[R] setwd and list.files / linux

[Lars Beckmann]

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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