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 B7A90200D33 for ; Wed, 8 Nov 2017 18:44:21 +0100 (CET) Received: by cust-asf.ponee.io (Postfix) id B6001160BDA; Wed, 8 Nov 2017 17:44:21 +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 5CA961609E0 for ; Wed, 8 Nov 2017 18:44:20 +0100 (CET) Received: (qmail 22824 invoked by uid 500); 8 Nov 2017 17:44:19 -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 22815 invoked by uid 99); 8 Nov 2017 17:44:19 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd1-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 08 Nov 2017 17:44:19 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd1-us-west.apache.org (ASF Mail Server at spamd1-us-west.apache.org) with ESMTP id C06FED274F for ; Wed, 8 Nov 2017 17:44:18 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd1-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 2.299 X-Spam-Level: ** X-Spam-Status: No, score=2.299 tagged_above=-999 required=6.31 tests=[KAM_ASCII_DIVIDERS=0.8, KAM_LAZY_DOMAIN_SECURITY=1, KAM_NUMSUBJECT=0.5, RP_MATCHES_RCVD=-0.001] autolearn=disabled Received: from mx1-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd1-us-west.apache.org [10.40.0.7]) (amavisd-new, port 10024) with ESMTP id wUZjNRI0fUDs for ; Wed, 8 Nov 2017 17:44:16 +0000 (UTC) Received: from mailrelay1-us-west.apache.org (mailrelay1-us-west.apache.org [209.188.14.139]) by mx1-lw-eu.apache.org (ASF Mail Server at mx1-lw-eu.apache.org) with ESMTP id 37B9B611E9 for ; Wed, 8 Nov 2017 17:44:10 +0000 (UTC) Received: from jenkins-master.apache.org (unknown [62.210.60.235]) by mailrelay1-us-west.apache.org (ASF Mail Server at mailrelay1-us-west.apache.org) with ESMTP id 3A705E069F for ; Wed, 8 Nov 2017 17:44:09 +0000 (UTC) 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 1FAE2A068D for ; Wed, 8 Nov 2017 17:44:06 +0000 (UTC) Date: Wed, 8 Nov 2017 17:44:05 +0000 (UTC) From: Apache Jenkins Server To: notifications@ctakes.apache.org Message-ID: <1865885269.805.1510163046128.JavaMail.jenkins@jenkins-master.apache.org> In-Reply-To: <704133463.783.1510160023741.JavaMail.jenkins@jenkins-master.apache.org> References: <704133463.783.1510160023741.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_#22?= 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: Wed, 08 Nov 2017 17:44:21 -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] 2017-11-08 17:37:37,066 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - delimiter 9 encapsulator 65534 [java] 2017-11-08 17:37:37,074 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 17:37:37,543 INFO hsqldb.db..ENGINE - open start -= state not modified [java] 2017-11-08 17:37:37,611 INFO hsqldb.db..ENGINE - dataFileCach= e open start [java] 2017-11-08 17:37:37,627 INFO hsqldb.db..ENGINE - dataFileCach= e open end [java] 2017-11-08 17:37:37,671 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,672 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,673 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,674 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,674 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,675 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,676 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,678 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,678 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,679 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,681 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,682 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,683 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,683 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,684 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 2 rows [java] 2017-11-08 17:37:37,684 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 31 rows total [java] 2017-11-08 17:37:37,693 INFO hsqldb.db..ENGINE - dataFileCach= e commit start [java] 2017-11-08 17:37:37,699 INFO hsqldb.db..ENGINE - dataFileCach= e commit end [java] 2017-11-08 17:37:37,702 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/ytex1751788231.sql 08 Nov 2017 17:37:38 INFO ENGINE - open start - state not modified 08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache open start 08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex1751788231.sql 08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache commit start 08 Nov 2017 17:37:38 INFO ENGINE - dataFileCache commit end 08 Nov 2017 17:37:38 INFO ENGINE - Database closed [sql] 2 of 2 SQL statements executed successfully [delete] Deleting: /tmp/ytex1751788231.sql [delete] Deleting: /tmp/ytex2144289946use.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] 2017-11-08 17:37:42,633 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - delimiter 44 encapsulator 65534 [java] 2017-11-08 17:37:42,641 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - insert into PUBLIC.ref_stopword (stopword) values (?) [java] 2017-11-08 17:37:43,165 INFO hsqldb.db..ENGINE - open start -= state not modified [java] 2017-11-08 17:37:43,235 INFO hsqldb.db..ENGINE - dataFileCach= e open start [java] 2017-11-08 17:37:43,251 INFO hsqldb.db..ENGINE - dataFileCach= e open end [java] 2017-11-08 17:37:43,328 INFO org.apache.ctakes.jdl.data.loader= .CsvLoader - inserted 360 rows total [java] 2017-11-08 17:37:43,336 INFO hsqldb.db..ENGINE - dataFileCach= e commit start [java] 2017-11-08 17:37:43,346 INFO hsqldb.db..ENGINE - dataFileCach= e commit end [java] 2017-11-08 17:37:43,349 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/ytex1642712519.sql 08 Nov 2017 17:37:43 INFO ENGINE - open start - state not modified 08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache open start 08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex1642712519.sql 08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache commit start 08 Nov 2017 17:37:43 INFO ENGINE - dataFileCache commit end 08 Nov 2017 17:37:43 INFO ENGINE - Database closed [sql] 22 of 22 SQL statements executed successfully [delete] Deleting: /tmp/ytex1642712519.sql [delete] Deleting: /tmp/ytex348288983use.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/ytex702157901.sql 08 Nov 2017 17:37:44 INFO ENGINE - open start - state not modified 08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache open start 08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache open end [sql] Executing resource: /tmp/ytex702157901.sql 08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache commit start 08 Nov 2017 17:37:44 INFO ENGINE - dataFileCache commit end 08 Nov 2017 17:37:44 INFO ENGINE - Database closed [sql] 52 of 52 SQL statements executed successfully [delete] Deleting: /tmp/ytex702157901.sql [delete] Deleting: /tmp/ytex227994778use.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 2017-11-08 17:37:45,064 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 17:37:45 UTC= 2017]; root of context hierarchy 2017-11-08 17:37:45,126 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [jar:file: 2017-11-08 17:37:45,339 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [file: 2017-11-08 17:37:45,354 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: 2017-11-08 17:37:45,376 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@568bf312: defining bea= ns [kernelApplicationContext]; root of factory hierarchy 2017-11-08 17:37:45,451 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 17:37:45 UTC= 2017]; root of context hierarchy 2017-11-08 17:37:45,458 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-datasource.xml] 2017-11-08 17:37:45,661 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.hbm.xml] 2017-11-08 17:37:45,688 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.xml] 2017-11-08 17:37:45,834 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-08 17:37:45,835 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex.properties] 2017-11-08 17:37:45,835 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-08 17:37:45,875 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@63475ace: 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 2017-11-08 17:37:45,918 INFO org.springframework.beans.factory.config.Prop= ertiesFactoryBean - Loading properties file from class path resource [org/= apache/ctakes/ytex/ytex.properties] 2017-11-08 17:37:46,708 INFO org.hibernate.annotations.common.Version - H= CANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-08 17:37:46,720 INFO org.hibernate.Version - HHH000412: Hibernate= Core {4.2.6.Final} 2017-11-08 17:37:46,723 INFO org.hibernate.cfg.Environment - HHH000206: h= ibernate.properties not found 2017-11-08 17:37:46,724 INFO org.hibernate.cfg.Environment - HHH000021: B= ytecode provider name : javassist 2017-11-08 17:37:47,461 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-11-08 17:37:47,536 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-11-08 17:37:47,545 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-11-08 17:37:47,602 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-11-08 17:37:47,604 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-11-08 17:37:47,607 INFO hsqldb.db..ENGINE - Database closed 2017-11-08 17:37:47,745 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-11-08 17:37:47,794 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-11-08 17:37:47,794 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-11-08 17:37:47,829 INFO org.hibernate.dialect.Dialect - HHH000400: U= sing dialect: org.hibernate.dialect.HSQLDialect 2017-11-08 17:37:47,946 INFO org.hibernate.engine.transaction.internal.Tra= nsactionFactoryInitiator - HHH000399: Using default transaction strategy (= direct JDBC transactions) 2017-11-08 17:37:47,950 INFO org.hibernate.hql.internal.ast.ASTQueryTransl= atorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-08 17:37:48,087 INFO org.hibernate.cache.spi.UpdateTimestampsCache= - HHH000250: Starting update timestamps cache at region: org.hibernate.ca= che.spi.UpdateTimestampsCache 2017-11-08 17:37:48,092 INFO org.hibernate.cache.internal.StandardQueryCac= he - HHH000248: Starting query cache at region: org.hibernate.cache.intern= al.StandardQueryCache 2017-11-08 17:37:48,637 INFO org.springframework.orm.hibernate4.HibernateT= ransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSou= rce@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-08 17:37:48,822 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@63475ace: 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 2017-11-08 17:37:48,834 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-11-08 17:37:48,836 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-11-08 17:37:48,839 INFO hsqldb.db..ENGINE - Database closed 2017-11-08 17:37:48,940 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@568bf312: defining beans [ker= nelApplicationContext]; root of factory hierarchy Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.117 sec <= << FAILURE! Running org.apache.ctakes.ytex.ConceptDaoTest 2017-11-08 17:37:49,664 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@2344fc66: startup date [Wed Nov 08 17:37:49 UTC= 2017]; root of context hierarchy 2017-11-08 17:37:49,723 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [jar:file: 2017-11-08 17:37:49,916 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from URL [file: 2017-11-08 17:37:49,929 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: 2017-11-08 17:37:49,947 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@568bf312: defining bea= ns [kernelApplicationContext]; root of factory hierarchy 2017-11-08 17:37:50,017 INFO org.springframework.context.support.ClassPath= XmlApplicationContext - Refreshing org.springframework.context.support.Cla= ssPathXmlApplicationContext@1f0f1111: startup date [Wed Nov 08 17:37:50 UTC= 2017]; root of context hierarchy 2017-11-08 17:37:50,019 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-datasource.xml] 2017-11-08 17:37:50,224 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.hbm.xml] 2017-11-08 17:37:50,249 INFO org.springframework.beans.factory.xml.XmlBean= DefinitionReader - Loading XML bean definitions from class path resource [= org/apache/ctakes/ytex/beans-kernel.xml] 2017-11-08 17:37:50,413 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-default.properties] 2017-11-08 17:37:50,414 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex.properties] 2017-11-08 17:37:50,414 INFO org.springframework.beans.factory.config.Prop= ertyPlaceholderConfigurer - Loading properties file from class path resour= ce [org/apache/ctakes/ytex/ytex-umls.properties] 2017-11-08 17:37:50,461 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Pre-instantiating singletons in org.springframew= ork.beans.factory.support.DefaultListableBeanFactory@63475ace: 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 2017-11-08 17:37:50,509 INFO org.springframework.beans.factory.config.Prop= ertiesFactoryBean - Loading properties file from class path resource [org/= apache/ctakes/ytex/ytex.properties] 2017-11-08 17:37:51,292 INFO org.hibernate.annotations.common.Version - H= CANN000001: Hibernate Commons Annotations {4.0.2.Final} 2017-11-08 17:37:51,302 INFO org.hibernate.Version - HHH000412: Hibernate= Core {4.2.6.Final} 2017-11-08 17:37:51,304 INFO org.hibernate.cfg.Environment - HHH000206: h= ibernate.properties not found 2017-11-08 17:37:51,306 INFO org.hibernate.cfg.Environment - HHH000021: B= ytecode provider name : javassist 2017-11-08 17:37:52,033 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-11-08 17:37:52,134 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-11-08 17:37:52,143 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-11-08 17:37:52,231 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-11-08 17:37:52,232 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-11-08 17:37:52,236 INFO hsqldb.db..ENGINE - Database closed 2017-11-08 17:37:52,366 INFO hsqldb.db..ENGINE - open start - state not m= odified 2017-11-08 17:37:52,402 INFO hsqldb.db..ENGINE - dataFileCache open start 2017-11-08 17:37:52,402 INFO hsqldb.db..ENGINE - dataFileCache open end 2017-11-08 17:37:52,434 INFO org.hibernate.dialect.Dialect - HHH000400: U= sing dialect: org.hibernate.dialect.HSQLDialect 2017-11-08 17:37:52,549 INFO org.hibernate.engine.transaction.internal.Tra= nsactionFactoryInitiator - HHH000399: Using default transaction strategy (= direct JDBC transactions) 2017-11-08 17:37:52,553 INFO org.hibernate.hql.internal.ast.ASTQueryTransl= atorFactory - HHH000397: Using ASTQueryTranslatorFactory 2017-11-08 17:37:52,681 INFO org.hibernate.cache.spi.UpdateTimestampsCache= - HHH000250: Starting update timestamps cache at region: org.hibernate.ca= che.spi.UpdateTimestampsCache 2017-11-08 17:37:52,685 INFO org.hibernate.cache.internal.StandardQueryCac= he - HHH000248: Starting query cache at region: org.hibernate.cache.intern= al.StandardQueryCache 2017-11-08 17:37:53,278 INFO org.springframework.orm.hibernate4.HibernateT= ransactionManager - Using DataSource [org.apache.commons.dbcp.BasicDataSou= rce@5b22b970] of Hibernate SessionFactory for HibernateTransactionManager 2017-11-08 17:37:53,501 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@63475ace: 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 2017-11-08 17:37:53,513 INFO hsqldb.db..ENGINE - dataFileCache commit sta= rt 2017-11-08 17:37:53,515 INFO hsqldb.db..ENGINE - dataFileCache commit end 2017-11-08 17:37:53,518 INFO hsqldb.db..ENGINE - Database closed 2017-11-08 17:37:53,619 INFO org.springframework.beans.factory.support.Def= aultListableBeanFactory - Destroying singletons in org.springframework.bea= ns.factory.support.DefaultListableBeanFactory@568bf312: defining beans [ker= nelApplicationContext]; root of factory hierarchy Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.208 sec <= << FAILURE! 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.AppJdlTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.514 sec Running org.apache.ctakes.jdl.AppMainTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.487 sec Running org.apache.ctakes.jdl.data.xml.ValidationTest Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.646 sec Running org.apache.ctakes.jdl.data.xml.DomParserTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec Running org.apache.ctakes.jdl.data.xml.DomUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.346 sec Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 sec Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.637 sec Running org.apache.ctakes.jdl.data.base.JdlConnectionTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.5 sec Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 sec Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest 2017-11-08 17:38:02,236 INFO org.apache.ctakes.jdl.data.loader.CsvLoader = - delimiter 44 encapsulator 65534 2017-11-08 17:38:02,258 INFO org.apache.ctakes.jdl.data.loader.CsvLoader = - delimiter 59 encapsulator 65534 Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.651 sec Running org.apache.ctakes.jdl.common.SingletonTest Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec Running org.apache.ctakes.jdl.common.PropertiesFileTest Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec Running org.apache.ctakes.jdl.common.FileUtilTest Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 sec Running org.apache.ctakes.jdl.common.PropFileTest Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 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