Completely new error. I have taken this offline until we figure out what is going on.
-----Original Message----- From: vijay garla [mailto:vnga...@gmail.com] Sent: Monday, April 28, 2014 1:47 PM To: dev@ctakes.apache.org Subject: Re: ytex merged into trunk Hello All, I can't reproduce this build error. It appears that maven does not want to run copy-dependencies in the compile phase. However, I have tried building this with maven 3.2.1 and maven 3.1.0 and it works fine for both. @Sean - can you send me the output of mvn -x clean install -pl ctakes-ytex (executed from ctakes root dir) This is the plugin that maven is complaining about: <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-dependency-plugin</artifactId> <executions> <execution> <id>copy-dependencies</id> <phase>compile</phase> <goals> <goal>copy-dependencies</goal> </goals> <configuration> <outputDirectory>${basedir}/target/lib</outputDirectory> <overWriteReleases>false</overWriteReleases> <overWriteSnapshots>false</overWriteSnapshots> <overWriteIfNewer>true</overWriteIfNewer> </configuration> </execution> </executions> </plugin> On Mon, Apr 28, 2014 at 1:26 PM, vijay garla <vnga...@gmail.com> wrote: > sorry about that. I will investigate. > > -vj > > > On Mon, Apr 28, 2014 at 11:00 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > >> Hi Vijay, >> >> I did a checkout this morning and I'm getting compile errors from Maven. >> >> If I just run mvn compile then I get an error while building ytex >> claiming that the package has not been created. Is there a reversed >> dependency? >> >> If I run mvn compile package then ytex seems to run through, but >> there is an error in the test of ytex-uima (see below). >> >> Any ideas? >> >> Thanks, >> Sean >> >> >> Running org.apache.ctakes.ytex.uima.annotators.SparseDataExporterTest >> ... >> 2014-04-28 10:50:43,074 INFO org.hibernate.dialect.Dialect - HHH000400: >> Using dialect: org.hibernate.dialect.HSQLDialect >> 2014-04-28 10:50:43,112 WARN >> org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: -22, >> SQLState: S0002 >> 2014-04-28 10:50:43,112 ERROR >> org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table not found >> in statement [select uimatype0_.ui ma_type_id as uima_typ1_21_, >> uimatype0_.uima_type_name as uima_typ2_21_, uimatype0_.table_name as >> table_na3_21_ from PUBLIC.ref_uima _type uimatype0_] ... >> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 6.277 >> sec <<< FAILURE! >> >> Results : >> >> Tests in error: >> test(org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest): >> Unable to initialize group definition. Group resource name [c >> lasspath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory >> key [ytexApplicationContext]; nested exception is org.springframe >> work.beans.factory.BeanCreationException: Error creating bean with >> name 'ytexApplicationContext' defined in URL [file:/C:/Spiffy/Dev >> /ApacheCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]: >> Instantiation of bean failed; >> nested exception is >> org.springframework.beans.BeanInstantiationException: Could not >> instantiate bean class [org.springframework.con >> text.support.ClassPathXmlApplicationContext]: Constructor threw >> exception; nested exception is org.springframework.beans.factory.Bea >> nCreationException: Error creating bean with name 'documentMapperService' >> defined in class path resource [org/apache/ctakes/ytex/uim >> a/beans-uima-mapper.xml]: Invocation of init method failed; nested >> exception is org.hibernate.exception.SQLGrammarException: could n ot >> prepare statement >> org.apache.ctakes.ytex.uima.annotators.DBConsumerTest: Unable to >> initialize group definition. Group resource name [classpath*:org/ >> apache/ctakes/ytex/uima/beanRefContext.xml], factory key >> [ytexApplicationContext]; nested exception is >> org.springframework.beans.fac >> tory.BeanCreationException: Error creating bean with name >> 'ytexApplicationContext' defined in URL >> [file:/C:/Spiffy/Dev/ApacheCtakesT >> runk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]: >> Instantiation of bean failed; nested except ion is >> org.springframework.beans.BeanInstantiationException: Could not >> instantiate bean class [org.springframework.context.support.C >> lassPathXmlApplicationContext]: Constructor threw exception; nested >> exception is org.springframework.beans.factory.BeanCreationExcep >> tion: Error creating bean with name 'documentMapperService' defined >> in class path resource [org/apache/ctakes/ytex/uima/beans-uima-m >> apper.xml]: Invocation of init method failed; nested exception is >> org.hibernate.exception.SQLGrammarException: could not prepare sta >> tement >> org.apache.ctakes.ytex.uima.annotators.DBConsumerTest >> >> testDictionaryLookupIntegrated(org.apache.ctakes.ytex.uima.annotators.DictionaryLookupAnnotatorTest): >> Initialization of annotator >> class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator" >> failed. (Descriptor: file:/C:/Spiffy/Dev/ApacheCtakesTrunk/cta >> kes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml) >> >> testDictionaryLookupSimple(org.apache.ctakes.ytex.uima.annotators.Dic >> tionaryLookupAnnotatorTest) >> >> testDisambiguate(org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotatorTest): >> Unable to initialize group definition. G roup resource name >> [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory >> key [ytexApplicationContext]; nested excepti on is >> org.springframework.beans.factory.BeanCreationException: Error >> creating bean with name 'ytexApplicationContext' defined in URL >> >> [file:/C:/Spiffy/Dev/ApacheCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]: >> Instanti >> ation of bean failed; nested exception is >> org.springframework.beans.BeanInstantiationException: Could not >> instantiate bean class [or >> g.springframework.context.support.ClassPathXmlApplicationContext]: >> Constructor threw exception; nested exception is org.springframew >> ork.beans.factory.BeanCreationException: Error creating bean with >> name 'documentMapperService' defined in class path resource [org/a >> pache/ctakes/ytex/uima/beans-uima-mapper.xml]: Invocation of init >> method failed; nested exception is org.hibernate.exception.SQLGram >> marException: could not prepare statement >> org.apache.ctakes.ytex.uima.annotators.SparseDataExporterTest: >> Unable to initialize group definition. Group resource name [classpa >> th*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key >> [ytexApplicationContext]; nested exception is org.springframework.b >> eans.factory.BeanCreationException: Error creating bean with name >> 'ytexApplicationContext' defined in URL [file:/C:/Spiffy/Dev/Apach >> eCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]: >> Instantiation of bean failed; neste >> d exception is org.springframework.beans.BeanInstantiationException: >> Could not instantiate bean class [org.springframework.context.s >> upport.ClassPathXmlApplicationContext]: Constructor threw exception; >> nested exception is org.springframework.beans.factory.BeanCreat >> ionException: Error creating bean with name 'documentMapperService' >> defined in class path resource [org/apache/ctakes/ytex/uima/bean >> s-uima-mapper.xml]: Invocation of init method failed; nested >> exception is >> org.hibernate.exception.SQLGrammarException: could not pre pare >> statement >> >> Tests run: 12, Failures: 0, Errors: 7, Skipped: 0 ... >> >> [INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [ >> 1.089 s] >> [INFO] Apache cTAKES YTEX ................................ SUCCESS [ >> 14.592 s] >> [INFO] Apache cTAKES YTEX UIMA ........................... FAILURE >> [01:34 min] [INFO] Apache cTAKES ctakes-clinical-pipeline >> ............ SKIPPED [INFO] Apache cTAKES YTEX Web >> ............................ SKIPPED >> >> ... >> [ERROR] Failed to execute goal >> org.apache.maven.plugins:maven-surefire-plugin:2.12:test >> (default-test) on project ctakes-ytex-uima: >> There are test failures. >> >> >> -----Original Message----- >> From: vijay garla [mailto:vnga...@gmail.com] >> Sent: Sunday, April 27, 2014 10:56 PM >> To: dev@ctakes.apache.org >> Subject: ytex merged into trunk >> >> Hello All, >> >> I have merged YTEX into trunk, will keep the branch around a little >> while then delete it. Some non-ytex related changes (I will gladly >> change/revert if there are objections): >> * ctakes-temporal does not compile; from the email threads I take it >> that this is under development and the compilation failures are to be >> expected. >> I have commented out these modules from the root pom.xml so that >> ctakes builds. I wasn't able to use maven profiles to exclude >> ctakes-temporal, not sure why. >> * default max memory runctakesCPE/CVD.bat: I have increased this to >> 2G (was 1G). I do not think it is possible to run cTAKES with less >> memory (definitely not in a 64-bit jdk) when loading the assertion >> models (which is the 'default' pipeline). >> >> I will clean up the ytex docs shortly. >> >> Best, >> >> VJ >> > >
