[phenotips-notifications] Build failed in Jenkins: clinical-text-analysis-extension #144

ci at phenotips.org ci at phenotips.org
Sat Apr 18 00:10:55 EDT 2015


See <https://ci.phenotips.org/job/clinical-text-analysis-extension/144/changes>

Changes:

[Sergiu Dumitriu] Be more verbose about the make failure

[Sergiu Dumitriu] Proper make invocation

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[...truncated 79 lines...]
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:prepare-agent (jacoco-prepare) @ clinical-text-analysis-extension ---
[INFO] argLine set to -javaagent:/home/jenkins-agent/workspace/maven-repositories/0/org/jacoco/org.jacoco.agent/0.7.2.201409121644/org.jacoco.agent-0.7.2.201409121644-runtime.jar=destfile=<https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/target/jacoco.exec>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.5:process (license-resources) @ clinical-text-analysis-extension ---
[WARNING] Failed to getClass for org.codehaus.mojo.clirr.ClirrCheckMojo
[INFO] 
[INFO] --- clirr-maven-plugin:2.6.1:check (clirr-check) @ clinical-text-analysis-extension ---
[INFO] Not generating Clirr report as there are no classes generated by the project
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:check (jacoco-check) @ clinical-text-analysis-extension ---
[INFO] Skipping JaCoCo execution due to missing execution data <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/target/jacoco.exec>
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install (default-install) @ clinical-text-analysis-extension ---
[INFO] Installing <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/pom.xml> to /home/jenkins-agent/workspace/maven-repositories/0/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/clinical-text-analysis-extension-1.0-SNAPSHOT.pom
[INFO] 
[INFO] --- maven-deploy-plugin:2.8.2:deploy (default-deploy) @ clinical-text-analysis-extension ---
Downloading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/maven-metadata.xml
Downloaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/maven-metadata.xml (622 B at 0.4 KB/sec)
Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/clinical-text-analysis-extension-1.0-20150417.235413-133.pom
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/clinical-text-analysis-extension-1.0-20150417.235413-133.pom (2 KB at 22.8 KB/sec)
Downloading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/maven-metadata.xml
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Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/maven-metadata.xml
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Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/maven-metadata.xml
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension/maven-metadata.xml (303 B at 4.9 KB/sec)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building PhenoTips - Clinical Text Analysis - Java API 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-plugins) @ clinical-text-analysis-extension-api ---
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[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-commons-lang3) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-no-legacy-dependencies) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:prepare-agent (jacoco-prepare) @ clinical-text-analysis-extension-api ---
[INFO] argLine set to -javaagent:/home/jenkins-agent/workspace/maven-repositories/0/org/jacoco/org.jacoco.agent/0.7.2.201409121644/org.jacoco.agent-0.7.2.201409121644-runtime.jar=destfile=<https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/jacoco.exec>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.5:process (license-resources) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ clinical-text-analysis-extension-api ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:compile (default-compile) @ clinical-text-analysis-extension-api ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/classes>
[WARNING] <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/src/main/java/org/phenotips/textanalysis/TermAnnotationService.java>:[50,12] serializable class org.phenotips.textanalysis.TermAnnotationService.AnnotationException has no definition of serialVersionUID
[INFO] 
[INFO] --- maven-resources-plugin:2.7:testResources (default-testResources) @ clinical-text-analysis-extension-api ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/src/test/resources>
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:testCompile (default-testCompile) @ clinical-text-analysis-extension-api ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ clinical-text-analysis-extension-api ---
[JENKINS] Recording test results
[INFO] 
[INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ clinical-text-analysis-extension-api ---
[INFO] Building jar: <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/clinical-text-analysis-extension-api-1.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-checkstyle-plugin:2.13:check (default) @ clinical-text-analysis-extension-api ---
[INFO] Starting audit...
Audit done.

[INFO] 
[INFO] --- license-maven-plugin:2.6:check (default) @ clinical-text-analysis-extension-api ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-plugins) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-commons-lang3) @ clinical-text-analysis-extension-api ---
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[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-no-legacy-dependencies) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:prepare-agent (jacoco-prepare) @ clinical-text-analysis-extension-api ---
[INFO] argLine set to -javaagent:/home/jenkins-agent/workspace/maven-repositories/0/org/jacoco/org.jacoco.agent/0.7.2.201409121644/org.jacoco.agent-0.7.2.201409121644-runtime.jar=destfile=<https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/jacoco.exec>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.5:process (license-resources) @ clinical-text-analysis-extension-api ---
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ clinical-text-analysis-extension-api ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 2 resources
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:compile (default-compile) @ clinical-text-analysis-extension-api ---
[INFO] Nothing to compile - all classes are up to date
[WARNING] Failed to getClass for org.codehaus.mojo.clirr.ClirrCheckMojo
[INFO] 
[INFO] --- clirr-maven-plugin:2.6.1:check (clirr-check) @ clinical-text-analysis-extension-api ---
[INFO] Unable to find a previous version of the project in the repository
[INFO] Not generating Clirr report as there is no previous version of the library to compare against
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:check (jacoco-check) @ clinical-text-analysis-extension-api ---
[INFO] Skipping JaCoCo execution due to missing execution data <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/jacoco.exec>
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install (default-install) @ clinical-text-analysis-extension-api ---
[INFO] Installing <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/clinical-text-analysis-extension-api-1.0-SNAPSHOT.jar> to /home/jenkins-agent/workspace/maven-repositories/0/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-SNAPSHOT.jar
[INFO] Installing <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/pom.xml> to /home/jenkins-agent/workspace/maven-repositories/0/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-SNAPSHOT.pom
[INFO] 
[INFO] --- maven-deploy-plugin:2.8.2:deploy (default-deploy) @ clinical-text-analysis-extension-api ---
Downloading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/maven-metadata.xml
Downloaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/maven-metadata.xml (799 B at 22.9 KB/sec)
Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-20150417.235455-117.jar
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-20150417.235455-117.jar (23 KB at 221.6 KB/sec)
Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-20150417.235455-117.pom
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-20150417.235455-117.pom (4 KB at 88.5 KB/sec)
Downloading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/maven-metadata.xml
Downloaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/maven-metadata.xml (307 B at 9.4 KB/sec)
Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/maven-metadata.xml
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/maven-metadata.xml (799 B at 13.9 KB/sec)
Uploading: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/maven-metadata.xml
Uploaded: https://nexus.phenotips.org/nexus/content/repositories/snapshots/org/phenotips/clinical-text-analysis-extension-api/maven-metadata.xml (307 B at 5.4 KB/sec)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-plugins) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-commons-lang3) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-no-legacy-dependencies) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:prepare-agent (jacoco-prepare) @ clinical-text-analysis-extension-biolark ---
[INFO] argLine set to -javaagent:/home/jenkins-agent/workspace/maven-repositories/0/org/jacoco/org.jacoco.agent/0.7.2.201409121644/org.jacoco.agent-0.7.2.201409121644-runtime.jar=destfile=<https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/jacoco.exec>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.5:process (license-resources) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ clinical-text-analysis-extension-biolark ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:compile (default-compile) @ clinical-text-analysis-extension-biolark ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 5 source files to <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/classes>
[WARNING] <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/src/main/java/org/phenotips/textanalysis/internal/BuildException.java>:[27,8] serializable class org.phenotips.textanalysis.internal.BuildException has no definition of serialVersionUID
[INFO] 
[INFO] --- maven-resources-plugin:2.7:testResources (default-testResources) @ clinical-text-analysis-extension-biolark ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/src/test/resources>
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:testCompile (default-testCompile) @ clinical-text-analysis-extension-biolark ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 2 source files to <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/test-classes>
[INFO] 
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ clinical-text-analysis-extension-biolark ---
[INFO] Surefire report directory: <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/surefire-reports>
[INFO] parallel='classesAndMethods', perCoreThreadCount=true, threadCount=2, useUnlimitedThreads=false, threadCountSuites=0, threadCountClasses=0, threadCountMethods=0, parallelOptimized=true

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running org.phenotips.textanalysis.internal.BiolarkFileUtilsTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.972 sec - in org.phenotips.textanalysis.internal.BiolarkFileUtilsTest
Running org.phenotips.textanalysis.internal.BioLarkAnnotationServiceTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.294 sec - in org.phenotips.textanalysis.internal.BioLarkAnnotationServiceTest

Results :

Tests run: 3, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
[INFO] 
[INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ clinical-text-analysis-extension-biolark ---
[INFO] Building jar: <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/clinical-text-analysis-extension-biolark-1.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-checkstyle-plugin:2.13:check (default) @ clinical-text-analysis-extension-biolark ---
[INFO] Starting audit...
Audit done.

[INFO] 
[INFO] --- license-maven-plugin:2.6:check (default) @ clinical-text-analysis-extension-biolark ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-plugins) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-commons-lang3) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-no-legacy-dependencies) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:prepare-agent (jacoco-prepare) @ clinical-text-analysis-extension-biolark ---
[INFO] argLine set to -javaagent:/home/jenkins-agent/workspace/maven-repositories/0/org/jacoco/org.jacoco.agent/0.7.2.201409121644/org.jacoco.agent-0.7.2.201409121644-runtime.jar=destfile=<https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/jacoco.exec>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.5:process (license-resources) @ clinical-text-analysis-extension-biolark ---
[INFO] 
[INFO] --- maven-resources-plugin:2.7:resources (default-resources) @ clinical-text-analysis-extension-biolark ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 2 resources
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.2:compile (default-compile) @ clinical-text-analysis-extension-biolark ---
[INFO] Nothing to compile - all classes are up to date
[WARNING] Failed to getClass for org.codehaus.mojo.clirr.ClirrCheckMojo
[INFO] 
[INFO] --- clirr-maven-plugin:2.6.1:check (clirr-check) @ clinical-text-analysis-extension-biolark ---
[INFO] Unable to find a previous version of the project in the repository
[INFO] Not generating Clirr report as there is no previous version of the library to compare against
[INFO] 
[INFO] --- jacoco-maven-plugin:0.7.2.201409121644:check (jacoco-check) @ clinical-text-analysis-extension-biolark ---
[INFO] Analyzed bundle 'PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs' with 4 classes
[WARNING] Rule violated for bundle PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs: instructions covered ratio is 0.17, but expected minimum is 0.18
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] PhenoTips - Clinical Text Analysis ................ SUCCESS [13.291s]
[INFO] PhenoTips - Clinical Text Analysis - Java API ..... SUCCESS [41.542s]
[INFO] PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs  FAILURE [40.166s]
[INFO] PhenoTips - Clinical Text Analysis - User Interface Components  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:40.599s
[INFO] Finished at: Fri Apr 17 19:55:37 EDT 2015
[INFO] Final Memory: 66M/282M
[INFO] ------------------------------------------------------------------------
Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal org.jacoco:jacoco-maven-plugin:0.7.2.201409121644:check (jacoco-check) on project clinical-text-analysis-extension-biolark: Coverage checks have not been met. See log for details. -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :clinical-text-analysis-extension-biolark
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/pom.xml> to org.phenotips/clinical-text-analysis-extension-biolark/1.0-SNAPSHOT/clinical-text-analysis-extension-biolark-1.0-SNAPSHOT.pom
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/biolark/target/clinical-text-analysis-extension-biolark-1.0-SNAPSHOT.jar> to org.phenotips/clinical-text-analysis-extension-biolark/1.0-SNAPSHOT/clinical-text-analysis-extension-biolark-1.0-SNAPSHOT.jar
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/ui/pom.xml> to org.phenotips/clinical-text-analysis-extension-ui/1.0-SNAPSHOT/clinical-text-analysis-extension-ui-1.0-SNAPSHOT.pom
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/pom.xml> to org.phenotips/clinical-text-analysis-extension-api/1.0-SNAPSHOT/clinical-text-analysis-extension-api-1.0-SNAPSHOT.pom
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/api/target/clinical-text-analysis-extension-api-1.0-SNAPSHOT.jar> to org.phenotips/clinical-text-analysis-extension-api/1.0-20150417.235455-117/clinical-text-analysis-extension-api-1.0-20150417.235455-117.jar
[JENKINS] Archiving <https://ci.phenotips.org/job/clinical-text-analysis-extension/ws/pom.xml> to org.phenotips/clinical-text-analysis-extension/1.0-SNAPSHOT/clinical-text-analysis-extension-1.0-SNAPSHOT.pom
Terminating xvnc.
channel stopped
$ vncserver -kill :82
Killing Xvnc process ID 4102
Setting commit status on GitHub for https://github.com/phenotips/clinical-text-analysis-extension/commit/f5c58df0fff0c704b7a142b2cb99460d9ac5bb56


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