See <https://builds.apache.org/job/ctakes-trunk-compiletest/792/changes>
Changes:
[clin] add parameters and code to do automatically add class-weights:
on Sharp data, with new-sent detector:
With class-wise weights:
Category:location_of freq:67374 weight:3.5372696
Category:-NONE- freq:238320 weight:1.0
Best model:
P R F1 #gold #system #correct
0.760 0.723 0.741 441 420 319 OVERALL
ParameterSettings{dataWriterClass=org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter,
configurationParameters=[ProbabilityOfKeepingANegativeExample, 1.0],
trainingArguments=[-s, 0, -c, 1.0]}
ConfusionMatrix{matrix={null=[location_of x 101], location_of=[null x 122,
location_of x 319]}}
Without class-wise weights:
Best model:
P R F1 #gold #system #correct
0.803 0.676 0.734 441 371 298 OVERALL
ParameterSettings{dataWriterClass=org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter,
configurationParameters=[ProbabilityOfKeepingANegativeExample, 1.0],
trainingArguments=[-s, 0, -c, 100.0]}
ConfusionMatrix{matrix={null=[location_of x 73], location_of=[null x 143,
location_of x 298]}}
------------------------------------------
[...truncated 11653 lines...]
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/stopWords.data>
(No such file or directory)
** Error: problem of opening/reading stop words file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/stopWords.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/nonInfoWords.data>
(No such file or directory)
** Error: problem of opening/reading non-Info words file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/nonInfoWords.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/conjunctionWord.data>
(No such file or directory)
** Error: problem of opening/reading conjunction words file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/conjunctionWord.data'.>
** ERR: problem of opening/reading diacritics file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/diacriticMap.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/diacriticMap.data>
(No such file or directory)
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/ligatureMap.data>
(No such file or directory)
** Error: problem of opening/reading ligature file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/ligatureMap.data'.>
** Error: problem of opening/reading symbol synonym file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/synonymMap.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/synonymMap.data>
(No such file or directory)
**Error: problem of opening/reading file
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/removeS.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/misc/removeS.data>
(No such file or directory)
** Error: problem of opening/reading Unicode symbol file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/symbolMap.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/symbolMap.data>
(No such file or directory)
** Error: problem of opening/reading Unicode file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/unicodeMap.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/unicodeMap.data>
(No such file or directory)
** Error: problem of opening/reading nonStripMap file:
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/nonStripMap.data'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/Unicode/nonStripMap.data>
(No such file or directory)
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/im.rul>
(No such file or directory)
**Error: problem of opening/reading file
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/im.rul'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/im.rul>
(No such file or directory)
**Error: problem of opening/reading file
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/im.rul'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/dm.rul>
(No such file or directory)
**Error: problem of opening/reading file
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/dm.rul'.>
Exception: java.io.FileNotFoundException:
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/data/rules/dm.rul>
(No such file or directory)
**Error: problem of opening/reading file
'<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal//data/rules/dm.rul'.>
25 Apr 2016 19:37:28 INFO LvgCmdApiResourceImpl - cd
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
25 Apr 2016 19:37:28 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
25 Apr 2016 19:37:28 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
25 Apr 2016 19:37:29 INFO SentenceDetector - Starting processing.
25 Apr 2016 19:37:29 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
25 Apr 2016 19:37:29 INFO LvgAnnotator - process(JCas)
25 Apr 2016 19:37:30 INFO ContextDependentTokenizerAnnotator - process(JCas)
25 Apr 2016 19:37:30 INFO POSTagger - process(JCas)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
Null value found in Feature(<Time-Class->, <NULL>)
25 Apr 2016 19:37:31 INFO EventTimeRelationAnnotatorTest - Relation:
RelationArgument
id: 0
argument: TimeMention
sofa: _InitialView
begin: 58
end: 66
id: 0
ontologyConceptArr: <null>
typeID: 0
segmentID: <null>
sentenceID: <null>
discoveryTechnique: 0
confidence: 0.0
polarity: 0
uncertainty: 0
conditional: false
generic: false
subject: <null>
historyOf: 0
originalText: <null>
date: <null>
time: <null>
timeClass: <null>
role: "Arg1"
participatesIn: <null>
RelationArgument
id: 0
argument: EventMention
sofa: _InitialView
begin: 67
end: 76
id: 0
ontologyConceptArr: <null>
typeID: 0
segmentID: <null>
sentenceID: <null>
discoveryTechnique: 0
confidence: 1.3807402
polarity: 0
uncertainty: 0
conditional: false
generic: false
subject: <null>
historyOf: 0
originalText: <null>
event: Event
id: 0
ontologyConcept: <null>
mentions: <null>
discoveryTechnique: 0
confidence: 0.0
conditional: false
generic: false
subject: <null>
polarity: 0
uncertainty: 0
historyOf: 0
properties: EventProperties
contextualModality: <null>
contextualAspect: <null>
permanence: <null>
category: <null>
aspect: <null>
docTimeRel: <null>
degree: <null>
polarity: 0
role: "Arg2"
participatesIn: <null>
Category: CONTAINS
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 27.797 sec
Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest
25 Apr 2016 19:37:35 INFO ClearNLPDependencyParserAE - using Morphy analysis?
true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
...........Java HotSpot(TM) 64-Bit Server VM warning: INFO:
os::commit_memory(0x0000000744000000, 409993216, 0) failed; error='Cannot
allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 409993216 bytes for committing
reserved memory.
# An error report file with more information is saved as:
#
<https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal/hs_err_pid23006.log>
Results :
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0
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[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [5.103s]
[INFO] Apache cTAKES common type system .................. SUCCESS [12.435s]
[INFO] Apache cTAKES utils ............................... SUCCESS [3.808s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [3.782s]
[INFO] Apache cTAKES core ................................ SUCCESS [36.361s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [1.819s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [5.521s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [1.634s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [3.569s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [3.522s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [18.464s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [5.879s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [7.005s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [34.227s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [5.325s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [2.112s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [6.758s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [2.377s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [3.284s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [2.247s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [1.834s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [6.520s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [29.923s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [23.273s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [7.840s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [2.076s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [6.740s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.876s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [9.164s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [1.637s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [11.477s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.295s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [7.956s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [1.895s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [2.749s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [2.546s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [2.903s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [11.756s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [1.741s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [10.588s]
[INFO] Apache cTAKES YTEX UIMA ........................... SUCCESS [9.731s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [8.113s]
[INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [55.314s]
[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: 7:02.327s
[INFO] Finished at: Mon Apr 25 19:37:38 UTC 2016
[INFO] Final Memory: 103M/777M
[INFO] ------------------------------------------------------------------------
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[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test (default-test) on
project ctakes-temporal: Execution default-test of goal
org.apache.maven.plugins:maven-surefire-plugin:2.12.1:test failed: The forked
VM terminated without saying properly goodbye. VM crash or System.exit called ?
-> [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/PluginExecutionException
[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]
channel stopped
