .................... > > *SUCCESS* [ 0.711 > > s] > > > > [*INFO*] Apache cTAKES Resources drug-ner ................... > > *SUCCESS* [ 0.272 > > s] > > > > [*INFO*] Apache cTAKES Drug NER ............................. > > *SUCCESS* [ 1.158 > > s] > > > > [*INFO*] Apache cTAKES Resources side-effect ................ > > *SUCCESS* [ 0.268 > > s] > > > > [*INFO*] Apache cTAKES Side Effects ......................... > > *SUCCESS* [ 0.837 > > s] > > > > [*INFO*] Apache cTAKES Resources smoking-status ............. > > *SUCCESS* [ 0.347 > > s] > > > > [*INFO*] Apache cTAKES Smoking Status ....................... > > *SUCCESS* [ 1.081 > > s] > > > > [*INFO*] Apache cTAKES Resources assertion-zoner ............ > > *SUCCESS* [ 0.296 > > s] > > > > [*INFO*] Apache cTAKES Assertion's zoner .................... > > *SUCCESS* [ 0.686 > > s] > > > > [*INFO*] ctakes-examples-res ................................ > > *SUCCESS* [ 0.443 > > s] > > > > [*INFO*] ctakes-examples .................................... > > *SUCCESS* [ 1.060 > > s] > > > > [*INFO*] Apache cTAKES Resources ctakes-ytex-res ............ > > *SUCCESS* [ 0.321 > > s] > > > > [*INFO*] Apache cTAKES YTEX ................................. > > *FAILURE* [ 0.666 > > 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: 02:34 min > > > > [*INFO*] Finished at: 2019-07-17T17:53:36-07:00 > > > > [*INFO*] > > > *------------------------------------------------------------------------* > > > > --------------------------------------------------- > > > > constituent[0]: file:/Users/mamir/apache-maven-3.6.1/conf/logging/ > > > > constituent[1]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-settings-builder-3.6.1.jar > > > > constituent[2]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven- > > resolver-transport-wagon-1.3.3.jar > > > > constituent[3]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-compat-3.6.1.jar > > > > constituent[4]: file:/Users/mamir/apache-maven-3.6.1/lib/aopalliance-1. > > 0.jar > > > > constituent[5]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-plugin-api-3.6.1.jar > > > > constituent[6]: > > file:/Users/mamir/apache-maven-3.6.1/lib/plexus-cipher-1.7.jar > > > > constituent[7]: > > file:/Users/mamir/apache-maven-3.6.1/lib/plexus-interpolation-1.25.jar > > > > constituent[8]: > > file:/Users/mamir/apache-maven-3.6.1/lib/guice-4.2.1-no_aop.jar > > > > constituent[9]: > > file:/Users/mamir/apache-maven-3.6.1/lib/slf4j-api-1.7.25.jar > > > > constituent[10]: > > > file:/Users/mamir/apache-maven-3.6.1/lib/error_prone_annotations-2.1.3.jar > > > > constituent[11]: file:/Users/mamir/apache-maven-3.6.1/lib/cdi-api-1.0.jar > > > > constituent[12]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-slf4j-provider-3.6.1.jar > > > > constituent[13]: > > file:/Users/mamir/apache-maven-3.6.1/lib/jcl-over-slf4j-1.7.25.jar > > > > constituent[14]: > > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-resolver-provider-3.6.1.jar > > > > constituent[15]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-artifact-3.6.1.jar > > > > constituent[16]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-resolver-spi-1.3.3.jar > > > > constituent[17]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-resolver-util-1.3.3.jar > > > > constituent[18]: > > file:/Users/mamir/apache-maven-3.6.1/lib/wagon-http-3.3.2-shaded.jar > > > > constituent[19]: > > file:/Users/mamir/apache-maven-3.6.1/lib/plexus-sec-dispatcher-1.4.jar > > > > constituent[20]: > > file:/Users/mamir/apache-maven-3.6.1/lib/plexus- > > component-annotations-1.7.1.jar > > > > constituent[21]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven- > > repository-metadata-3.6.1.jar > > > > constituent[22]: > > file:/Users/mamir/apache-maven-3.6.1/lib/plexus-utils-3.2.0.jar > > > > constituent[23]: > > file:/Users/mamir/apache-maven-3.6.1/lib/commons-cli-1.4.jar > > > > constituent[24]: file:/Users/mamir/apache-maven-3.6.1/lib/commons-io-2. > > 5.jar > > > > constituent[25]: > file:/Users/mamir/apache-maven-3.6.1/lib/jansi-1.17.1.jar > > > > constituent[26]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-resolver-impl-1.3.3.jar > > > > constituent[27]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-embedder-3.6.1.jar > > > > constituent[28]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-model-builder-3.6.1.jar > > > > constituent[29]: > > file:/Users/mamir/apache-maven-3.6.1/lib/checker-compat-qual-2.0.0.jar > > > > constituent[30]: > > file:/Users/mamir/apache-maven-3.6.1/lib/j2objc-annotations-1.1.jar > > > > constituent[31]: > > > file:/Users/mamir/apache-maven-3.6.1/lib/org.eclipse.sisu.inject-0.3.3.jar > > > > constituent[32]: > > file:/Users/mamir/apache-maven-3.6.1/lib/wagon-file-3.3.2.jar > > > > constituent[33]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-model-3.6.1.jar > > > > constituent[34]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-settings-3.6.1.jar > > > > constituent[35]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-resolver-api-1.3.3.jar > > > > constituent[36]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven- > > resolver-connector-basic-1.3.3.jar > > > > constituent[37]: > > file:/Users/mamir/apache-maven-3.6.1/lib/animal- > > sniffer-annotations-1.14.jar > > > > constituent[38]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-builder-support-3.6.1.jar > > > > constituent[39]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-shared-utils-3.2.1.jar > > > > constituent[40]: > > > file:/Users/mamir/apache-maven-3.6.1/lib/org.eclipse.sisu.plexus-0.3.3.jar > > > > constituent[41]: > file:/Users/mamir/apache-maven-3.6.1/lib/jsr305-3.0.2.jar > > > > constituent[42]: > > file:/Users/mamir/apache-maven-3.6.1/lib/maven-core-3.6.1.jar > > > > constituent[43]: file:/Users/mamir/apache-maven-3.6.1/lib/javax.inject- > > 1.jar > > > > constituent[44]: > > file:/Users/mamir/apache-maven-3.6.1/lib/commons-lang3-3.8.1.jar > > > > constituent[45]: > > file:/Users/mamir/apache-maven-3.6.1/lib/guava-25.1-android.jar > > > > constituent[46]: file:/Users/mamir/apache-maven-3.6.1/lib/jsr250-api-1. > > 0.jar > > > > constituent[47]: > > file:/Users/mamir/apache-maven-3.6.1/lib/wagon-provider-api-3.3.2.jar > > > > --------------------------------------------------- > > > > Exception in thread "main" 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:137) > > > > at > > org.apache.maven.lifecycle.internal.MojoExecutor.execute( > > MojoExecutor.java:210) > > > > at > > org.apache.maven.lifecycle.internal.MojoExecutor.execute( > > MojoExecutor.java:156) > > > > at > > org.apache.maven.lifecycle.internal.MojoExecutor.execute( > > MojoExecutor.java:148) > > > > 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:56) > > > > at > > org.apache.maven.lifecycle.internal.LifecycleStarter. > > execute(LifecycleStarter.java:128) > > > > at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305) > > > > at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192) > > > > at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105) > > > > at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956) > > > > at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288) > > > > at org.apache.maven.cli.MavenCli.main(MavenCli.java:192) > > > > 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:567) > > > > at > > org.codehaus.plexus.classworlds.launcher.Launcher. > > launchEnhanced(Launcher.java:282) > > > > at > > org.codehaus.plexus.classworlds.launcher.Launcher. > > launch(Launcher.java:225) > > > > at > > org.codehaus.plexus.classworlds.launcher.Launcher. > > mainWithExitCode(Launcher.java:406) > > > > at org.codehaus.plexus.classworlds.launcher.Launcher. > > main(Launcher.java:347) > > > > 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.DelegatingConstructorAccessorI > > mpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > > > at > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller( > > Constructor.java:500) > > > > at java.base/java.lang.reflect.Constructor.newInstance( > > Constructor.java:481) > > > > at com.sun.tools.xjc.reader.Ring.get(Ring.java:102) > > > > ... 29 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) > > > > ... 35 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.DelegatingConstructorAccessorI > > mpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > > > at > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller( > > Constructor.java:500) > > > > at java.base/java.lang.reflect.Constructor.newInstance( > > Constructor.java:481) > > > > at com.sun.tools.xjc.reader.Ring.get(Ring.java:102) > > > > ... 38 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:3143) > > > > at java.base/java.lang.Class.getConstructor0(Class.java:3348) > > > > at java.base/java.lang.Class.getDeclaredConstructor(Class.java:2559) > > > > 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) > > > > ... 44 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) > > > > ... 51 more > > > > > > > > > > I really appreciate any help. > > > > Thanks. > > Maral > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of others > !!!" >
