Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 97C53200D0F for ; Fri, 29 Sep 2017 21:12:12 +0200 (CEST) Received: by cust-asf.ponee.io (Postfix) id 9643C1609D1; Fri, 29 Sep 2017 19:12:12 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id 184BA1609BC for ; Fri, 29 Sep 2017 21:12:10 +0200 (CEST) Received: (qmail 64926 invoked by uid 500); 29 Sep 2017 19:12:10 -0000 Mailing-List: contact notifications-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list notifications@ctakes.apache.org Received: (qmail 64917 invoked by uid 99); 29 Sep 2017 19:12:10 -0000 Received: from Unknown (HELO jenkins-master.apache.org) (62.210.60.235) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 29 Sep 2017 19:12:10 +0000 Received: from jenkins-master.apache.org (localhost [127.0.0.1]) by jenkins-master.apache.org (ASF Mail Server at jenkins-master.apache.org) with ESMTP id 99FD3A01DE for ; Fri, 29 Sep 2017 19:12:05 +0000 (UTC) Date: Fri, 29 Sep 2017 19:12:05 +0000 (UTC) From: Apache Jenkins Server To: notifications@ctakes.apache.org Message-ID: <1187101466.1141.1506712325629.JavaMail.jenkins@jenkins-master.apache.org> In-Reply-To: <1387392892.1111.1506708744431.JavaMail.jenkins@jenkins-master.apache.org> References: <1387392892.1111.1506708744431.JavaMail.jenkins@jenkins-master.apache.org> Subject: =?UTF-8?Q?Build_failed_in_Jenkins:_cTAKES-tru?= =?UTF-8?Q?nk-Java-1.8_=C2=BB_Apache_cTAKES_YTEX_#5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Instance-Identity: MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkqVKZPv7YyHBB3FvWfV7XQehwe/Ga3aadzSNknt8g382X3uN8A3SOQ+Ixq9HxS+ZlN6XR4TECySmSRy2JN5Rx8svxAD0TjtSF9LuU98dD+LniNDP7Lq6gvRFuJhbMHoS0nuTizDZLsK4X8TW5MyV9w+jFbdoZfRE5O/Mse0fkOeL5uoIS/3Vvu/W+x9QSjDkB7CaU56bPFlQjqqJBl3Cn9r34CkXQZYnLb/NjW4vcpw0+TgMUAPTIVEr5BTPZRshz19g7huwg3zANT5HBIZnzV4hsVY9w4JHkceFdKi/ibNnjPjsFs9pm0HSGJ/RDxjIvSTYT02eH4+m1RAYaj2E9QIDAQAB X-Jenkins-Job: cTAKES-trunk-Java-1.8/org.apache.ctakes:ctakes-ytex X-Jenkins-Result: FAILURE archived-at: Fri, 29 Sep 2017 19:12:12 -0000 See ------------------------------------------ [...truncated 43.26 KB...] [echo] jdl.format examples/fracture_demo.xml [echo] jdl.data examples/fracture_demo.txt [echo] umls.prefix=20 [copy] Copying 1 file to /tmp [java] 2017-09-29 19:10:06,589 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - delimiter 9 encapsulator 65534 [java] 2017-09-29 19:10:06,600 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - insert into PUBLIC.fracture_demo (site_id,note_text,fracture,= note_set) values (?,?,?,?) [java] 2017-09-29 19:10:07,218 INFO hsqldb.db..ENGINE - open start -= state not modified [java] 2017-09-29 19:10:07,289 INFO hsqldb.db..ENGINE - dataFileCach= e open start [java] 2017-09-29 19:10:07,324 INFO hsqldb.db..ENGINE - dataFileCach= e open end [java] 2017-09-29 19:10:07,381 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,382 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,383 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,384 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,385 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,386 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,387 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,389 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,389 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,390 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,392 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,393 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,403 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,404 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,405 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-09-29 19:10:07,406 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 31 rows total [java] 2017-09-29 19:10:07,421 INFO hsqldb.db..ENGINE - dataFileCach= e commit start [java] 2017-09-29 19:10:07,428 INFO hsqldb.db..ENGINE - dataFileCach= e commit end [java] 2017-09-29 19:10:07,432 INFO hsqldb.db..ENGINE - Database clo= sed jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog=20 [echo] execute ./hsql/uima/fracture_demo.sql [copy] Copying 1 file to /tmp [echo] executing /tmp/ytex897090839.sql 29 Sep 2017 19:10:07 INFO ENGINE - open start - state not modified 29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache open start 29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex897090839.sql 29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache commit start 29 Sep 2017 19:10:08 INFO ENGINE - dataFileCache commit end 29 Sep 2017 19:10:08 INFO ENGINE - Database closed [sql] 2 of 2 SQL statements executed successfully [delete] Deleting: /tmp/ytex897090839.sql [delete] Deleting: /tmp/ytex1929446082use.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=20 [copy] Copying 1 file to /tmp [java] 2017-09-29 19:10:12,526 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - delimiter 44 encapsulator 65534 [java] 2017-09-29 19:10:12,534 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?) [java] 2017-09-29 19:10:13,172 INFO hsqldb.db..ENGINE - open start -= state not modified [java] 2017-09-29 19:10:13,250 INFO hsqldb.db..ENGINE - dataFileCach= e open start [java] 2017-09-29 19:10:13,281 INFO hsqldb.db..ENGINE - dataFileCach= e open end [java] 2017-09-29 19:10:13,380 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 360 rows total [java] 2017-09-29 19:10:13,390 INFO hsqldb.db..ENGINE - dataFileCach= e commit start [java] 2017-09-29 19:10:13,405 INFO hsqldb.db..ENGINE - dataFileCach= e commit end [java] 2017-09-29 19:10:13,408 INFO hsqldb.db..ENGINE - Database clo= sed uima.all: kernel.drop: jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog=20 [echo] execute ./hsql/kernel/drop_tables.sql [copy] Copying 1 file to /tmp [echo] executing /tmp/ytex1291228459.sql 29 Sep 2017 19:10:14 INFO ENGINE - open start - state not modified 29 Sep 2017 19:10:14 INFO ENGINE - dataFileCache open start 29 Sep 2017 19:10:14 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex1291228459.sql 29 Sep 2017 19:10:15 INFO ENGINE - dataFileCache commit start 29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache commit end 29 Sep 2017 19:10:16 INFO ENGINE - Database closed [sql] 22 of 22 SQL statements executed successfully [delete] Deleting: /tmp/ytex1291228459.sql [delete] Deleting: /tmp/ytex564695223use.sql kernel.create: jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog=20 [echo] execute ./hsql/kernel/create_tables.sql [copy] Copying 1 file to /tmp [echo] executing /tmp/ytex1195843211.sql 29 Sep 2017 19:10:16 INFO ENGINE - open start - state not modified 29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache open start 29 Sep 2017 19:10:16 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex1195843211.sql 29 Sep 2017 19:10:18 INFO ENGINE - dataFileCache commit start 29 Sep 2017 19:10:19 INFO ENGINE - dataFileCache commit end 29 Sep 2017 19:10:21 INFO ENGINE - Database closed [sql] 52 of 52 SQL statements executed successfully [delete] Deleting: /tmp/ytex1195843211.sql [delete] Deleting: /tmp/ytex1363463702use.sql kernel.all: all: [INFO] Executed tasks [INFO]=20 [INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex --= - [INFO] Surefire report directory: ------------------------------------------------------- T E S T S ------------------------------------------------------- ------------------------------------------------------- T E S T S ------------------------------------------------------- Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest 2017-09-29 19:10:23,222 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 19:10:23 UTC= 2017]; root of context hierarchy 2017-09-29 19:10:23,289 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [jar:file: 2017-09-29 19:10:23,526 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [file: 2017-09-29 19:10:23,543 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Overriding bean definition for bean 'kernelAppli= cationContext': replacing [Generic bean: class [org.springframework.context= .support.ClassPathXmlApplicationContext]; scope=3D; abstract=3Dfalse; lazyI= nit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowireCandidate=3Dtru= e; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodName=3Dnull; initM= ethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [jar:file: with [Generic bean: class [org.springframework= .context.support.ClassPathXmlApplicationContext]; scope=3D; abstract=3Dfals= e; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowireCandida= te=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodName=3Dnul= l; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [file: 2017-09-29 19:10:23,576 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@29f69090: defining bea= ns [kernelApplicationContext]; root of factory hierarchy 2017-09-29 19:10:23,667 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@670002: startup date [Fri Sep 29 19:10:23 UTC 2= 017]; root of context hierarchy 2017-09-29 19:10:23,670 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-datasource.xml] 2017-09-29 19:10:23,941 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.hbm.xml] 2017-09-29 19:10:23,991 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.xml] 2017-09-29 19:10:24,223 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-default.properties] 2017-09-29 19:10:24,223 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex.properties] 2017-09-29 19:10:24,224 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-umls.properties] 2017-09-29 19:10:24,287 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@2de23121: defining bea= ns [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#= 0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTempl= ateNew,transactionManager,sessionFactory,org.springframework.aop.config.int= ernalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaI= mporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperatio= n,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultB= eanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFact= oryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsE= xporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImport= er,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,lib= svmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributePro= ductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelU= til,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLi= ghtParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,spar= seDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmL= inFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFo= rmatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeE= val,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoCont= entEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscap= eHelper,abstractKernelCacheAdvice,pageRankService]; root of factory hierarc= hy 2017-09-29 19:10:24,345 INFO org.springframework.beans.factory.config.Prop= ertiesFactoryBean - Loading properties file from class path resource [org/= apache/ctakes/ytex/ytex.properties] 2017-09-29 19:10:25,288 INFO org.hibernate.annotations.common.Version - H= CANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-09-29 19:10:25,294 INFO org.hibernate.Version - HHH000412: Hibernate= Core {4.2.6.Final} 2017-09-29 19:10:25,296 INFO org.hibernate.cfg.Environment - HHH000206: h= ibernate.properties not found 2017-09-29 19:10:25,299 INFO org.hibernate.cfg.Environment - HHH000021: B= ytecode provider name : javassist 2017-09-29 19:10:26,259 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-09-29 19:10:26,381 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-09-29 19:10:26,395 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-09-29 19:10:26,493 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-09-29 19:10:26,494 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-09-29 19:10:26,497 INFO hsqldb.db..ENGINE - Database closed 2017-09-29 19:10:26,639 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-09-29 19:10:26,724 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-09-29 19:10:26,725 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-09-29 19:10:26,817 INFO org.hibernate.dialect.Dialect - HHH000400: U= sing dialect: org.hibernate.dialect.HSQLDialect 2017-09-29 19:10:26,924 INFO org.hibernate.engine.transaction.internal.Tra= nsactionFactoryInitiator - HHH000399: Using default transaction strategy (= direct JDBC transactions) 2017-09-29 19:10:26,929 INFO org.hibernate.hql.internal.ast.ASTQueryTransl= atorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-09-29 19:10:27,115 INFO org.hibernate.cache.spi.UpdateTimestampsCache= - HHH000250: Starting update timestamps cache at region: org.hibernate.ca= che.spi.UpdateTimestampsCache 2017-09-29 19:10:27,121 INFO org.hibernate.cache.internal.StandardQueryCac= he - HHH000248: Starting query cache at region: org.hibernate.cache.intern= al.StandardQueryCache 2017-09-29 19:10:27,910 INFO org.springframework.orm.hibernate4.HibernateT= ransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSou= rce@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager 2017-09-29 19:10:28,207 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org= .springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexP= roperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,= transactionManager,sessionFactory,org.springframework.aop.config.internalAu= toProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter= ,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultB= eanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFact= oryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPoin= tcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter= ,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,clas= sifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil= ,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKer= nel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,bas= eClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightPars= er,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataF= ormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinForma= tterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatter= Factory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,ran= kerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEval= uator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper= ,abstractKernelCacheAdvice,pageRankService]; root of factory hierarchy 2017-09-29 19:10:28,246 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-09-29 19:10:28,248 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-09-29 19:10:28,250 INFO hsqldb.db..ENGINE - Database closed 2017-09-29 19:10:28,352 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@29f69090: defining beans [ker= nelApplicationContext]; root of factory hierarchy Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.439 sec <= << FAILURE! Running org.apache.ctakes.ytex.ConceptDaoTest 2017-09-29 19:10:29,193 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@2669b199: startup date [Fri Sep 29 19:10:29 UTC= 2017]; root of context hierarchy 2017-09-29 19:10:29,255 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [jar:file: 2017-09-29 19:10:29,472 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [file: 2017-09-29 19:10:29,481 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Overriding bean definition for bean 'kernelAppli= cationContext': replacing [Generic bean: class [org.springframework.context= .support.ClassPathXmlApplicationContext]; scope=3D; abstract=3Dfalse; lazyI= nit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowireCandidate=3Dtru= e; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodName=3Dnull; initM= ethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [jar:file: with [Generic bean: class [org.springframework= .context.support.ClassPathXmlApplicationContext]; scope=3D; abstract=3Dfals= e; lazyInit=3Dfalse; autowireMode=3D0; dependencyCheck=3D0; autowireCandida= te=3Dtrue; primary=3Dfalse; factoryBeanName=3Dnull; factoryMethodName=3Dnul= l; initMethodName=3Dnull; destroyMethodName=3Dnull; defined in URL [file: 2017-09-29 19:10:29,504 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@29f69090: defining bea= ns [kernelApplicationContext]; root of factory hierarchy 2017-09-29 19:10:29,574 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@670002: startup date [Fri Sep 29 19:10:29 UTC 2= 017]; root of context hierarchy 2017-09-29 19:10:29,577 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-datasource.xml] 2017-09-29 19:10:29,842 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.hbm.xml] 2017-09-29 19:10:29,876 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.xml] 2017-09-29 19:10:30,055 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-default.properties] 2017-09-29 19:10:30,056 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex.properties] 2017-09-29 19:10:30,056 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-umls.properties] 2017-09-29 19:10:30,097 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@2de23121: defining bea= ns [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#= 0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTempl= ateNew,transactionManager,sessionFactory,org.springframework.aop.config.int= ernalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaI= mporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperatio= n,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultB= eanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFact= oryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsE= xporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImport= er,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,lib= svmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributePro= ductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelU= til,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLi= ghtParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,spar= seDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmL= inFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFo= rmatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeE= val,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoCont= entEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscap= eHelper,abstractKernelCacheAdvice,pageRankService]; root of factory hierarc= hy 2017-09-29 19:10:30,149 INFO org.springframework.beans.factory.config.Prop= ertiesFactoryBean - Loading properties file from class path resource [org/= apache/ctakes/ytex/ytex.properties] 2017-09-29 19:10:30,956 INFO org.hibernate.annotations.common.Version - H= CANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-09-29 19:10:30,962 INFO org.hibernate.Version - HHH000412: Hibernate= Core {4.2.6.Final} 2017-09-29 19:10:30,965 INFO org.hibernate.cfg.Environment - HHH000206: h= ibernate.properties not found 2017-09-29 19:10:30,972 INFO org.hibernate.cfg.Environment - HHH000021: B= ytecode provider name : javassist 2017-09-29 19:10:31,891 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-09-29 19:10:32,007 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-09-29 19:10:32,019 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-09-29 19:10:32,159 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-09-29 19:10:32,159 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-09-29 19:10:32,162 INFO hsqldb.db..ENGINE - Database closed 2017-09-29 19:10:32,321 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-09-29 19:10:32,405 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-09-29 19:10:32,406 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-09-29 19:10:32,453 INFO org.hibernate.dialect.Dialect - HHH000400: U= sing dialect: org.hibernate.dialect.HSQLDialect 2017-09-29 19:10:32,594 INFO org.hibernate.engine.transaction.internal.Tra= nsactionFactoryInitiator - HHH000399: Using default transaction strategy (= direct JDBC transactions) 2017-09-29 19:10:32,600 INFO org.hibernate.hql.internal.ast.ASTQueryTransl= atorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-09-29 19:10:32,783 INFO org.hibernate.cache.spi.UpdateTimestampsCache= - HHH000250: Starting update timestamps cache at region: org.hibernate.ca= che.spi.UpdateTimestampsCache 2017-09-29 19:10:32,790 INFO org.hibernate.cache.internal.StandardQueryCac= he - HHH000248: Starting query cache at region: org.hibernate.cache.intern= al.StandardQueryCache 2017-09-29 19:10:33,615 INFO org.springframework.orm.hibernate4.HibernateT= ransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSou= rce@1a5f7e7c] of Hibernate SessionFactory for HibernateTransactionManager 2017-09-29 19:10:33,893 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@2de23121: defining beans [org= .springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexP= roperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,= transactionManager,sessionFactory,org.springframework.aop.config.internalAu= toProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter= ,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.s= pringframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springfr= amework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework= .aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.su= pport.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.D= efaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultB= eanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFact= oryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPoin= tcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter= ,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,clas= sifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil= ,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKer= nel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,bas= eClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightPars= er,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataF= ormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinForma= tterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatter= Factory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,ran= kerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEval= uator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper= ,abstractKernelCacheAdvice,pageRankService]; root of factory hierarchy 2017-09-29 19:10:33,951 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-09-29 19:10:33,952 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-09-29 19:10:33,956 INFO hsqldb.db..ENGINE - Database closed 2017-09-29 19:10:34,058 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@29f69090: defining beans [ker= nelApplicationContext]; root of factory hierarchy Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 5.172 sec <= << FAILURE! Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.846 sec Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.936 sec Running org.apache.ctakes.jdl.data.xml.DomParserTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec Running org.apache.ctakes.jdl.data.xml.DomUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 sec Running org.apache.ctakes.jdl.data.xml.ValidationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.832 sec Running org.apache.ctakes.jdl.data.base.JdlConnectionTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.621 sec Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.867 sec Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest 2017-09-29 19:10:43,011 INFO org.apache.ctakes.jdl.data.loader.CsvLoader = - delimiter 44 encapsulator 65534 2017-09-29 19:10:43,128 INFO org.apache.ctakes.jdl.data.loader.CsvLoader = - delimiter 59 encapsulator 65534 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.893 sec Running org.apache.ctakes.jdl.common.SingletonTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.102 sec Running org.apache.ctakes.jdl.common.FileUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 sec Running org.apache.ctakes.jdl.common.PropFileTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 sec Running org.apache.ctakes.jdl.common.PropertiesFileTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec Running org.apache.ctakes.jdl.AppTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec Running org.apache.ctakes.jdl.AppJdlTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.782 sec Running org.apache.ctakes.jdl.AppMainTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.62 sec Results : Tests in error:=20 testGetAllAuiStr(org.apache.ctakes.ytex.umls.dao.UMLSDaoTest): Unable to = initialize group definition. Group resource name [classpath*:org/apache/cta= kes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext];= nested exception is org.springframework.beans.factory.BeanCreationExceptio= n: Error creating bean with name 'kernelApplicationContext' defined in URL = [file:: Instantiation of bean failed; nested exception is org.spri= ngframework.beans.BeanInstantiationException: Could not instantiate bean cl= ass [org.springframework.context.support.ClassPathXmlApplicationContext]: C= onstructor threw exception; nested exception is org.springframework.beans.f= actory.BeanCreationException: Error creating bean with name 'gramMatrixExpo= rter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.x= ml]: 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.In= trospectionException: type mismatch between read and write methods testCreateConceptGraph(org.apache.ctakes.ytex.ConceptDaoTest): Unable to = initialize group definition. Group resource name [classpath*:org/apache/cta= kes/ytex/kernelBeanRefContext.xml], factory key [kernelApplicationContext];= nested exception is org.springframework.beans.factory.BeanCreationExceptio= n: Error creating bean with name 'kernelApplicationContext' defined in URL = [file:: Instantiation of bean failed; nested exception is org.spri= ngframework.beans.BeanInstantiationException: Could not instantiate bean cl= ass [org.springframework.context.support.ClassPathXmlApplicationContext]: C= onstructor threw exception; nested exception is org.springframework.beans.f= actory.BeanCreationException: Error creating bean with name 'gramMatrixExpo= rter' defined in class path resource [org/apache/ctakes/ytex/beans-kernel.x= ml]: 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.In= trospectionException: type mismatch between read and write methods Tests run: 36, Failures: 0, Errors: 2, Skipped: 4 [JENKINS] Recording test results [JENKINS] Archiving disabled