tbigdeli wrote:
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,..)
}
1. This should do the same for interactive and batch mode given the
relevant things are not hidden in "...".
2. You are running both inteactive and batch under the same user?
3. Why do you change working directories all the time, you could give
full path names instead.
4. 1:length(files$V1) is dangerous in loops (if length becomes 0),
hence use seq_along(files$V1)
Uwe Ligges
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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