"Problem Installing RapidAnalytics: errors running sh script run.sh"

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  fischer Member Posts: 439 Maven

  January 2011

  Hi,
  
  stange. The warnings you post seem to be irrelevant to me. The "16:50:39,233 WARNING [Injector] duplicate class definition bug occured? Please report this : de/rapidanalytics/web/service" is the one that the manual mentions. Don't report it. It's not the reason.
  
  What happens in the 12 seconds between this and "16:50:47,746 ERROR [[/RA]] Exception starting filter de.rapidanalytics.web.filter.AccessLogFilter: java.lang.RuntimeException: Unable to inject jndi dependency: "? Can you post the full log?
  
  Best,
  Simon

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  Ethan Member Posts: 4 Contributor I

  January 2011

  Simon,
  
  I'd like to, but I hit the maximum allowable characters for a forum post.  Can I attach a file, or email the text?  Here's the section you asked about:
  
  15:56:37,858 WARNING [Injector] duplicate class definition bug occured? Please report this : de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;: java.lang.ClassFormatError: Illegal class name "de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;" in class file de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;
  at java.lang.ClassLoader.defineClass1(Native Method)
  at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
  at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
  at java.lang.ClassLoader.defineClass(ClassLoader.java:466)
  at sun.reflect.GeneratedMethodAccessor123.invoke(Unknown Source)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
  at java.lang.reflect.Method.invoke(Method.java:597)
  at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.inject(Injector.java:205)
  at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.inject(Injector.java:85)
  at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:89)
  at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:114)
  at com.sun.xml.bind.v2.runtime.reflect.Accessor$GetterSetterReflection.optimize(Accessor.java:369)
  at com.sun.xml.bind.v2.runtime.property.ArrayProperty.<init>(ArrayProperty.java:65)
  at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.<init>(ArrayERProperty.java:84)
  at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.<init>(ArrayElementProperty.java:96)
  at com.sun.xml.bind.v2.runtime.property.ArrayElementLeafProperty.<init>(ArrayElementLeafProperty.java:66)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:124)
  at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:179)
  at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:515)
  at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:534)
  at com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>(SingleElementNodeProperty.java:101)
  at sun.reflect.GeneratedConstructorAccessor45.newInstance(Unknown Source)
  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:124)
  at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:179)
  at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:515)
  at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:330)
  at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1140)
  at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:154)
  at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:121)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
  at java.lang.reflect.Method.invoke(Method.java:597)
  at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:201)
  at javax.xml.bind.ContextFinder.find(ContextFinder.java:362)
  at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:618)
  at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:565)
  at org.jboss.ws.core.jaxws.CustomizableJAXBContextFactory.createContext(CustomizableJAXBContextFactory.java:76)
  at org.jboss.ws.metadata.umdm.EndpointMetaData.eagerInitializeAccessors(EndpointMetaData.java:670)
  at org.jboss.ws.metadata.umdm.EndpointMetaData.initializeInternal(EndpointMetaData.java:550)
  at org.jboss.ws.metadata.umdm.EndpointMetaData.eagerInitialize(EndpointMetaData.java:538)
  at org.jboss.ws.metadata.umdm.ServiceMetaData.eagerInitialize(ServiceMetaData.java:433)
  at org.jboss.ws.metadata.umdm.UnifiedMetaData.eagerInitialize(UnifiedMetaData.java:199)
  at org.jboss.wsf.stack.jbws.EagerInitializeDeploymentAspect.start(EagerInitializeDeploymentAspect.java:48)
  at org.jboss.webservices.integration.deployers.WSDeploymentAspectDeployer.internalDeploy(WSDeploymentAspectDeployer.java:107)
  at org.jboss.deployers.spi.deployer.helpers.AbstractRealDeployer.deploy(AbstractRealDeployer.java:55)
  at org.jboss.deployers.plugins.deployers.DeployerWrapper.deploy(DeployerWrapper.java:179)
  at org.jboss.deployers.plugins.deployers.DeployersImpl.doDeploy(DeployersImpl.java:1660)
  at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1378)
  at org.jboss.deployers.plugins.deployers.DeployersImpl.doInstallParentFirst(DeployersImpl.java:1431)
  at org.jboss.deployers.plugins.deployers.DeployersImpl.install(DeployersImpl.java:1319)
  at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:378)
  at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:2029)
  at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:1050)
  at org.jboss.dependency.plugins.AbstractController.executeOrIncrementStateDirectly(AbstractController.java:1289)
  at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1213)
  at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1107)
  at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:918)
  at org.jboss.dependency.plugins.AbstractController.change(AbstractController.java:633)
  at org.jboss.deployers.plugins.deployers.DeployersImpl.process(DeployersImpl.java:898)
  at org.jboss.deployers.plugins.main.MainDeployerImpl.process(MainDeployerImpl.java:677)
  at org.jboss.system.server.profileservice.repository.MainDeployerAdapter.process(MainDeployerAdapter.java:117)
  at org.jboss.system.server.profileservice.repository.ProfileDeployAction.install(ProfileDeployAction.java:70)
  at org.jboss.system.server.profileservice.repository.AbstractProfileAction.install(AbstractProfileAction.java:53)
  at org.jboss.system.server.profileservice.repository.AbstractProfileService.install(AbstractProfileService.java:403)
  at org.jboss.dependency.plugins.AbstractControllerContext.install(AbstractControllerContext.java:378)
  at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:2029)
  at org.jboss.dependency.plugins.AbstractController.incrementState(AbstractController.java:1050)
  at org.jboss.dependency.plugins.AbstractController.executeOrIncrementStateDirectly(AbstractController.java:1289)
  at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1213)
  at org.jboss.dependency.plugins.AbstractController.resolveContexts(AbstractController.java:1107)
  at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:873)
  at org.jboss.dependency.plugins.AbstractController.install(AbstractController.java:620)
  at org.jboss.system.server.profileservice.repository.AbstractProfileService.registerProfile(AbstractProfileService.java:308)
  at org.jboss.system.server.profileservice.ProfileServiceBootstrap.start(ProfileServiceBootstrap.java:259)
  at org.jboss.system.server.profileservice.ProfileServiceBootstrap.start(ProfileServiceBootstrap.java:100)
  at org.jboss.bootstrap.impl.base.server.AbstractServer.startBootstraps(AbstractServer.java:860)
  at org.jboss.bootstrap.impl.base.server.AbstractServer$StartServerTask.run(AbstractServer.java:441)
  at java.lang.Thread.run(Thread.java:680)
  
  15:56:37,881 INFO  [WSDLFilePublisher] WSDL published to: file:/Applications/rapidanalytics/server/default/data/wsdl/RapidAnalytics.ear/RapidRepositoryWebService.war/RepositoryService6471260153992731918.wsdl
  15:56:37,890 INFO  [WSDLFilePublisher] WSDL published to: file:/Applications/rapidanalytics/server/default/data/wsdl/RapidAnalytics.ear/RapidRepositoryWebService.war/ProcessService5199971243466470240.wsdl
  15:56:38,467 INFO  [TomcatDeployment] deploy, ctxPath=/RA
  15:56:38,562 INFO  [config] Initializing Mojarra 2.0.2 (FCS b10) for context '/RA'
  15:56:45,646 INFO  [CacheManager] Selected [org.ajax4jsf.cache.LRUMapCacheFactory] cache factory
  15:56:45,646 INFO  [LRUMapCacheFactory] Creating LRUMap cache instance using parameters: {com.sun.faces.forceLoadConfiguration=true, org.richfaces.CONTROL_SKINNING=enable, org.ajax4jsf.VIEW_HANDLERS=com.sun.facelets.FaceletViewHandler, com.sun.faces.duplicateJARPattern=^tmp\d+(\S*\.jar), com.sun.faces.injectionProvider=org.jboss.web.jsf.integration.injection.JBossDelegatingInjectionProvider, javax.faces.DATETIMECONVERTER_DEFAULT_TIMEZONE_IS_SYSTEM_TIMEZONE=true, javax.faces.DISABLE_FACELET_JSF_VIEWHANDLER=true, javax.faces.SKIP_COMMENTS=true, javax.faces.DEFAULT_SUFFIX=.xhtml}
  15:56:45,646 INFO  [LRUMapCacheFactory] Creating LRUMap cache instance of default capacity
  15:56:45,649 INFO  [CacheManager] Selected [org.ajax4jsf.cache.LRUMapCacheFactory] cache factory
  15:56:45,649 INFO  [LRUMapCacheFactory] Creating LRUMap cache instance using parameters: {com.sun.faces.forceLoadConfiguration=true, org.richfaces.CONTROL_SKINNING=enable, org.ajax4jsf.VIEW_HANDLERS=com.sun.facelets.FaceletViewHandler, com.sun.faces.duplicateJARPattern=^tmp\d+(\S*\.jar), com.sun.faces.injectionProvider=org.jboss.web.jsf.integration.injection.JBossDelegatingInjectionProvider, javax.faces.DATETIMECONVERTER_DEFAULT_TIMEZONE_IS_SYSTEM_TIMEZONE=true, javax.faces.DISABLE_FACELET_JSF_VIEWHANDLER=true, javax.faces.SKIP_COMMENTS=true, javax.faces.DEFAULT_SUFFIX=.xhtml}
  15:56:45,650 INFO  [LRUMapCacheFactory] Creating LRUMap cache instance of default capacity
  

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  fischer Member Posts: 439 Maven

  January 2011

  Hi,
  
  I have received the complete log file by email. To me it looks like you did not define a data source, did you?
  
  Best,
  Simon

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  Ethan Member Posts: 4 Contributor I

  January 2011

  Simon,
  
  I used the Optionally section in the Install manual under 1.1.1; i.e. I have RapidMiner 5.1 installed, vice a SQL database.  I did not see in a further section where I needed to define a data source... unlike when using an SQL database.  Obviously I've missed a step....
  
  Can you provide some guidance when installing with RapidMiner 5.1 without using an SQL database such as MySQL?
  
  Thank you,
  Ethan

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  Ethan Member Posts: 4 Contributor I

  January 2011

  Okay, I managed to get this installed now.
  
  I misunderstood the install manual, such that I read you either needed a SQL database OR optionally RapidMiner.  I've installed MySQL, followed the instructions, and RapidAnalytics installed without difficulty.
  
  Thank you Simon.
  
  

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  mmargett Member Posts: 4 Contributor I

  January 2011

  I am also having a problem installing rapidanalytics.  The errors in the boot.log start with:
  
  10:04:55,649 INFO  [PersistenceUnitDeployment] Starting persistence unit persistence.unit:unitName=RapidAnalytics.ear/lib/RapidRepositoryEntity.jar#RapidRepositoryEntity
  10:04:55,681 ERROR [AbstractKernelController] Error installing to Start: name=persistence.unit:unitName=RapidAnalytics.ear/lib/RapidRepositoryEntity.jar#RapidRepositoryEntity state=Create: javax.naming.NameNotFoundException: jdbc not bound
  at org.jnp.server.NamingServer.getBinding
  
  I've followed the instructions in the manual for the bundled install.  I'm confident that my rapidanalytics-ds.xml is correct and the jdbc jar was copied to the rapidanalytics/server/default/lib directory.
  
  If you need the full log please tell me how/where to put the log.  BTW I'm using Oracle 11gR2 as the DB, installing RapidAnalytics on Windows 2008R2 64bit in a VM with 1 proc and 4GB RAM
  
  Please advise.

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  fischer Member Posts: 439 Maven

  January 2011

  Hi,
  
  your data source uses the wrong JNDI name. Try adding to the -ds.xml:
  
  <use-java-context>false</use-java-context>
  
  Best,
  Simon

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  mmargett Member Posts: 4 Contributor I

  January 2011

  getting closer.  After adding <use-java-context>false</use-java-context> I get
  [JBossManagedConnectionPool] Throwable while attempting to get a new connection: null: org.jboss.resource.JBossResourceException: Could not create connection; - nested throwable: (java.sql.SQLException: Io exception: The Network Adapter could not establish the connection)
  
  which looks like either the connection url is wrong or the server cant find the jdbc jar.  I've tested the url in another app that it works fine.  I've also copied the ojdbc14.jar to rapidanalytics/common/lib and rapidanalytics/server/default/lib just to make sure. 
  what else is needed?

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  mmargett Member Posts: 4 Contributor I

  January 2011

  I had an old JDBC version.  I've replaced that and now I'm getting the following error in the boot.log
  ERROR [[/RA]] Exception starting filter de.rapidanalytics.web.filter.AccessLogFilter: java.lang.RuntimeException: Unable to inject jndi dependency: env/de.rapidanalytics.web.filter.AccessLogFilter/accessLogEJB into property de.rapidanalytics.web.filter.AccessLogFilter.accessLogEJB: RapidAnalytics not bound
  
  

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  mmargett Member Posts: 4 Contributor I

  January 2011

  Problem resolved.  The machine that I installed RapidAnalytics needed the domain appended to the host name.  Duh!!!

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  fischer Member Posts: 439 Maven

  January 2011

  Hi,
  
  that's it. JBoss will add the hostname to the WSDL it generates, so the hostname must be one that is actually working from the machine that connects to RA.
  
  Best,
  Simon

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  riyao Member Posts: 4 Contributor I

  February 2011

  Hi Simon,
  
  I have the similar problem with the two person above, and tried all the methods you suggested above, like check the jdbc version. But the problem is still there. Have spent more than 3 hours on it, hope that you can help. Thanks a lot in advance!
  
  
  I will email you the whole log. Again, thanks!
  
  PS: I am sure the jdbc part is fine, followed the manual, create the db, rapidanalytics and create a user with the name rapidanalytics. And I also grant all the privileges to that user. I tried to connect this database to Crystal Reports, it works fine.
  
  

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  fischer Member Posts: 439 Maven

  February 2011

  Dear Riyao,
  
  there are some issues with this posting:
  
  - You are providing virtually no information except the fact that things don't work.
  - This thread is becoming a general "things don't work thread". Please try be more specific and open new threads for new topics
  - Looking at the log file in your email, I don't see any hint that the datasource is configured properly. Please check in the JBoss admin-console (http://localhost:8080/admin-console)
  - I did not ask for private email. If you need email support, please get an enterprise edition.
  
  Best,
  Simon
  

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  riyao Member Posts: 4 Contributor I

  February 2011

  Hi Simon,
  
  Thanks for your reply. I feel sorry for the vague explanation of the problem. I will post a new thread with specific problems.
  
  PS: I am very interested in data mining and machine learning field, that is why i choose this software to explore.

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  cyberbugsy Member Posts: 1 Contributor I

  April 2011

  Hello Ethan,
  
  I have got the same warning, but I had an other problem with my datasource. Perhaps this warning is not important:
  
  13:45:11,493 WARNING [Injector] duplicate class definition bug occured? Please report this : de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;: java.lang.ClassFormatError: Illegal class name "de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;" in class file de/rapidanalytics/web/service/ProcessResponse$JaxbAccessorM_getOutputLocations_setOutputLocations_[Ljava_lang_String;
  
  If you have a startup problem, you will see this warning first and perhaps try to fix the wrong bug.
  
  My problem was not to copy the *-ds.xml.template file to the correct name.
  
  Here are my hints for checking the data source:
  
  1.
  Please make shure you have the rapidanalytics-mysql-ds.xml file copied
  
  stop server:
  rapidanalytics/bin/shutdown.sh -S
  
  cd rapidanalytics/server/default/deploy
  cp rapidanalytics-mysql-ds.xml rapidanalytics-ds.xml
  
  2.
  change password "XXX_PASSWORD" to your password previosly set for the user rapidanalytics in mysql.
  Be shure not corrupt the file rapidanalytics-ds.xml.
  
  3.
  startup again:
  
  rapidanalytics/bin/run.sh
  
  4.
  Open http://localhost:8080/admin-console
  and check Resources -> Datasources . there mus be two data sources configured and up: "DefaultDS" and "jdbc/RapidAnalyticsDS"
  
  Greetings, Bernd.
  

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