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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #1150
Date Sun, 26 Nov 2017 16:33:51 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/1150/display/redirect?page=changes>

Changes:

[seanfinan] CTAKES-485 : Add thread safe default clinical pipeline

------------------------------------------
[...truncated 508.64 KB...]
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "E-EXAMPLE A-EXAMPLE U-EXAMPLE X-EXAMPLE AGRO-EXAMPLE ANTE-EXAMPLE ANTI-EXAMPLE
ARCH-EXAMPLE BE-EXAMPLE BI-EXAMPLE BIO-EXAMPLE CO-EXAMPLE COUNTER-EXAMPLE CROSS-EXAMPLE CYBER-EXAMPLE
DE-EXAMPLE ECO-EXAMPLE EXAMPLE-ESQUE EXAMPLE-ETTE EX-EXAMPLE EXTRA-EXAMPLE EXAMPLE-FEST EXAMPLE-FOLD
EXAMPLE-GATE INTER-EXAMPLE INTRA-EXAMPLE EXAMPLE-ITIS EXAMPLE-LESS MACRO-EXAMPLE MEGA-EXAMPLE
MICRO-EXAMPLE MID-EXAMPLE MINI-EXAMPLE MM-HM MM-MM EXAMPLE-MOST MULTI-EXAMPLE NEO-EXAMPLE
NON-EXAMPLE O-KAY EXAMPLE-O-TORIUM OVER-EXAMPLE PAN-EXAMPLE PARA-EXAMPLE PERI-EXAMPLE POST-EXAMPLE
PRE-EXAMPLE PRO-EXAMPLE PSEUDO-EXAMPLE QUASI-EXAMPLE EXAMPLE-RAMA RE-EXAMPLE SEMI-EXAMPLE
SUB-EXAMPLE SUPER-EXAMPLE TRI-EXAMPLE UH-HUH UH-OH ULTRA-EXAMPLE UN-EXAMPLE UNI-EXAMPLE VICE-EXAMPLE
EXAMPLE-WISE SUB-EXAMPLE-WISE ULTRA-EXAMPLE-FEST   "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 65 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "e.g.abc e.g. abc injury.[16]  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 12 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "Mr. Smith! Dr. Smith! Ste. 6! sign e.g. edema! 210 A.D.! injury.[16][17]
 "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 24 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "w3c.f 1.0 version 1.0.3f Mrs.? Mr.! bldg.: Stabile  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 15 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "ClinicalNLP@mayo.edu http://www.mayoclinic.org http://mayo.edu  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 3 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "http://www.islamonline.net/Arabic/news/2004-12/05/images/pic05b.jpg http://www.mofa.gov.sa/detail.asp?InNewsItemID=59090&InTemplateKey=print
rayhanenajib@menara.ma  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 3 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "he ... she  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 3 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "5-1212 1-800-555-1212 55901-9999  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 3 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "80's P'yongyang 'Assad 2000's  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 4 token(s) using assertions.
26 Nov 2017 16:32:00  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - -
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Test PTB Tokenizer for string (shown
here in quotes) "80's-esque  "
26 Nov 2017 16:32:00  INFO TokenizerAnnotatorPTBTests - Verified 1 token(s) using assertions.
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.203 sec
Running org.apache.ctakes.core.ae.SentenceDetectorAnnotatorTest
26 Nov 2017 16:32:01  INFO CDASegmentAnnotator - Reading Section File org/apache/ctakes/core/sections/ccda_sections.txt
26 Nov 2017 16:32:01  INFO CDASegmentAnnotator - Warning: Skipped reading sections config
row: []
26 Nov 2017 16:32:01  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
26 Nov 2017 16:32:01  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:01  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
26 Nov 2017 16:32:01  INFO SentenceDetector - Starting processing.
26 Nov 2017 16:32:01  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
26 Nov 2017 16:32:01  INFO SentenceDetector - Starting processing.
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec
Running org.apache.ctakes.core.ae.SimpleSegmentAnnotatorTests
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.251 sec
Running org.apache.ctakes.core.ci.HyphenTextModifierImplTests
OK to see the following 4 had been written to stderr:
Orig: Non  Hodgkin's the x  ray without any non small  cell complications.
Non-Hodgkin Orig: 0-12 New: 0-11
x-ray Orig: 19-25 New: 18-23
non-small-cell Orig: 38-53 New: 36-50
Orig: Non Hodgkin's the x ray without any non small cell complications.
New:  Non-Hodgkin's the x-ray without any non-small-cell complications.
Non-Hodgkin Orig: 0-11 New: 0-11
x-ray Orig: 18-23 New: 18-23
non-small-cell Orig: 36-50 New: 36-50
UNSUPPORTED: TextModification with offset changes.
UNSUPPORTED: TextModification with offset changes.
UNSUPPORTED: TextModification with offset changes.
New:  (new text not generated, see previous messages)
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec

Results :

Tests run: 6, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[JENKINS] Archiving disabled
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ctakes-gui 4.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-gui ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-gui ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-gui ---
[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-gui ---
[INFO] Compiling 78 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/target/classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[4,16]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java>:[355,18]
error: cannot find symbol
[ERROR]   symbol:   method addUserPackage(String)
  location: variable reader of type PiperFileReader
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[94,37]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[120,9]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[INFO] 4 errors 
[INFO] -------------------------------------------------------------
[JENKINS] Archiving disabled
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [4.742s]
[INFO] ctakes-gui-res .................................... SUCCESS [3.891s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [2.440s]
[INFO] Apache cTAKES common type system .................. SUCCESS [7.645s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.443s]
[INFO] Apache cTAKES core ................................ SUCCESS [1:06.634s]
[INFO] ctakes-gui ........................................ FAILURE [2.531s]
[INFO] Apache cTAKES Resources pos-tagger ................ SKIPPED
[INFO] Apache cTAKES part-of-speech tagger ............... SKIPPED
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SKIPPED
[INFO] Apache cTAKES chunker ............................. SKIPPED
[INFO] Apache cTAKES document preprocessor ............... SKIPPED
[INFO] Apache cTAKES Resources dictionary-lookup ......... SKIPPED
[INFO] Apache cTAKES dictionary lookup ................... SKIPPED
[INFO] Apache cTAKES context dependent tokenizer ......... SKIPPED
[INFO] Apache cTAKES Resources lvg ....................... SKIPPED
[INFO] Apache cTAKES LVG lexical tools ................... SKIPPED
[INFO] Apache cTAKES Resources ne-contexts ............... SKIPPED
[INFO] Apache cTAKES named entity contexts ............... SKIPPED
[INFO] Apache cTAKES Resources constituency-parser ....... SKIPPED
[INFO] Apache cTAKES Constituency Parser ................. SKIPPED
[INFO] Apache cTAKES Resources coreference ............... SKIPPED
[INFO] Apache cTAKES Resources temporal .................. SKIPPED
[INFO] Apache cTAKES Resources relation-extractor ........ SKIPPED
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res  SKIPPED
[INFO] Apache cTAKES dictionary lookup fast .............. SKIPPED
[INFO] Apache cTAKES Resources assertion ................. SKIPPED
[INFO] Apache cTAKES Resources dependency-parser ......... SKIPPED
[INFO] Apache cTAKES Dependency Parser ................... SKIPPED
[INFO] Apache cTAKES Assertion ........................... SKIPPED
[INFO] ctakes-clinical-pipeline-res ...................... SKIPPED
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
[INFO] Apache cTAKES Relation Extractor .................. SKIPPED
[INFO] Apache cTAKES Temporal Information Extraction ..... SKIPPED
[INFO] Apache cTAKES CoReference Resolver ................ SKIPPED
[INFO] Apache cTAKES Resources drug-ner .................. SKIPPED
[INFO] Apache cTAKES Drug NER ............................ SKIPPED
[INFO] Apache cTAKES Resources side-effect ............... SKIPPED
[INFO] Apache cTAKES Side Effects ........................ SKIPPED
[INFO] Apache cTAKES Resources smoking-status ............ SKIPPED
[INFO] Apache cTAKES Smoking Status ...................... SKIPPED
[INFO] Apache cTAKES Resources assertion-zoner ........... SKIPPED
[INFO] Apache cTAKES Assertion's zoner ................... SKIPPED
[INFO] ctakes-examples-res ............................... SKIPPED
[INFO] ctakes-examples ................................... SKIPPED
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SKIPPED
[INFO] Apache cTAKES YTEX ................................ SKIPPED
[INFO] Apache cTAKES YTEX UIMA ........................... 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] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:44.886s
[INFO] Finished at: Sun Nov 26 16:33:03 UTC 2017
[INFO] Final Memory: 46M/654M
[INFO] ------------------------------------------------------------------------
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Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.4:compile
(default-compile) on project ctakes-gui: Compilation failure: Compilation failure:
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[4,16]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java>:[355,18]
error: cannot find symbol
[ERROR] symbol:   method addUserPackage(String)
[ERROR] location: variable reader of type PiperFileReader
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[94,37]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[ERROR] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java>:[120,9]
SwingUtilities2 is internal proprietary API and may be removed in a future release
[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-gui
Sending e-mails to: notifications@ctakes.apache.org
channel stopped
[ctakes-trunk-compiletest] $ /bin/bash -xe /tmp/jenkins1415190492711144383.sh
+ rm -fr '/tmp/ctakes-*'

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