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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #473
Date Mon, 28 Apr 2014 16:35:53 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/473/changes>

Changes:

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[vjapache] #CTAKES-253, CTAKES-292 ytex merge

[tmill] Fixed reference to non-official model, and switched lvg to not post lemmas.

[tmill] CTAKES-297: First pass at some default pipelines. Full dictionary pipeline still WIP
but basics are set up.

[tmill] CTAKES-197: Update Dictionary module to java 7 (and java 5 and 6 while I was at it).

[tmill] CTAKES-297: Standardized Lvg static factory method by catching URI exception.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for ChunkAdjuster.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for Chunker.

[tmill] CTAKES-297: Added method for getting default descriptor & model-specifying descriptor
for POSTagger.

[tmill] CTAKES-297: Added method for getting default descriptor for ContextDependentTokenizerAnnotator.

[tmill] CTAKES-297: Added method for getting descriptor for LvgAnnotator. Added unit test.
Made some parameters optional with sane defaults.

[tmill] CTAKES-297: Added method for getting descriptor for TokenizerAnnotatorPTB

[tmill] CTAKES-16: Fix TokenizerAnnotatorPTB to use UIMAFit select instead of iterator.

[tmill] CTAKES-297: Added methods for getting descriptors for SentenceDetector.

[tmill] CTAKES-297: Added methods for getting descriptors for SimpleSegmentAnnotator.

[tmill] CTAKES-16: Fix to use UIMAFit select instead of iterator.

[dligach] added note name to the output

[chenpei] CTAKES-286 - Remove no longer used pad term spotter and related resources.
Full Thread here: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201402.mbox/%3C924DE05C19409B438EB81DE683A942D91066CE4B%40CHEXMBX1A.CHBOSTON.ORG%3E

[chenpei] CTAKES-294
Wrong PROJECT_ATTR in ctakes-core/resources/launch/UIMA_CVD--core.launch
Thanks  iglewski for identifying the issue.

[dligach] got rid of the loop and replaced it with an iterator

[dligach] now using cumulative probability as a feature

[tmill] CTAKES-295: Update CopyAnnotator to use UimaFit-style configuration.

[tmill] CTAKES-295: Update ChunkAdjuster to use UimaFit-style configuration parameters.

[tmill] CTAKES-197: Used java 7 style generics w/o unnecessary type specifications to remove
warnings.

[tmill] Minor cleanup -- added comment to undocumented empty method.

[tmill] CTAKES-295: Updated to use uima-fit configuration parameters.

[tmill] CTAKES-295: Update pos tagger to use uimafit configuratino parameters, some other
minor java 7 updates.

[tmill] CTAKES-295: Update ContextDependentTokenizerAnnotator to UIMAFit-style methods and
Java >=6 overrides.

[tmill] CTAKES-295: Update LVG to use UIMAFit style configuration parameters and resources
-- changes some arguments to being optional with sane default values.

[dligach] added event-time relations where arg1=event and arg2=time

[clin] fix a typo in CheckSpecialWordRelatinExtractor, which is used for event-time relation
discovery.

[clin] added three more feature extractors for event-time relation discovery.

[dligach] added event-time relations

[dligach] Added a class to display duration information for event arguments of event-event
relations. Did some refactoring for EventTimeDurationStatistics related to this.

[dligach] output durations in days (instead of normalized seconds)

[clin] fix a dependency error. added dependency distance as a feature

[clin] add transitive closure for event-time relation discovery. Closure was added for both
training and testing, and both gold relations and system predictions.

[dligach] only print contexts of up to 80 characters

[tmill] CTAKES-197: Java 7 updates (mainly type/generic stuff, some try-with-resources) to
LVG Annotator.

[dligach] now including relation context too

[tmill] Fixed order of annotators in TokensAndSentencesTAE descriptor.

[dligach] dump duration of event and time arguments of time-event relations  to a file

[tmill] CTAKES-295: Updated TokenizerAnnotatorPTB to use UIMAFit configuration.

[tmill] CTAKES-295: Updated CDA segmenter to use uimafit configurations.

[tmill] CTAKES-197: Updates for java 7 to remove warnings.

[tmill] CTAKES-295: Updates SentenceDetector to use UimaFit-style configuration.

[tmill] CTAKES-70: Adds unit test for sentence detector.

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Results :

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[INFO] 
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[INFO] Generating source...
[INFO] parsing a schema...
[INFO] compiling a schema...
[INFO] org/apache/ctakes/jdl/schema/xdl/ColumnCsvLoadType.java
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[INFO] org/apache/ctakes/jdl/schema/xdl/CsvLoadType.java
[INFO] org/apache/ctakes/jdl/schema/xdl/JdbcType.java
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[INFO] org/apache/ctakes/jdl/schema/xdl/ObjectFactory.java
[INFO] org/apache/ctakes/jdl/schema/xdl/XmlLoadType.java
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[debug] execute contextualize
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[JENKINS] Archiving disabled
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [20.962s]
[INFO] Apache cTAKES common type system .................. SUCCESS [11.655s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.115s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [2.067s]
[INFO] Apache cTAKES core ................................ SUCCESS [18.174s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [10.770s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.894s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [1.816s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [4.070s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [3.740s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [1.897s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [28.668s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [3.733s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [3.186s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [8.286s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [1.697s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [4.457s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [2.231s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [3.447s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [4.444s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [1.747s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [9.721s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [38.720s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [9.867s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [4.796s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [1.997s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [4.952s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [2.231s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [5.631s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [1.890s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [6.765s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.945s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [2.273s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [3.098s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [5.589s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [2.038s]
[INFO] Apache cTAKES YTEX ................................ FAILURE [15.327s]
[INFO] Apache cTAKES YTEX UIMA ........................... SKIPPED
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
[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: 5:39.829s
[INFO] Finished at: Mon Apr 28 16:35:19 UTC 2014
[INFO] Final Memory: 68M/183M
[INFO] ------------------------------------------------------------------------
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[ERROR] Failed to execute goal org.apache.maven.plugins:maven-dependency-plugin:2.6:copy-dependencies
(copy-dependencies) on project ctakes-ytex: Artifact has not been packaged yet. When used
on reactor artifact, copy should be executed after packaging: see MDEP-187. -> [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 :ctakes-ytex
Sending e-mails to: notifications@ctakes.apache.org vngarla@gmail.com
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