R help - Feb 2012 - Help needed! Error in setwd(newdir) : cannot change working directory

Hi Guys,

I am new to R and just trying to write a small script to automate a couple
commands. But I run into the setwd(): cannot change working directory.
I googled a little bit and tried all fixes/suggestions with no success.
Basically I have a script that works from inside a directory with my data
(/home/sean/Rtest/Data01). Now I want to modify the script to make it run from
the upper directory (/home/sean/Rtest) because I have many data directories
under /Rtest, such as /home/sean/Rtest/Data01, /home/sean/Rtest/Data02,
/home/sean/Rtest/Data03,.....
I want to modify my script so that it will run from /Rtest, and with the data
directory name as arg passed to my R script. Here is my mytest02.R
script:
>># retrieve args>>args <- commandArgs(TRUE);>># store the
current directory>>initial.dir <- getwd();>>newdir <-
paste(initial.dir,args,sep="/");>>outfilename <-
paste(args,"out",sep=".");>># change to the new
directory>>setwd(newdir);>># load the necessary
libraries>>library("A"); 
#>>library("B");>>library("C");>># set the
output file>>sink(outfilename);>>........    #data
processing>>........    #data processing>>........    #data
processing>># close the output file>>sink();>># unload the
libraries>>detach("package:A"); 
#>>detach("package:B");>>detach("package:C");>>#
change back to the original directory>>setwd(initial.dir);
Then I run the script by
>>sean@I7-3930K:~/Rtest$ R --slave --args Data01 < mytest02.R
I got the error message:
>>sean@I7-3930K:~/Rtest$ R --slave --args Data01 <
mytest02.R>>Attempting to load the environment
‘package:R.utils’>>Loading required package:
R.methodsS3>>R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See
?R.methodsS3 for help.>>Loading required package: utils>>R.oo v1.8.3
(2011-11-01) successfully loaded. See ?R.oo for help.>>>>Attaching
package: ‘R.oo’>>>>The following object(s) are masked from
‘package:R.methodsS3’:>> >>   throw.default>>>>The
following object(s) are masked from ‘package:methods’:>> >>  
getClass, getClasses, getMethods>>>>The following object(s) are
masked from ‘package:base’:>> >>   attach, detach, environment, gc,
load, save>>>>R.utils v1.9.11 (2012-01-17) successfully loaded. See
?R.utils for help.>>>>Attaching package:
‘R.utils’>>>>The following object(s) are masked from
‘package:utils’:>>>>    timestamp>>>>The following
object(s) are masked from ‘package:base’:>>>>    cat, commandArgs,
getOption, inherits, isOpen, lapply, parse,>>    remove,
warnings>>>>[1] "/home/sean/Rtest">>[1]
"/home/sean/Rtest/NA"       "/home/sean/Rtest/TRUE"   
>>[3] "/home/sean/Rtest/Data01">>[1] "NA.out"   
"TRUE.out"     "Data01.out">>Error in setwd(newdir) :
cannot change working directory>>Execution halted
What did I do wrong?
One more question, is there anyway to modify this script to make it work on all
data directories under /home/sean/Rtest by itself?
Thanks a lot for the help!
Ying
 		 	   		   		 	   		  
	[[alternative HTML version deleted]]

This is a mess -- please resend in plain text.

Also, there are not, to my knowledge, packages (not libraries) called
"A", "B", or "C" so your script doesn't even
begin to look
reproducible were it legible.

Do you have read/write access to the directories in question?

Michael

On Sat, Feb 25, 2012 at 11:25 PM, ying chen <ying_chen at live.com>
wrote:
>
> Hi Guys,
>
> I am new to R and just trying to write a small script to automate a couple
commands. But I run into the setwd(): cannot change working directory.
> I googled a little bit and tried all fixes/suggestions with no success.
> Basically I have a script that works from inside a directory with my data
(/home/sean/Rtest/Data01). Now I want to modify the script to make it run from
the upper directory (/home/sean/Rtest) because I have many data directories
under /Rtest, such as /home/sean/Rtest/Data01, /home/sean/Rtest/Data02,
/home/sean/Rtest/Data03,.....
> I want to modify my script so that it will run from /Rtest, and with the
data directory name as arg passed to my R script. Here is my mytest02.R script:
>>># retrieve args>>args <- commandArgs(TRUE);>># store
the current directory>>initial.dir <- getwd();>>newdir <-
paste(initial.dir,args,sep="/");>>outfilename <-
paste(args,"out",sep=".");>># change to the new
directory>>setwd(newdir);>># load the necessary
libraries>>library("A");
?#>>library("B");>>library("C");>># set
the output file>>sink(outfilename);>>........ ? ?#data
processing>>........ ? ?#data processing>>........ ? ?#data
processing>># close the output file>>sink();>># unload the
libraries>>detach("package:A");
?#>>detach("package:B");>>detach("package:C");>>#
change back to the original directory>>setwd(initial.dir);
> Then I run the script by
>>>sean at I7-3930K:~/Rtest$ R --slave --args Data01 < mytest02.R
> I got the error message:
>>>sean at I7-3930K:~/Rtest$ R --slave --args Data01 <
mytest02.R>>Attempting to load the environment
?package:R.utils?>>Loading required package:
R.methodsS3>>R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See
?R.methodsS3 for help.>>Loading required package: utils>>R.oo v1.8.3
(2011-11-01) successfully loaded. See ?R.oo for help.>>>>Attaching
package: ?R.oo?>>>>The following object(s) are masked from
?package:R.methodsS3?:>> >> ? throw.default>>>>The
following object(s) are masked from ?package:methods?:>> >> ?
getClass, getClasses, getMethods>>>>The following object(s) are
masked from ?package:base?:>> >> ? attach, detach, environment, gc,
load, save>>>>R.utils v1.9.11 (2012-01-17) successfully loaded. See
?R.utils for help.>>>>Attaching package:
?R.utils?>>>>The following object(s) are masked from
?package:utils?:>>>> ? ?timestamp>>>>The following
object(s) are masked from ?package:base?:>>>> ? ?cat, commandArgs,
getOption, inherits, isOpen, lapply, parse,>> ? ?remove,
warnings>>>>[1] "/home/sean/Rtest">>[1]
"/home/sean/Rtest/NA" ? ? ? "/home/sean/Rtest/TRUE" ?
?>>[3] "/home/sean/Rtest/Data01">>[1] "NA.out" ?
? ? "TRUE.out" ? ? "Data01.out">>Error in
setwd(newdir) : cannot change working directory>>Execution halted
> What did I do wrong?
> One more question, is there anyway to modify this script to make it work on
all data directories under /home/sean/Rtest by itself?
> Thanks a lot for the help!
> Ying
>
> ? ? ? ?[[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

try setwd(choose.dir()) 

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