See
<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/5/display/redirect?page=changes>
Changes:
[tmill] Add script for extracting markables from a corpus for analysis.
------------------------------------------
[...truncated 990.78 KB...]
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 19:10:58 INFO RegressionPipelineTest - Creating directory:
testdata/generatedoutput/RegressionPipelineCPETest
29 Sep 2017 19:10:58 INFO RegressionPipelineTest - Parsing CPE
Descriptor:RegressionPipelineCPETest.xml
29 Sep 2017 19:10:59 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using left , right scope sizes: 7
, 7
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
29 Sep 2017 19:11:01 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
29 Sep 2017 19:11:01 INFO NegationContextAnalyzer - initBoundaryData() called
for ContextInitializer
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
29 Sep 2017 19:11:01 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
29 Sep 2017 19:11:01 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
29 Sep 2017 19:11:01 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
29 Sep 2017 19:11:01 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using left , right scope sizes:
10 , 10
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
29 Sep 2017 19:11:02 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.status.StatusContextAnalyzer
29 Sep 2017 19:11:02 INFO StatusContextAnalyzer - initBoundaryData() called
for ContextInitializer
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.status.StatusContextHitConsumer
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
29 Sep 2017 19:11:02 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
29 Sep 2017 19:11:02 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
29 Sep 2017 19:11:02 INFO AbstractJCasTermAnnotator - Using dictionary lookup
window type: org.apache.ctakes.typesystem.type.textspan.Sentence
29 Sep 2017 19:11:02 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 19:11:02 INFO AbstractJCasTermAnnotator - Using minimum term text
span: 3
29 Sep 2017 19:11:02 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
29 Sep 2017 19:11:02 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
29 Sep 2017 19:11:02 ERROR UmlsUserApprover - User CHANGE_ME not allowed. It
is a placeholder reminder.
29 Sep 2017 19:11:02 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: 4.771 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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[JENKINS] Archiving disabled[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ...................................... SUCCESS [ 5.142 s]
[INFO] ctakes-gui-res ..................................... SUCCESS [ 4.294 s]
[INFO] Apache cTAKES Resources core ....................... SUCCESS [ 2.778 s]
[INFO] Apache cTAKES common type system ................... SUCCESS [ 8.497 s]
[INFO] Apache cTAKES utils ................................ SUCCESS [ 4.380 s]
[INFO] Apache cTAKES core ................................. SUCCESS [ 25.868 s]
[INFO] ctakes-gui ......................................... SUCCESS [ 5.074 s]
[INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [ 3.169 s]
[INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [ 6.199 s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [ 3.341 s]
[INFO] Apache cTAKES chunker .............................. SUCCESS [ 3.614 s]
[INFO] Apache cTAKES document preprocessor ................ SUCCESS [ 3.834 s]
[INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [ 10.866 s]
[INFO] Apache cTAKES dictionary lookup .................... SUCCESS [ 4.792 s]
[INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [ 5.451 s]
[INFO] Apache cTAKES Resources lvg ........................ SUCCESS [ 32.104 s]
[INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [ 4.674 s]
[INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [ 2.372 s]
[INFO] Apache cTAKES named entity contexts ................ SUCCESS [ 4.679 s]
[INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [ 4.969 s]
[INFO] Apache cTAKES Constituency Parser .................. SUCCESS [ 3.508 s]
[INFO] Apache cTAKES Resources coreference ................ SUCCESS [ 6.962 s]
[INFO] Apache cTAKES Resources temporal ................... SUCCESS [ 2.875 s]
[INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [ 2.459 s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [ 3.265 s]
[INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [ 3.962 s]
[INFO] Apache cTAKES Resources assertion .................. SUCCESS [ 4.194 s]
[INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [ 24.732 s]
[INFO] Apache cTAKES Dependency Parser .................... SUCCESS [ 47.550 s]
[INFO] Apache cTAKES Assertion ............................ SUCCESS [ 7.027 s]
[INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [ 2.379 s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [ 6.802 s]
[INFO] Apache cTAKES Relation Extractor ................... SUCCESS [ 11.615 s]
[INFO] Apache cTAKES Temporal Information Extraction ...... FAILURE [ 24.405 s]
[INFO] Apache cTAKES CoReference Resolver ................. SKIPPED
[INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [ 2.501 s]
[INFO] Apache cTAKES Drug NER ............................. SUCCESS [ 7.604 s]
[INFO] Apache cTAKES Resources side-effect ................ SUCCESS [ 2.596 s]
[INFO] Apache cTAKES Side Effects ......................... SUCCESS [ 6.907 s]
[INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [ 2.501 s]
[INFO] Apache cTAKES Smoking Status ....................... SUCCESS [ 6.657 s]
[INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [ 2.595 s]
[INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [ 3.149 s]
[INFO] ctakes-examples-res ................................ SUCCESS [ 2.432 s]
[INFO] ctakes-examples .................................... SKIPPED
[INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [ 2.442 s]
[INFO] Apache cTAKES YTEX ................................. FAILURE [01:23 min]
[INFO] Apache cTAKES YTEX UIMA ............................ SKIPPED
[INFO] Apache cTAKES YTEX Web ............................. SKIPPED
[INFO] Apache cTAKES Distribution ......................... SKIPPED
[INFO] Apache cTAKES Regression-test ...................... FAILURE [ 12.854 s]
[INFO] Apache cTAKES template filler ...................... SUCCESS [ 12.159 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 09:05 min
[INFO] Finished at: 2017-09-29T19:11:53Z
[INFO] Final Memory: 123M/1535M
[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
Sending e-mails to: [email protected]
Sending e-mails to: [email protected]
Sending e-mails to: [email protected]
channel stopped
