See
<https://builds.apache.org/job/ctakes-trunk-package/535/display/redirect?page=changes>
Changes:
[seanfinan] Mixed Versions : trying to get rid of version conflicts. 3rd party
dependencies are bringing in conflicting 4th-to-3rd party dependencies
[seanfinan] TODO : dependencies yadda yadda
[seanfinan] TODO : remove unnecessary dependencies
[seanfinan] TODO : remove unwanted dependencies
[seanfinan] TODO : Pom / Dependencies should be simplified
[james-masanz] CTAKES-330 - autoload pipeline if it exists to save new user a
step
[james-masanz] CTAKES-178 don't allow space(s) in the "number" attribute of a
MedicationStrength.
[james-masanz] CTAKES-39 Update mini LVG-style dictionary in ctakes-lvg-res to
hsqldb 2.3.4 format
[seanfinan] Temporary!!! Commented tests until hsqldb versions are synchronized
[seanfinan] updated hsqldb version
[seanfinan] ctakes-424 : improved source vocabulary use
------------------------------------------
[...truncated 932.92 KB...]
[delete] Deleting: /tmp/ytex1440355415.sql
[delete] Deleting: /tmp/ytex1752072325use.sql
init:
init.conn:
[copy] Copying 1 file to /tmp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] 2017-03-29 11:59:46,396 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2017-03-29 11:59:46,403 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword
(stopword) values (?)
[java] 2017-03-29 11:59:46,863 INFO hsqldb.db..ENGINE - open start -
state not modified
[java] 2017-03-29 11:59:46,908 INFO hsqldb.db..ENGINE - dataFileCache
open start
[java] 2017-03-29 11:59:46,922 INFO hsqldb.db..ENGINE - dataFileCache
open end
[java] 2017-03-29 11:59:46,999 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
[java] 2017-03-29 11:59:47,011 INFO hsqldb.db..ENGINE - dataFileCache
commit start
[java] 2017-03-29 11:59:47,039 INFO hsqldb.db..ENGINE - dataFileCache
commit end
[java] 2017-03-29 11:59:47,049 INFO hsqldb.db..ENGINE - Database closed
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex739246523.sql
29 Mar 2017 11:59:47 INFO ENGINE - open start - state not modified
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache open start
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex739246523.sql
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache commit start
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache commit end
29 Mar 2017 11:59:47 INFO ENGINE - Database closed
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: /tmp/ytex739246523.sql
[delete] Deleting: /tmp/ytex350208584use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex1179251641.sql
29 Mar 2017 11:59:47 INFO ENGINE - open start - state not modified
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache open start
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache open end
[sql] Executing resource: /tmp/ytex1179251641.sql
[sql] Failed to execute: CREATE CACHED TABLE classifier_eval_svm (
classifier_eval_id int not null , cost double DEFAULT '0', weight varchar(50),
degree int DEFAULT '0', gamma double DEFAULT '0', kernel int NULL,
supportVectors int null, vcdim double null )
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache commit start
29 Mar 2017 11:59:47 INFO ENGINE - dataFileCache commit end
29 Mar 2017 11:59:47 INFO ENGINE - Database closed
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [13.766s]
[INFO] ctakes-gui-res .................................... SUCCESS [6.044s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [4.371s]
[INFO] Apache cTAKES common type system .................. SUCCESS [15.736s]
[INFO] Apache cTAKES utils ............................... SUCCESS [4.278s]
[INFO] Apache cTAKES core ................................ SUCCESS [14.127s]
[INFO] ctakes-gui ........................................ SUCCESS [10.484s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [4.737s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [4.963s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [3.712s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [5.715s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [4.955s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [20.640s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [8.669s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [6.489s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [17.748s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [7.051s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [9.097s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [3.753s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [8.850s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [5.810s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [7.620s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [4.111s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [20.385s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [14.343s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [11.139s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [5.470s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [10.407s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [5.220s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [5.437s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [4.289s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [1:20.490s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [1:05.348s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [3.877s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [32.938s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [4.185s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [7.983s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [4.038s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [8.620s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [5.139s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [4.470s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [4.295s]
[INFO] Apache cTAKES YTEX ................................ FAILURE [45.398s]
[INFO] Apache cTAKES YTEX UIMA ........................... SKIPPED
[INFO] ctakes-clinical-pipeline-res ...................... SKIPPED
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
[INFO] ctakes-examples-res ............................... SKIPPED
[INFO] ctakes-examples ................................... 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: 12:47.234s
[INFO] Finished at: Wed Mar 29 11:59:59 UTC 2017
[INFO] Final Memory: 101M/868M
[INFO] ------------------------------------------------------------------------
Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-antrun-plugin:1.6:run (generate-test-config) on
project ctakes-ytex: An Ant BuildException has occured: The following error
occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/build-setup.xml>:149:
The following error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/build.xml>:552:
The following error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/build.xml>:441:
java.sql.SQLSyntaxErrorException: incompatible data types in combination
[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/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <goals> -rf :ctakes-ytex
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Compressed 123.83 MB of artifacts by 99.0% relative to #534
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No prior successful build to compare, so performing full copy of artifacts
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