Hi Reed, As Gundolf mentioned, you got to use the following to get away from test failures:
mvn clean install -Dmaven.test.skip=true Regards, Gandhi From: Schenk, Gundolf [mailto:[email protected]] Sent: Friday, March 23, 2018 6:01 AM To: [email protected] Subject: Re: User wishing to use version 4.0.1 from developer install for bug fixes, experiencing setup problems HI Reed, Perhaps, this should go to the developers list. I am getting those test errors, too. Curious to hear any thoughts about why they happen. If you just want an installation you can skip the tests by using -DskipTests=false and a zip or tar.gz file should be produced at the end of the compilation. Cheers, Gundolf. From: Reed Villanueva <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Thursday, March 22, 2018 at 16:55 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Fwd: User wishing to use version 4.0.1 from developer install for bug fixes, experiencing setup problems I am a user experiencing an error when trying to use the simple piper fabricator gui ($CTAKES_HOME/bin/runPiperCreator.sh): Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.getTableCellRendererComponent(SynthTableHeaderUI.java:234) at org.apache.ctakes.gui.pipeline.MainPanel2.createWestPanel(MainPanel2.java:94) Looking at this previously archived message (https://issues.apache.org/jira/browse/CTAKES-442), it appears that the problem has been resolved in version 4.0.1. However, binaries of this version are not yet available on the downloads page of the cTAKES site (https://ctakes.apache.org/downloads.cgi) (if available elsewhere please let me know). Thus, I am attempting to install the dev version following the associated guide (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide). Have created the dev home ~/projects/ctakes as recommeded by the guide, checked out the code (via svn), and at this point I have two questions: 1. Once I have the trunk directory, how do I use the files therein (have no experience with subversion repositories or using maven projects beyond reading basic overviews)? I assume that I need to "install" the project with maven, but doing so leads into the build errors in question 2... 2. Running the dev guide's build instructions (see https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide#cTAKES4.0DeveloperInstallGuide-Build): $ rm -fr /tmp/ctakes-* $ exports MAVEN_OPTS='-Xms3072m -Xmx4g -Xss128M -XX:+CMSClassUnloadingEnabled -XX:-UseGCOverheadLimit -Dmaven.test.failure.ignore=false' $ mvn --fail-at-end --errors --update-snapshots clean install sonar:sonar -DskipTests=false -Dsonar.scm.provider=svn -Dsonar.host.url=https://builds.apache.org<http://apache.org>/analysis I get the error [INFO] Apache cTAKES YTEX ................................. FAILURE [01:10 min] [INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED [INFO] Apache cTAKES YTEX Web ............................. SKIPPED [INFO] Apache cTAKES Distribution ......................... SKIPPED [INFO] Apache cTAKES Regression-test ...................... SUCCESS [ 26.852 s] [INFO] Apache cTAKES template filler 4.0.1-SNAPSHOT ....... SUCCESS [ 0.659 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13:36 min [INFO] Finished at: 2018-03-22T12:38:47-10:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-failsafe-plugin:2.20.1:verify (default) on project ctakes-ytex: There are test failures. [ERROR] [ERROR] Please refer to /home/reedv/projects/ctakes/trunk/ctakes-ytex/target/failsafe-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream. [ERROR] -> [Help 1] org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-failsafe-plugin:2.20.1:verify (default) on project ctakes-ytex: There are test failures. Please refer to /home/reedv/projects/ctakes/trunk/ctakes-ytex/target/failsafe-reports for the individual test results. Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream. at org.apache.maven.lifecycle.int<https://protect2.fireeye.com/url?k=ee86a0c549dbe000.ee8687d8-f27dec8e1fd55dbb&u=http://org.apache.maven.lifecycle.int>ernal.MojoExecutor.execute (MojoExecutor.java:213) at org.apache.maven.lifecycle.int<https://protect2.fireeye.com/url?k=ee86a0c549dbe000.ee8687d8-f27dec8e1fd55dbb&u=http://org.apache.maven.lifecycle.int>ernal.MojoExecutor.execute (MojoExecutor.java:154) (could not determine a next course of action after visiting http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException). Trying "$mvn clean install" did not seem to help either. Though running the UMLS tests (see https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide#cTAKES4.0DeveloperInstallGuide-Testing), the output looks successful, eg. Results : Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Apache cTAKES 4.0.1-SNAPSHOT ....................... SUCCESS [ 0.525 s] [INFO] ctakes-gui-res ..................................... SUCCESS [ 0.668 s] [INFO] Apache cTAKES Resources coreference ................ SUCCESS [ 1.742 s] [INFO] Apache cTAKES Resources temporal ................... SUCCESS [ 0.504 s] [INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [ 0.257 s] [INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [ 3.642 s] [INFO] Apache cTAKES Resources core ....................... SUCCESS [ 0.291 s] [INFO] Apache cTAKES common type system ................... SUCCESS [ 2.374 s] [INFO] Apache cTAKES utils ................................ SUCCESS [ 0.919 s] [INFO] Apache cTAKES core ................................. SUCCESS [ 4.496 s] [INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [ 0.677 s] [INFO] Apache cTAKES document preprocessor ................ SUCCESS [ 0.770 s] [INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 52.623 s] [INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [ 0.482 s] [INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [ 0.127 s] [INFO] Apache cTAKES named entity contexts ................ SUCCESS [ 1.065 s] [INFO] Apache cTAKES Resources assertion .................. SUCCESS [ 1.169 s] [INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [ 1.340 s] [INFO] Apache cTAKES Constituency Parser .................. SUCCESS [ 0.497 s] [INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 9.191 s] [INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [ 0.578 s] [INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [ 1.393 s] [INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 20.204 s] [INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [ 1.880 s] [INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [ 4.408 s] [INFO] Apache cTAKES chunker .............................. SUCCESS [ 3.969 s] [INFO] Apache cTAKES Assertion ............................ SUCCESS [ 3.322 s] [INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [ 0.148 s] [INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [ 0.714 s] [INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 2.400 s] [INFO] Apache cTAKES Temporal Information Extraction ...... SUCCESS [ 56.517 s] [INFO] Apache cTAKES CoReference Resolver ................. SUCCESS [ 1.532 s] [INFO] ctakes-gui ......................................... SUCCESS [ 1.081 s] [INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 11.038 s] [INFO] Apache cTAKES dictionary lookup .................... SUCCESS [ 0.523 s] [INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [ 0.204 s] [INFO] Apache cTAKES Drug NER ............................. SUCCESS [ 0.794 s] [INFO] Apache cTAKES Resources side-effect ................ SUCCESS [ 0.260 s] [INFO] Apache cTAKES Side Effects ......................... SUCCESS [ 0.554 s] [INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [ 0.731 s] [INFO] Apache cTAKES Smoking Status ....................... SUCCESS [ 3.608 s] [INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [ 1.294 s] [INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [ 1.721 s] [INFO] ctakes-examples-res ................................ SUCCESS [ 6.022 s] [INFO] ctakes-examples .................................... SUCCESS [ 2.195 s] [INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [ 3.440 s] [INFO] Apache cTAKES YTEX ................................. SUCCESS [ 5.740 s] [INFO] Apache cTAKES YTEX UIMA ............................ SUCCESS [ 0.906 s] [INFO] Apache cTAKES YTEX Web ............................. SUCCESS [ 1.976 s] [INFO] Apache cTAKES Distribution ......................... SUCCESS [ 0.742 s] [INFO] Apache cTAKES Regression-test ...................... SUCCESS [ 25.546 s] [INFO] Apache cTAKES template filler 4.0.1-SNAPSHOT ....... SUCCESS [ 0.511 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 04:09 min [INFO] Finished at: 2018-03-22T12:52:09-10:00 [INFO] ------------------------------------------------------------------------ What does this mean? Is there any significance to this? Thank you. Note: I get the feeling that some elements of this post maybe should be split into separate emails, but (again) I am not experienced in using maven, subversion, or cTAKES so could not say for sure. Extra details: ➜ ~ java -version java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode) ➜ ~ javac -version javac 1.8.0_161 ➜ trunk echo $JAVA_HOME /usr/lib/jvm/java-8-oracle ➜ ~ svn --version svn, version 1.9.3 (r1718519) compiled Aug 10 2017, 16:59:15 on x86_64-pc-linux-gnu Copyright (C) 2015 The Apache Software Foundation. This software consists of contributions made by many people; see the NOTICE file for more information. Subversion is open source software, see http://subversion.apache.org/ The following repository access (RA) modules are available: * ra_svn : Module for accessing a repository using the svn network protocol. - with Cyrus SASL authentication - handles 'svn' scheme * ra_local : Module for accessing a repository on local disk. - handles 'file' scheme * ra_serf : Module for accessing a repository via WebDAV protocol using serf. - using serf 1.3.8 (compiled with 1.3.8) - handles 'http' scheme - handles 'https' scheme The following authentication credential caches are available: * Plaintext cache in $HOME/.subversion * Gnome Keyring * GPG-Agent * KWallet (KDE) ➜ ~ mvn -version Apache Maven 3.5.3 (3383c37e1f9e9b3bc3df5050c29c8aff9f295297; 2018-02-24T09:49:05-10:00) Maven home: $HOME/apache-maven-3.5.3 Java version: 1.8.0_161, vendor: Oracle Corporation Java home: /usr/lib/jvm/java-8-oracle/jre Default locale: en_US, platform encoding: UTF-8 OS name: "linux", version: "4.13.0-36-generic", arch: "amd64", family: "unix" ➜ ~ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04.4 LTS Release: 16.04 Codename: xenial This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
