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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: cTAKES-trunk-Java-1.8 » Apache cTAKES YTEX #21
Date Wed, 08 Nov 2017 16:53:43 GMT
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/21/display/redirect>

------------------------------------------
[...truncated 43.94 KB...]
     [echo] jdl.format examples/fracture_demo.xml
     [echo] jdl.data examples/fracture_demo.txt
     [echo] umls.prefix 
     [copy] Copying 1 file to /tmp
     [java] 2017-11-08 16:46:27,469 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter
9 encapsulator 65534
     [java] 2017-11-08 16:46:27,479 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - insert
into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
     [java] 2017-11-08 16:46:28,061 INFO  hsqldb.db..ENGINE  - open start - state not modified
     [java] 2017-11-08 16:46:28,141 INFO  hsqldb.db..ENGINE  - dataFileCache open start
     [java] 2017-11-08 16:46:28,160 INFO  hsqldb.db..ENGINE  - dataFileCache open end
     [java] 2017-11-08 16:46:28,252 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,254 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,255 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,256 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,258 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,259 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,261 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,263 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,265 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,266 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,268 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,270 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,272 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,272 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,273 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-11-08 16:46:28,274 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
31 rows total
     [java] 2017-11-08 16:46:28,435 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
     [java] 2017-11-08 16:46:28,653 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
     [java] 2017-11-08 16:46:28,781 INFO  hsqldb.db..ENGINE  - Database closed

jdbc.sqlcmd:
     [echo] db.schemaPUBLIC
     [echo] umls.schema ${db.schema}
     [echo] umls.catalog 
     [echo] execute ./hsql/uima/fracture_demo.sql
     [copy] Copying 1 file to /tmp
     [echo] executing /tmp/ytex1328227159.sql
08 Nov 2017 16:46:29  INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:29  INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:29  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex1328227159.sql
08 Nov 2017 16:46:29  INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:29  INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:29  INFO ENGINE - Database closed
      [sql] 2 of 2 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex1328227159.sql
   [delete] Deleting: /tmp/ytex1315143500use.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] 2017-11-08 16:46:34,191 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter
44 encapsulator 65534
     [java] 2017-11-08 16:46:34,200 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - insert
into PUBLIC.ref_stopword (stopword) values (?)
     [java] 2017-11-08 16:46:34,731 INFO  hsqldb.db..ENGINE  - open start - state not modified
     [java] 2017-11-08 16:46:34,817 INFO  hsqldb.db..ENGINE  - dataFileCache open start
     [java] 2017-11-08 16:46:34,845 INFO  hsqldb.db..ENGINE  - dataFileCache open end
     [java] 2017-11-08 16:46:35,009 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
360 rows total
     [java] 2017-11-08 16:46:35,145 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
     [java] 2017-11-08 16:46:35,371 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
     [java] 2017-11-08 16:46:35,482 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/ytex1264790108.sql
08 Nov 2017 16:46:36  INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex1264790108.sql
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:36  INFO ENGINE - Database closed
      [sql] 22 of 22 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex1264790108.sql
   [delete] Deleting: /tmp/ytex2147318110use.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/ytex1773679046.sql
08 Nov 2017 16:46:36  INFO ENGINE - open start - state not modified
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache open start
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex1773679046.sql
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache commit start
08 Nov 2017 16:46:36  INFO ENGINE - dataFileCache commit end
08 Nov 2017 16:46:37  INFO ENGINE - Database closed
      [sql] 52 of 52 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex1773679046.sql
   [delete] Deleting: /tmp/ytex1549224809use.sql

kernel.all:

all:
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory: <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/target/surefire-reports>

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2017-11-08 16:46:37,929 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66:
startup date [Wed Nov 08 16:46:37 UTC 2017]; root of context hierarchy
2017-11-08 16:46:37,985 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:38,171 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:38,180 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Overriding bean definition for bean 'kernelApplicationContext': replacing [Generic bean:
class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false;
lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false;
factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext];
scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true;
primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 16:46:38,199 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 16:46:38,262 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111:
startup date [Wed Nov 08 16:46:38 UTC 2017]; root of context hierarchy
2017-11-08 16:46:38,264 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 16:46:38,466 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 16:46:38,493 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 16:46:38,653 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 16:46:38,654 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:38,654 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 16:46:38,709 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace:
defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-11-08 16:46:38,752 INFO  org.springframework.beans.factory.config.PropertiesFactoryBean
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:39,446 INFO  org.hibernate.annotations.common.Version  - HCANN000001: Hibernate
Commons Annotations {4.0.2.Final}
2017-11-08 16:46:39,452 INFO  org.hibernate.Version  - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 16:46:39,454 INFO  org.hibernate.cfg.Environment  - HHH000206: hibernate.properties
not found
2017-11-08 16:46:39,455 INFO  org.hibernate.cfg.Environment  - HHH000021: Bytecode provider
name : javassist
2017-11-08 16:46:40,161 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-11-08 16:46:40,255 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-11-08 16:46:40,268 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-11-08 16:46:40,538 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-11-08 16:46:40,580 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-11-08 16:46:40,690 INFO  hsqldb.db..ENGINE  - Database closed
2017-11-08 16:46:40,823 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-11-08 16:46:40,860 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-11-08 16:46:40,861 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-11-08 16:46:40,895 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 16:46:41,004 INFO  org.hibernate.engine.transaction.internal.TransactionFactoryInitiator
 - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 16:46:41,009 INFO  org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory  -
HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 16:46:41,152 INFO  org.hibernate.cache.spi.UpdateTimestampsCache  - HHH000250:
Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 16:46:41,156 INFO  org.hibernate.cache.internal.StandardQueryCache  - HHH000248:
Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 16:46:41,743 INFO  org.springframework.orm.hibernate4.HibernateTransactionManager
 - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory
for HibernateTransactionManager
2017-11-08 16:46:41,910 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace:
defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-11-08 16:46:42,469 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-11-08 16:46:42,520 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-11-08 16:46:42,638 INFO  hsqldb.db..ENGINE  - Database closed
2017-11-08 16:46:42,739 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.056 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-11-08 16:46:43,308 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2344fc66:
startup date [Wed Nov 08 16:46:43 UTC 2017]; root of context hierarchy
2017-11-08 16:46:43,370 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:43,557 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-11-08 16:46:43,566 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Overriding bean definition for bean 'kernelApplicationContext': replacing [Generic bean:
class [org.springframework.context.support.ClassPathXmlApplicationContext]; scope=; abstract=false;
lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true; primary=false;
factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in URL [jar:file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
with [Generic bean: class [org.springframework.context.support.ClassPathXmlApplicationContext];
scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; autowireCandidate=true;
primary=false; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null;
defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]>
2017-11-08 16:46:43,584 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-11-08 16:46:43,658 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@1f0f1111:
startup date [Wed Nov 08 16:46:43 UTC 2017]; root of context hierarchy
2017-11-08 16:46:43,661 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-11-08 16:46:43,890 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-11-08 16:46:43,912 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-11-08 16:46:44,054 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-11-08 16:46:44,055 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:44,055 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-11-08 16:46:44,091 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace:
defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-11-08 16:46:44,129 INFO  org.springframework.beans.factory.config.PropertiesFactoryBean
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-11-08 16:46:44,859 INFO  org.hibernate.annotations.common.Version  - HCANN000001: Hibernate
Commons Annotations {4.0.2.Final}
2017-11-08 16:46:44,882 INFO  org.hibernate.Version  - HHH000412: Hibernate Core {4.2.6.Final}
2017-11-08 16:46:44,887 INFO  org.hibernate.cfg.Environment  - HHH000206: hibernate.properties
not found
2017-11-08 16:46:44,891 INFO  org.hibernate.cfg.Environment  - HHH000021: Bytecode provider
name : javassist
2017-11-08 16:46:45,599 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-11-08 16:46:45,698 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-11-08 16:46:45,709 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-11-08 16:46:45,959 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-11-08 16:46:46,015 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-11-08 16:46:46,150 INFO  hsqldb.db..ENGINE  - Database closed
2017-11-08 16:46:46,283 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-11-08 16:46:46,323 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-11-08 16:46:46,324 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-11-08 16:46:46,361 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-11-08 16:46:46,483 INFO  org.hibernate.engine.transaction.internal.TransactionFactoryInitiator
 - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-11-08 16:46:46,491 INFO  org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory  -
HHH000397: Using ASTQueryTranslatorFactory
2017-11-08 16:46:46,641 INFO  org.hibernate.cache.spi.UpdateTimestampsCache  - HHH000250:
Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-11-08 16:46:46,646 INFO  org.hibernate.cache.internal.StandardQueryCache  - HHH000248:
Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-11-08 16:46:47,259 INFO  org.springframework.orm.hibernate4.HibernateTransactionManager
 - Using DataSource [org.apache.commons.dbcp.BasicDataSource@5b22b970] of Hibernate SessionFactory
for HibernateTransactionManager
2017-11-08 16:46:47,434 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@63475ace:
defining beans [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2017-11-08 16:46:47,611 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-11-08 16:46:47,653 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-11-08 16:46:47,771 INFO  hsqldb.db..ENGINE  - Database closed
2017-11-08 16:46:47,872 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@568bf312:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.791 sec <<< FAILURE!
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.429 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-11-08 16:46:51,245 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter 44
encapsulator 65534
2017-11-08 16:46:51,272 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter 59
encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.456 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.575 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.345 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.579 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.467 sec

Results :

Tests in error: 
  testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to initialize group
definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml],
factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>:
Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException:
Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods
  testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to initialize group
definition. Group resource name [classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml],
factory key [kernelApplicationContext]; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'kernelApplicationContext' defined in URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>:
Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException:
Could not instantiate bean class [org.springframework.context.support.ClassPathXmlApplicationContext]:
Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'gramMatrixExporter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.xml]:
Initialization of bean failed; nested exception is org.springframework.beans.FatalBeanException:
Failed to obtain BeanInfo for class [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
nested exception is java.beans.IntrospectionException: type mismatch between read and write
methods

Tests run: 36, Failures: 0, Errors: 2, Skipped: 4

[JENKINS] Recording test results
[JENKINS] Archiving disabled

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