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 <[EMAIL PROTECTED]>
> An: Lars Beckmann <[EMAIL PROTECTED]>
> CC: r-help@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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