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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 #9
Date Mon, 02 Oct 2017 21:39:51 GMT
See <https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/9/display/redirect>

------------------------------------------
[...truncated 51.76 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] 2017-10-02 21:38:08,028 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter
9 encapsulator 65534
     [java] 2017-10-02 21:38:08,038 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - insert
into PUBLIC.fracture_demo (site_id,note_text,fracture,note_set) values (?,?,?,?)
     [java] 2017-10-02 21:38:08,614 INFO  hsqldb.db..ENGINE  - open start - state not modified
     [java] 2017-10-02 21:38:08,717 INFO  hsqldb.db..ENGINE  - dataFileCache open start
     [java] 2017-10-02 21:38:08,741 INFO  hsqldb.db..ENGINE  - dataFileCache open end
     [java] 2017-10-02 21:38:08,796 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,797 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,798 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,799 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,800 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,801 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,803 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,804 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,805 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,806 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,808 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,809 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,810 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,811 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,812 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
2 rows
     [java] 2017-10-02 21:38:08,813 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
31 rows total
     [java] 2017-10-02 21:38:08,821 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
     [java] 2017-10-02 21:38:08,826 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
     [java] 2017-10-02 21:38:08,829 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/ytex265782330.sql
02 Oct 2017 21:38:09  INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:09  INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:09  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex265782330.sql
02 Oct 2017 21:38:09  INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:09  INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:09  INFO ENGINE - Database closed
      [sql] 2 of 2 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex265782330.sql
   [delete] Deleting: /tmp/ytex1427625299use.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] 2017-10-02 21:38:13,573 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter
44 encapsulator 65534
     [java] 2017-10-02 21:38:13,589 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - insert
into PUBLIC.ref_stopword (stopword) values (?)
     [java] 2017-10-02 21:38:14,181 INFO  hsqldb.db..ENGINE  - open start - state not modified
     [java] 2017-10-02 21:38:14,262 INFO  hsqldb.db..ENGINE  - dataFileCache open start
     [java] 2017-10-02 21:38:14,288 INFO  hsqldb.db..ENGINE  - dataFileCache open end
     [java] 2017-10-02 21:38:14,385 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - inserted
360 rows total
     [java] 2017-10-02 21:38:14,400 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
     [java] 2017-10-02 21:38:14,410 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
     [java] 2017-10-02 21:38:14,413 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/ytex824337993.sql
02 Oct 2017 21:38:14  INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex824337993.sql
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15  INFO ENGINE - Database closed
      [sql] 22 of 22 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex824337993.sql
   [delete] Deleting: /tmp/ytex1487798293use.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/ytex177981942.sql
02 Oct 2017 21:38:15  INFO ENGINE - open start - state not modified
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache open start
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache open end
      [sql] Executing resource: /tmp/ytex177981942.sql
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache commit start
02 Oct 2017 21:38:15  INFO ENGINE - dataFileCache commit end
02 Oct 2017 21:38:15  INFO ENGINE - Database closed
      [sql] 52 of 52 SQL statements executed successfully
   [delete] Deleting: /tmp/ytex177981942.sql
   [delete] Deleting: /tmp/ytex621876601use.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
2017-10-02 21:38:16,266 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,328 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,546 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:16,555 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]]>
2017-10-02 21:38:16,576 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-02 21:38:16,649 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup
date [Mon Oct 02 21:38:16 UTC 2017]; root of context hierarchy
2017-10-02 21:38:16,651 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:16,884 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:16,916 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:17,118 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:17,119 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:17,119 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:17,162 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
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
2017-10-02 21:38:17,206 INFO  org.springframework.beans.factory.config.PropertiesFactoryBean
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:18,134 INFO  org.hibernate.annotations.common.Version  - HCANN000001: Hibernate
Commons Annotations {4.0.2.Final}
2017-10-02 21:38:18,141 INFO  org.hibernate.Version  - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 21:38:18,144 INFO  org.hibernate.cfg.Environment  - HHH000206: hibernate.properties
not found
2017-10-02 21:38:18,146 INFO  org.hibernate.cfg.Environment  - HHH000021: Bytecode provider
name : javassist
2017-10-02 21:38:18,986 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-10-02 21:38:19,095 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-10-02 21:38:19,104 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-10-02 21:38:19,165 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-10-02 21:38:19,166 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-10-02 21:38:19,169 INFO  hsqldb.db..ENGINE  - Database closed
2017-10-02 21:38:19,330 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-10-02 21:38:19,368 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-10-02 21:38:19,369 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-10-02 21:38:19,403 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:19,543 INFO  org.hibernate.engine.transaction.internal.TransactionFactoryInitiator
 - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:19,550 INFO  org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory  -
HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 21:38:19,719 INFO  org.hibernate.cache.spi.UpdateTimestampsCache  - HHH000250:
Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:19,726 INFO  org.hibernate.cache.internal.StandardQueryCache  - HHH000248:
Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:20,539 INFO  org.springframework.orm.hibernate4.HibernateTransactionManager
 - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory
for HibernateTransactionManager
2017-10-02 21:38:20,784 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
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
2017-10-02 21:38:20,815 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-10-02 21:38:20,816 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-10-02 21:38:20,819 INFO  hsqldb.db..ENGINE  - Database closed
2017-10-02 21:38:20,920 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.945 sec <<< FAILURE!
Running org.apache.ctakes.ytex.ConceptDaoTest
2017-10-02 21:38:21,720 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2669b199:
startup date [Mon Oct 02 21:38:21 UTC 2017]; root of context hierarchy
2017-10-02 21:38:21,789 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$ctakes-ytex/ws/-res/target/ctakes-ytex-res-4.0.1-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,985 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from URL [file:<https://builds.apache.org/job/cTAKES-trunk-Java-1.8/org.apache.ctakes$ctakes-ytex/ws/-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]>
2017-10-02 21:38:21,994 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]]>
2017-10-02 21:38:22,025 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
2017-10-02 21:38:22,102 INFO  org.springframework.context.support.ClassPathXmlApplicationContext
 - Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@670002: startup
date [Mon Oct 02 21:38:22 UTC 2017]; root of context hierarchy
2017-10-02 21:38:22,105 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-datasource.xml]
2017-10-02 21:38:22,332 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2017-10-02 21:38:22,368 INFO  org.springframework.beans.factory.xml.XmlBeanDefinitionReader
 - Loading XML bean definitions from class path resource [org/apache/ctakes/ytex/beans-kernel.xml]
2017-10-02 21:38:22,583 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-default.properties]
2017-10-02 21:38:22,584 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:22,584 INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex-umls.properties]
2017-10-02 21:38:22,647 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
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
2017-10-02 21:38:22,705 INFO  org.springframework.beans.factory.config.PropertiesFactoryBean
 - Loading properties file from class path resource [org/apache/ctakes/ytex/ytex.properties]
2017-10-02 21:38:23,557 INFO  org.hibernate.annotations.common.Version  - HCANN000001: Hibernate
Commons Annotations {4.0.2.Final}
2017-10-02 21:38:23,565 INFO  org.hibernate.Version  - HHH000412: Hibernate Core {4.2.6.Final}
2017-10-02 21:38:23,568 INFO  org.hibernate.cfg.Environment  - HHH000206: hibernate.properties
not found
2017-10-02 21:38:23,574 INFO  org.hibernate.cfg.Environment  - HHH000021: Bytecode provider
name : javassist
2017-10-02 21:38:24,406 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-10-02 21:38:24,502 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-10-02 21:38:24,514 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-10-02 21:38:24,630 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-10-02 21:38:24,632 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-10-02 21:38:24,641 INFO  hsqldb.db..ENGINE  - Database closed
2017-10-02 21:38:24,803 INFO  hsqldb.db..ENGINE  - open start - state not modified
2017-10-02 21:38:24,852 INFO  hsqldb.db..ENGINE  - dataFileCache open start
2017-10-02 21:38:24,853 INFO  hsqldb.db..ENGINE  - dataFileCache open end
2017-10-02 21:38:24,903 INFO  org.hibernate.dialect.Dialect  - HHH000400: Using dialect: org.hibernate.dialect.HSQLDialect
2017-10-02 21:38:25,017 INFO  org.hibernate.engine.transaction.internal.TransactionFactoryInitiator
 - HHH000399: Using default transaction strategy (direct JDBC transactions)
2017-10-02 21:38:25,023 INFO  org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory  -
HHH000397: Using ASTQueryTranslatorFactory
2017-10-02 21:38:25,196 INFO  org.hibernate.cache.spi.UpdateTimestampsCache  - HHH000250:
Starting update timestamps cache at region: org.hibernate.cache.spi.UpdateTimestampsCache
2017-10-02 21:38:25,200 INFO  org.hibernate.cache.internal.StandardQueryCache  - HHH000248:
Starting query cache at region: org.hibernate.cache.internal.StandardQueryCache
2017-10-02 21:38:25,928 INFO  org.springframework.orm.hibernate4.HibernateTransactionManager
 - Using DataSource [org.apache.commons.dbcp.BasicDataSource@1a5f7e7c] of Hibernate SessionFactory
for HibernateTransactionManager
2017-10-02 21:38:26,231 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2de23121:
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
2017-10-02 21:38:26,243 INFO  hsqldb.db..ENGINE  - dataFileCache commit start
2017-10-02 21:38:26,245 INFO  hsqldb.db..ENGINE  - dataFileCache commit end
2017-10-02 21:38:26,248 INFO  hsqldb.db..ENGINE  - Database closed
2017-10-02 21:38:26,350 INFO  org.springframework.beans.factory.support.DefaultListableBeanFactory
 - Destroying singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@29f69090:
defining beans [kernelApplicationContext]; root of factory hierarchy
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.918 sec <<< FAILURE!
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.754 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.713 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.607 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.573 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2017-10-02 21:38:34,320 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter 44
encapsulator 65534
2017-10-02 21:38:34,348 INFO  org.apache.ctakes.jdl.data.loader.CsvLoader  - delimiter 59
encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.665 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.547 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.594 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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