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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #788
Date Thu, 14 Apr 2016 14:36:29 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/788/changes>

Changes:

[clin] enable "test-on-train" parameter.
remove timex-induced relations

------------------------------------------
[...truncated 12716 lines...]
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'.>
14 Apr 2016 14:35:37  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
14 Apr 2016 14:35:37  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Apr 2016 14:35:37  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
14 Apr 2016 14:35:38  INFO SentenceDetector - Starting processing.
14 Apr 2016 14:35:38  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Apr 2016 14:35:38  INFO LvgAnnotator - process(JCas)
14 Apr 2016 14:35:38  INFO ContextDependentTokenizerAnnotator - process(JCas)
14 Apr 2016 14:35:38  INFO POSTagger - process(JCas)
14 Apr 2016 14:35:38  INFO BackwardsTimeAnnotatorTest - Event: recently
14 Apr 2016 14:35:38  INFO BackwardsTimeAnnotatorTest - Event: 6 months ago
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.493 sec
Running org.apache.ctakes.temporal.ae.DocTimeRelAnnotatorTest
14 Apr 2016 14:35:41  INFO ClearNLPDependencyParserAE - using Morphy analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
14 Apr 2016 14:35:51  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
14 Apr 2016 14:35:51  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
14 Apr 2016 14:35:51  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file
= /tmp/lvg.properties
14 Apr 2016 14:35:51  INFO LvgCmdApiResourceImpl -   config file absolute path = /tmp/lvg.properties
14 Apr 2016 14:35:51  INFO LvgCmdApiResourceImpl - cwd = <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
14 Apr 2016 14:35:51  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
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'.>
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'.>
14 Apr 2016 14:35:51  INFO LvgCmdApiResourceImpl - cd <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-temporal>
14 Apr 2016 14:35:51  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Apr 2016 14:35:51  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
14 Apr 2016 14:35:52  INFO SentenceDetector - Starting processing.
14 Apr 2016 14:35:52  INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Apr 2016 14:35:52  INFO LvgAnnotator - process(JCas)
14 Apr 2016 14:35:52  INFO ContextDependentTokenizerAnnotator - process(JCas)
14 Apr 2016 14:35:52  INFO POSTagger - process(JCas)
14 Apr 2016 14:35:52  INFO DocTimeRelAnnotatorTest - Event: old DocTimeRel:OVERLAP
14 Apr 2016 14:35:52  INFO DocTimeRelAnnotatorTest - Event: referred DocTimeRel:BEFORE
14 Apr 2016 14:35:52  INFO DocTimeRelAnnotatorTest - Event: diagnosed DocTimeRel:BEFORE
14 Apr 2016 14:35:52  INFO DocTimeRelAnnotatorTest - Event: cancer DocTimeRel:OVERLAP
14 Apr 2016 14:35:52  INFO DocTimeRelAnnotatorTest - Event: blood DocTimeRel:OVERLAP
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.69 sec
Running org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest
14 Apr 2016 14:35:55  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(0x000000072fd80000,
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_pid4985.log>

Results :

Tests run: 2, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[JENKINS] Archiving disabled
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [4.850s]
[INFO] Apache cTAKES common type system .................. SUCCESS [10.773s]
[INFO] Apache cTAKES utils ............................... SUCCESS [2.704s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [1.364s]
[INFO] Apache cTAKES core ................................ SUCCESS [31.399s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [1.661s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [4.647s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [1.279s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [2.187s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [2.918s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [17.832s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [3.609s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [3.850s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [1:01.562s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [3.756s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [1.384s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [3.309s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [1.471s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [2.045s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [1.408s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [1.234s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [3.801s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [23.496s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [8.477s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [8.637s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [1.400s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [5.374s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.340s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [6.576s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [2.192s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [6.702s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [1.748s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [5.684s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [1.343s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.922s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [1.310s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res  SUCCESS [2.575s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [9.157s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [1.267s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [7.140s]
[INFO] Apache cTAKES YTEX UIMA ........................... SUCCESS [7.363s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [4.992s]
[INFO] Apache cTAKES Temporal Information Extraction ..... FAILURE [50.100s]
[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: 6:03.182s
[INFO] Finished at: Thu Apr 14 14:35:57 UTC 2016
[INFO] Final Memory: 110M/648M
[INFO] ------------------------------------------------------------------------
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Waiting for Jenkins to finish collecting data
[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
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