[R] re ad.table() and setwd() in unix batch mode

[tbigdeli]

My apologies for being overly brief before..

I submit an R script to batch mode as follows:

a list of files (object = 'files').  In each iteration, the next file is
read, alterations made, working directory changed, and output file written
out.  R will take an inordinate amount of time processing the first file,
after which no files seem to be read-in.  For batch mode, are my paths
inappropriate?  Thanks!

setwd("/home/bigdelitb/chr20/merlin/sim/d5/ped")
files<-read.table("d5.rf.list",stringsAsFactors=FALSE)

for(i in 1:length(files$V1)){
	setwd("/home/bigdelitb/chr20/merlin/sim/d5/ped")
	count <- 1
	name<-files$V1[i]
	ped <- read.table(name,header=FALSE,stringsAsFactors=FALSE)
        ...
        ...
        setwd("/home/bigdelitb/chr20/merlin/sim/d5/ped/pdt/")
        write.table(ped,name,quote=FALSE,..)
}

Uwe Ligges-3 wrote:
> 
> 
> 
> tbigdeli wrote:
>> I continually receive the error
>> 
>> Error in file(file, "r") : cannot open the connection, when running in
>> batch
>> mode, but not when inputing directly into R. 
> 
> Have you given the full path name?
> If not, do you start both R instances from the same working directory?
> 
> Otherwise, do you have the same credentials in both cases?
> 
> Uwe Ligges
> 
> 
> 
> 
> 
>> 
>> Any ideas?
>> 
>> Thanks!
>> 
>> TB
> 
> ______________________________________________
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> PLEASE do read the posting guide
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> 
> 

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