setwd and list.files / linux
Hey Marc,
sorry I forgot to mention it. I am the owner of the path, which is in my home directory. I can change the read/write/execute privileges. All users have - at least - read privileges for all files and the directory:
hpc36 40: ls -la *.tped
-rw-r--r-- 1 cremer C020 205487231 Dec 3 17:35 chr10.tped
-rw-r--r-- 1 cremer C020 192067641 Dec 3 17:37 chr11.tped
-rw-r--r-- 1 cremer C020 192243483 Dec 3 17:38 chr12.tped
etc
A workaround I found now is to start R in the respective directory from the command line, which will set working directory to current directory. list.files will work then too:
list.file(".",pattern="\\.tped")
The problem now is to start a script via R CMD BATCH from a different directory, because setwd() will not work:
datapath<-'/nfs/home/m/cremer/gaw/data/traws_chrs/' getwd()
[1] "/nfs/home/m/cremer/gaw/code/plink"
setwd(datapath)
Error in setwd(datapath) : cannot change working directory Execution halted Lars -------- Original-Nachricht --------
Datum: Thu, 04 Dec 2008 10:58:16 -0600 Von: Marc Schwartz <marc_schwartz at comcast.net> An: Lars Beckmann <Lars.Beckmann at gmx.net> CC: r-help at r-project.org Betreff: Re: [R] setwd and list.files / linux
on 12/04/2008 10:38 AM Lars Beckmann wrote:
Hey, two questions regarding setwd and list.files: I try to use the function list.files:
datapath<-'/nfs/home/m/cremer/gaw/data/traws_chrs'
fl<-list.files(datapath, pattern="\\.tped")
but I get the following error message: Warning message: In list.files(datapath, pattern = "\\.tped") : list.files: '/nfs/home/m/cremer/gaw/data/traws_chrs/' is not a
readable directory
fl
character(0) The use of setwd also does not work:
setwd(datapath)
Error in setwd(datapath) : cannot change working directory datapath exists and it doesn't matter whether I use single quotes ' or
double quotes "
Any help? Lars
You do not have read privileges to the path in question. Either you or your SysAdmin will have to grant the appropriate privileges so that you can read the files in the path. HTH, Marc Schwartz
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