See <https://builds.apache.org/job/ctakes-trunk-package/413/changes>
Changes:
[clin] use the new sentence dectector
[clin] 1. use the newest sentence detector
2. change the data split, so we can test on the real test set
3. normalize timex to string
------------------------------------------
[...truncated 4942 lines...]
[delete] Deleting: /tmp/ytex1675812738.sql
[delete] Deleting: /tmp/ytex1482075101use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex959592506.sql
[sql] Executing resource: /tmp/ytex959592506.sql
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: /tmp/ytex959592506.sql
[delete] Deleting: /tmp/ytex1056999955use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex-uima
---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @
ctakes-ytex-uima ---
[INFO] Installing
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-uima/target/ctakes-ytex-uima-3.2.3-SNAPSHOT.jar>
to
/home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-ytex-uima/3.2.3-SNAPSHOT/ctakes-ytex-uima-3.2.3-SNAPSHOT.jar
[INFO] Installing
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-uima/pom.xml>
to
/home/jenkins/jenkins-slave/maven-repositories/1/org/apache/ctakes/ctakes-ytex-uima/3.2.3-SNAPSHOT/ctakes-ytex-uima-3.2.3-SNAPSHOT.pom
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES ctakes-clinical-pipeline 3.2.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @
ctakes-clinical-pipeline ---
[INFO]
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @
ctakes-clinical-pipeline ---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @
ctakes-clinical-pipeline ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/src/main/resources>
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
ctakes-clinical-pipeline ---
[INFO] Compiling 5 source files to
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target/classes>
[WARNING]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java>:[92,55]
[unchecked] unchecked cast
[WARNING] required: Class<T>
found: Type
where T is a type-variable:
T extends Annotation declared in class BagOfAnnotationsGenerator
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java>:[152,23]
[unchecked] unchecked call to add(E) as a member of the raw type Set
[INFO]
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @
ctakes-clinical-pipeline ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/src/test/resources>
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @
ctakes-clinical-pipeline ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @
ctakes-clinical-pipeline ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-clinical-pipeline ---
[INFO] Building jar:
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target/ctakes-clinical-pipeline-3.2.3-SNAPSHOT.jar>
[INFO]
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @
ctakes-clinical-pipeline ---
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @
ctakes-clinical-pipeline ---
[INFO] Installing
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target/ctakes-clinical-pipeline-3.2.3-SNAPSHOT.jar>
to
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[INFO] Installing
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to
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[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Temporal Information Extraction 3.2.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading:
http://repository.apache.org/snapshots/org/apache/ctakes/ctakes-sentdetect-cleartk/3.2.3-SNAPSHOT/maven-metadata.xml
Downloading:
http://repository.apache.org/snapshots/org/apache/ctakes/ctakes-sentdetect-cleartk/3.2.3-SNAPSHOT/ctakes-sentdetect-cleartk-3.2.3-SNAPSHOT.pom
[WARNING] The POM for
org.apache.ctakes:ctakes-sentdetect-cleartk:jar:3.2.3-SNAPSHOT is missing, no
dependency information available
Downloading:
http://repository.apache.org/snapshots/org/apache/ctakes/ctakes-sentdetect-cleartk/3.2.3-SNAPSHOT/ctakes-sentdetect-cleartk-3.2.3-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [2.257s]
[INFO] Apache cTAKES common type system .................. SUCCESS [7.014s]
[INFO] Apache cTAKES utils ............................... SUCCESS [2.521s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [0.499s]
[INFO] Apache cTAKES core ................................ SUCCESS [4.408s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [1.704s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [1.297s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [1.559s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [0.957s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.037s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [11.067s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [3.655s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [0.817s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [42.483s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [2.531s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [0.473s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [1.030s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [3.179s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [0.960s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [4.683s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [0.536s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [19.821s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [4.168s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [7.845s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [7.414s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [0.505s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [4.697s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [0.513s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [5.285s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [0.532s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [5.179s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.327s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [8.738s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [0.414s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [0.950s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [1.048s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [1.113s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [1.236s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [0.535s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [39.888s]
[INFO] Apache cTAKES YTEX UIMA ........................... SUCCESS [37.469s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [5.622s]
[INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [2.173s]
[INFO] Apache cTAKES YTEX Web ............................ SKIPPED
[INFO] Apache cTAKES Distribution ........................ SKIPPED
[INFO] Apache cTAKES Regression-test ..................... SKIPPED
[INFO] Apache cTAKES template filler ..................... SKIPPED
[INFO] ctakes-examples ................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4:24.568s
[INFO] Finished at: Sat Mar 12 11:50:27 UTC 2016
[INFO] Final Memory: 107M/915M
[INFO] ------------------------------------------------------------------------
Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal on project ctakes-temporal: Could not resolve
dependencies for project org.apache.ctakes:ctakes-temporal:jar:3.2.3-SNAPSHOT:
Could not find artifact
org.apache.ctakes:ctakes-sentdetect-cleartk:jar:3.2.3-SNAPSHOT in Nexus
(http://repository.apache.org/snapshots) -> [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/DependencyResolutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <goals> -rf :ctakes-temporal
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