On 28/10/2010 15:10, Bambhania, Anand M. wrote:
> Hi all,
Hello
> I'm using Rshell to process multiple sample files. I read all files as a
> string vector called "Files". It also gives number of samples with length
> function but when I try to read them tab delimited for further processing, it
> gives me following error for output port "temp":
>
> [error]
> org.rosuda.REngine.Rserve.RserveException: cannot open the connection
>
> net.sf.taverna.t2.activities.rshell.RshellActivity$1.run(RshellActivity.java:217)
> java.lang.Thread.run(Thread.java:662)
> [error]
>
> I'm trying very simple code:
>
> #Files are sample files(.txt) read as string vector
> Sample_length<-length(Files)
So the script is OK up to here?
> #looping through string vector and reading each sample file tab delimited
> for (i in 1:24)
> {
> #Read in as temporary data, process it, then assign as SampleName
> temp<- read.delim(Files[i], skip=13, sep=";", header=F, na.strings=NA,
> fill=T)
> }
>
> I'm unable to find what causes this error. Any idea?
Are the files on the R server? Looking at the code, I think R is
complaining it "cannot open the connection" to one of the files.
> Thanks,
>
> Anand
Alan
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