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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #195
Date Wed, 06 Nov 2013 18:52:34 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/195/changes>

Changes:

[tmill] Fix typo in method name and reference to it.

[tmill] Fixes CTAKES-257. Implements two different forms - Dependency Word (DW) and Grammatical
Relation and Word (GRW) from Nguyen et al. (2009) emnlp paper.

[tmill] Made escape method public.

[tmill] Remove commented out method.

[chenpei] CTAKES-253 - Didn't need an additional .length()>0 in NumTokenAdapter check since
Strings.isNullOrEmpty() does it already

[chenpei] CTAKES-251 - Infinite recursion in DrugMentionAnnotator.java Thanks Bruce.
Adding the temp patch for the interim while there will be a new drug module(s) coming soon...

[chenpei] CTAKES-150 - Apostrophe parsing is not thread safe because of global variable. 
Thanks Kim.

[chenpei] CTAKES-253 - YTEX ctakes patches port. Thanks Vijay Garla.
* ctakes-context-tokenizer\src\main\java\org\apache\ctakes\contexttokenizer\ae\ContextDependentTokenizerAnnotator.java

add null check: changed to avoid NPE in case BaseToken is null. Also ignore newline tokens
(they should be treated as whitespace). 
* ctakes-core\src\main\java\org\apache\ctakes\core\fsm\adapters\NumberTokenAdapter.java 
add null check: ignore empty numbertokens 
* ctakes-core\src\main\java\org\apache\ctakes\core\fsm\machine\DateFSM.java 
Modified to include years in dates

[chenpei] CTAKES-254 - Add empty string check Apostrophe in contraction breaks TokenizerPTB
CTAKES-256 - Add a test doc that contains various edge cases for regression testing

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[INFO] apache-ctakes-3.2.0-SNAPSHOT/resources/org/apache/ctakes already added, skipping
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[INFO] apache-ctakes-3.2.0-SNAPSHOT/resources/org/apache/ctakes/smokingstatus already added,
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[INFO] Building tar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-src.tar.gz>
[INFO] Building zip: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-src.zip>
[INFO] 
[INFO] --- maven-antrun-plugin:1.6:run (generate checksums for binary artifacts) @ ctakes-distribution
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[INFO] Executing tasks

main:
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-distribution ---
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-distribution/3.2.0-SNAPSHOT/ctakes-distribution-3.2.0-SNAPSHOT.pom
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-bin.tar.gz>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-distribution/3.2.0-SNAPSHOT/ctakes-distribution-3.2.0-SNAPSHOT-bin.tar.gz
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-bin.zip>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-distribution/3.2.0-SNAPSHOT/ctakes-distribution-3.2.0-SNAPSHOT-bin.zip
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-src.tar.gz>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-distribution/3.2.0-SNAPSHOT/ctakes-distribution-3.2.0-SNAPSHOT-src.tar.gz
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target/apache-ctakes-3.2.0-SNAPSHOT-src.zip>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-distribution/3.2.0-SNAPSHOT/ctakes-distribution-3.2.0-SNAPSHOT-src.zip
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[INFO] Building Apache cTAKES Regression-test 3.2.0-SNAPSHOT
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[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-regression-test ---
[INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target>
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[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-regression-test ---
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[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-regression-test
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[debug] execute contextualize
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[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-regression-test
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[debug] execute contextualize
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[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-regression-test
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[INFO] Compiling 1 source file to <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target/test-classes>
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[INFO] Tests are skipped.
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[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-regression-test ---
[INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target/ctakes-regression-test-3.2.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-regression-test
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[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target/ctakes-regression-test-3.2.0-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-regression-test/3.2.0-SNAPSHOT/ctakes-regression-test-3.2.0-SNAPSHOT.jar
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-regression-test/3.2.0-SNAPSHOT/ctakes-regression-test-3.2.0-SNAPSHOT.pom
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[INFO] Building Apache cTAKES template filler 3.2.0-SNAPSHOT
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[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-template-filler
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[INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/target/ctakes-template-filler-3.2.0-SNAPSHOT.jar>
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[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/target/ctakes-template-filler-3.2.0-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-template-filler/3.2.0-SNAPSHOT/ctakes-template-filler-3.2.0-SNAPSHOT.jar
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-template-filler/3.2.0-SNAPSHOT/ctakes-template-filler-3.2.0-SNAPSHOT.pom
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[INFO] ------------------------------------------------------------------------
[INFO] Building ctakes-examples 3.2.0-SNAPSHOT
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[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-examples ---
[INFO] Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target>
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-examples ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-examples ---
[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-examples ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-examples
---
[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-examples ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-examples ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-examples ---
[INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target/ctakes-examples-3.2.0-SNAPSHOT.jar>
[INFO] 
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-examples ---
[INFO] 
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-examples ---
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target/ctakes-examples-3.2.0-SNAPSHOT.jar>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-examples/3.2.0-SNAPSHOT/ctakes-examples-3.2.0-SNAPSHOT.jar
[INFO] Installing <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/pom.xml>
to /home/jenkins/jenkins-slave/maven-repositories/0/org/apache/ctakes/ctakes-examples/3.2.0-SNAPSHOT/ctakes-examples-3.2.0-SNAPSHOT.pom
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [34.472s]
[INFO] Apache cTAKES common type system .................. SUCCESS [21.662s]
[INFO] Apache cTAKES utils ............................... SUCCESS [55.166s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [19.109s]
[INFO] Apache cTAKES core ................................ SUCCESS [1:14.504s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [7.439s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [8.827s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [32.864s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [8.223s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [19.525s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [6.083s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [15.095s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [9.397s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [14.366s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [9.094s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [24.169s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [7.506s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [8.558s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [11.001s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [14.357s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [7.802s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [6.450s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [12.930s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [12.200s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [12.200s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [7.046s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [8.488s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [4.752s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [9.837s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [14.463s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [10.854s]
[INFO] Apache cTAKES Resources pad-term-spotter-res ...... SUCCESS [5.713s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [10.357s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [11.085s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [9.001s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [11.318s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [13.073s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [6.888s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [21.510s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [7.911s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [3:01.056s]
[INFO] Apache cTAKES Regression-test ..................... SUCCESS [10.467s]
[INFO] Apache cTAKES template filler ..................... SUCCESS [20.363s]
[INFO] ctakes-examples ................................... SUCCESS [1.628s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 25:39.374s
[INFO] Finished at: Wed Nov 06 18:51:33 UTC 2013
[INFO] Final Memory: 47M/410M
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Build step 'Deploy artifacts to Maven repository' changed build result to FAILURE

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