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]> Reply-To: "[email protected]" <[email protected]> Date: Thursday, March 22, 2018 at 16:55 To: "[email protected]" <[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
