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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk-Java-1.8 #4
Date Fri, 29 Sep 2017 18:12:29 GMT
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/4/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 1.01 MB...]
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
29 Sep 2017 18:11:16  INFO RegressionPipelineTest - Creating directory: testdata/generatedoutput/RegressionPipelineCPETest
29 Sep 2017 18:11:16  INFO RegressionPipelineTest - Parsing CPE Descriptor:RegressionPipelineCPETest.xml
29 Sep 2017 18:11:17  INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using left , right scope sizes: 7 , 7
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using scope order: LEFT,RIGHT
29 Sep 2017 18:11:19  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using context analyzer: org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
29 Sep 2017 18:11:19  INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using context consumer: org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using focus type: org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
29 Sep 2017 18:11:19  INFO ContextAnnotator - Using context type: org.apache.ctakes.typesystem.type.syntax.BaseToken
29 Sep 2017 18:11:19  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
29 Sep 2017 18:11:19  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
29 Sep 2017 18:11:19  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using left , right scope sizes: 10 , 10
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using scope order: LEFT,RIGHT
29 Sep 2017 18:11:20  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using context analyzer: org.apache.ctakes.necontexts.status.StatusContextAnalyzer
29 Sep 2017 18:11:20  INFO StatusContextAnalyzer - initBoundaryData() called for ContextInitializer
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using context consumer: org.apache.ctakes.necontexts.status.StatusContextHitConsumer
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using focus type: org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
29 Sep 2017 18:11:20  INFO ContextAnnotator - Using context type: org.apache.ctakes.typesystem.type.syntax.BaseToken
29 Sep 2017 18:11:20  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
29 Sep 2017 18:11:20  INFO AbstractJCasTermAnnotator - Using dictionary lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 18:11:20  INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD DT EX
IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB 
29 Sep 2017 18:11:20  INFO AbstractJCasTermAnnotator - Using minimum term text span: 3
29 Sep 2017 18:11:20  INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
29 Sep 2017 18:11:20  INFO DictionaryDescriptorParser - Parsing dictionary specifications:

29 Sep 2017 18:11:20 ERROR UmlsUserApprover -   User CHANGE_ME not allowed.  It is a placeholder
reminder.
29 Sep 2017 18:11:20 ERROR UmlsUserApprover -    Verify that you are setting command-line
option --user or ctakes property umlsUser or environment variable ctakes.umlsuser properly.
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.451 sec <<< FAILURE!

Results :

Tests in error: 
  testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest): Initialization of CAS
Processor with name "RegressionPipelineAggregateTest" failed.  

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0

[JENKINS] Recording test results
[JENKINS] Archiving disabled
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES template filler 4.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-template-filler ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-template-filler ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-template-filler
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 0 resource
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-template-filler ---
[INFO] Compiling 1 source file to <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-template-filler/target/classes>
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-template-filler
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 0 resource
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-template-filler
---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @ ctakes-template-filler ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-template-filler/target/surefire-reports>

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

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

[JENKINS] Recording test results
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-template-filler ---
[INFO] Building jar: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-template-filler/target/ctakes-template-filler-4.0.1-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-template-filler
---
[INFO] 
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-template-filler ---
[INFO] Installing <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-template-filler/target/ctakes-template-filler-4.0.1-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-template-filler/4.0.1-SNAPSHOT/ctakes-template-filler-4.0.1-SNAPSHOT.jar
[INFO] Installing <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-template-filler/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-template-filler/4.0.1-SNAPSHOT/ctakes-template-filler-4.0.1-SNAPSHOT.pom
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[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ...................................... SUCCESS [  6.981 s]
[INFO] ctakes-gui-res ..................................... SUCCESS [  5.321 s]
[INFO] Apache cTAKES Resources core ....................... SUCCESS [  2.619 s]
[INFO] Apache cTAKES common type system ................... SUCCESS [  9.057 s]
[INFO] Apache cTAKES utils ................................ SUCCESS [  4.428 s]
[INFO] Apache cTAKES core ................................. SUCCESS [ 26.313 s]
[INFO] ctakes-gui ......................................... SUCCESS [  4.958 s]
[INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [  3.376 s]
[INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [  5.817 s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [  3.323 s]
[INFO] Apache cTAKES chunker .............................. SUCCESS [  3.572 s]
[INFO] Apache cTAKES document preprocessor ................ SUCCESS [  3.789 s]
[INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 27.523 s]
[INFO] Apache cTAKES dictionary lookup .................... SUCCESS [  4.723 s]
[INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [  5.159 s]
[INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 50.280 s]
[INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [  5.956 s]
[INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [  2.369 s]
[INFO] Apache cTAKES named entity contexts ................ SUCCESS [  4.617 s]
[INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [  4.901 s]
[INFO] Apache cTAKES Constituency Parser .................. SUCCESS [  3.334 s]
[INFO] Apache cTAKES Resources coreference ................ SUCCESS [  7.143 s]
[INFO] Apache cTAKES Resources temporal ................... SUCCESS [  3.006 s]
[INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [  2.548 s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [  4.002 s]
[INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [  3.687 s]
[INFO] Apache cTAKES Resources assertion .................. SUCCESS [  4.184 s]
[INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 22.276 s]
[INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 51.679 s]
[INFO] Apache cTAKES Assertion ............................ SUCCESS [  7.161 s]
[INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [  2.468 s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [  6.828 s]
[INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 11.458 s]
[INFO] Apache cTAKES Temporal Information Extraction ...... FAILURE [ 27.303 s]
[INFO] Apache cTAKES CoReference Resolver ................. SKIPPED
[INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [  2.687 s]
[INFO] Apache cTAKES Drug NER ............................. SUCCESS [  8.027 s]
[INFO] Apache cTAKES Resources side-effect ................ SUCCESS [  2.687 s]
[INFO] Apache cTAKES Side Effects ......................... SUCCESS [  6.602 s]
[INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [  3.229 s]
[INFO] Apache cTAKES Smoking Status ....................... SUCCESS [  6.880 s]
[INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [  2.512 s]
[INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [  3.333 s]
[INFO] ctakes-examples-res ................................ SUCCESS [  2.417 s]
[INFO] ctakes-examples .................................... SKIPPED
[INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [  2.580 s]
[INFO] Apache cTAKES YTEX ................................. FAILURE [01:18 min]
[INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED
[INFO] Apache cTAKES YTEX Web ............................. SKIPPED
[INFO] Apache cTAKES Distribution ......................... SKIPPED
[INFO] Apache cTAKES Regression-test ...................... FAILURE [ 16.767 s]
[INFO] Apache cTAKES template filler ...................... SUCCESS [  7.937 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 09:55 min
[INFO] Finished at: 2017-09-29T18:12:10Z
[INFO] Final Memory: 125M/1591M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test
(default-test) on project ctakes-temporal: There are test failures.
[ERROR] 
[ERROR] Please refer to <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-temporal/target/surefire-reports>
for the individual test results.
[ERROR] -> [Help 1]
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test
(surefire-it) on project ctakes-ytex: There are test failures.
[ERROR] 
[ERROR] Please refer to <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-ytex/target/surefire-reports>
for the individual test results.
[ERROR] -> [Help 1]
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test
(default-test) on project ctakes-regression-test: There are test failures.
[ERROR] 
[ERROR] Please refer to <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/ws/ctakes-regression-test/target/surefire-reports>
for the individual test results.
[ERROR] -> [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/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :ctakes-temporal
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