org.rosuda.REngine.Rserve.RserveException

There are no available Samebug tips for this exception. Do you have an idea how to solve this issue? A short tip would help users who saw this issue last week.

  • Can't create a notebook on Mac
    via GitHub by csu
    ,
  • GitHub comment 2690#147036470
    via GitHub by ArthurZ
    ,
  • R backend error
    via GitHub by upendrak
    ,
  • GitHub comment 3422#175901250
    via GitHub by bcaller
    ,
  • R Error
    via GitHub by kartikdesikan
    ,
  • Running Paul's http://www.myexperiment.org/workflows/10 causes: WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196) - Failed (INVOCATION) invoking net.sf.taverna.t2.activitie .rshell.RshellActivity@1e1d497 for job DispatchJobEvent facade4:MicroarrayCELfi etocandidatepathways:AffyDataAnalysis[]: Could not establish connection to loca host using port 6311: Cannot connect: Connection refused: connect org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused: onnect at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88) at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60) at net.sf.taverna.t2.activities.rshell.RshellConnection.<init>(RshellCo nection.java:50) at net.sf.taverna.t2.activities.rshell.RshellConnectionManager.createCo nection(RshellConnectionManager.java:87) at net.sf.taverna.t2.activities.rshell.RshellActivity$1.run(RshellActiv ty.java:136) at java.lang.Thread.run(Thread.java:619) WARN 2009-11-22 15:46:03,466 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196) - Failed (INVOCATION) invoking net.sf.taverna.t2.activitie .rshell.RshellActivity@1e1d497 for job DispatchJobEvent facade4:MicroarrayCELfi etocandidatepathways:AffyDataAnalysis[]: Uncaught exception while invoking net. f.taverna.t2.activities.rshell.RshellActivity@1e1d497 java.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [Ljava.lang String; at net.sf.taverna.t2.activities.rshell.RshellActivity.javaToRExp(Rshell ctivity.java:429) at net.sf.taverna.t2.activities.rshell.RshellActivity.access$400(Rshell ctivity.java:69) at net.sf.taverna.t2.activities.rshell.RshellActivity$1.run(RshellActiv ty.java:163) at java.lang.Thread.run(Thread.java:619)
    via by Alan Williams,
    • org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88) at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60) at edu.harvard.iq.dataverse.rserve.RemoteDataFrameService.runDataPreprocessing(RemoteDataFrameService.java:556) at edu.harvard.iq.dataverse.dataaccess.DataFileConverter.runFormatConversion(DataFileConverter.java:257) at edu.harvard.iq.dataverse.dataaccess.DataFileConverter.performFormatConversion(DataFileConverter.java:120) at edu.harvard.iq.dataverse.api.DownloadInstanceWriter.writeTo(DownloadInstanceWriter.java:109) at edu.harvard.iq.dataverse.api.DownloadInstanceWriter.writeTo(DownloadInstanceWriter.java:40) at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263) at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250) at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) at org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:106) at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:89) at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) at org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154) at org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:621) at org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:377) at org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:367) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:274) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) at org.glassfish.jersey.internal.Errors.process(Errors.java:315) at org.glassfish.jersey.internal.Errors.process(Errors.java:297) at org.glassfish.jersey.internal.Errors.process(Errors.java:267) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:297) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028) at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:372) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344) at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221) at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:205) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:162) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:30) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:575) at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546) at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:378) at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174) at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545) at java.lang.Thread.run(Thread.java:745)

    Users with the same issue

    Unknown visitor1 times, last one,
    Unknown visitor1 times, last one,
    Unknown visitor1 times, last one,
    Unknown visitor1 times, last one,
    Unknown visitor1 times, last one,
    5 more bugmates