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 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]]

Hi,
I am sorry about the format it showed up. I do not know what happened
as it looks fine when I read it using chrome on ubuntu 11.10 64bit. The
packages A, B, C are not the real package names.  Basically I have 
scriptA.R 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. My point is that when I put the
scriptA.R in data directory such as Data01, it works. Here are my
scriptB.R script:
######################scriptA.R#########################################
# load the necessary librarieslibrary("A");  # A fake package
namelibrary("B");  # B fake package namelibrary("C");  # C fake package
name........    #data processing........    #data processing........   
#data processing# unload the librariesdetach("package:A"); 
detach("package:B");detach("package:C");q();#######################################################################
But, when I tried to modify scriptA.R to scriptB.R to run it from the
directory just above Data directories, I got the error message.
###########################scriptB.R#######################################
# retrieve argsargs <- commandArgs(TRUE);# store the current
directoryinitial.dir <- getwd();newdir <-
paste(initial.dir,args,sep="/");outfilename <-
paste(args,"out",sep=".");# change to the new directorysetwd(newdir);#
load the necessary librarieslibrary("A");  # A fake package
namelibrary("B");  # B fake package namelibrary("C");  # C fake package
name# set the output filesink(outfilename);........    #data
processing........    #data processing........    #data processing#
close the output filesink();# unload the librariesdetach("package:A"); 
#detach("package:B");detach("package:C");# change back to the original
directorysetwd(initial.dir);
##################################################################
I run the scriptB.R by
sean at I7-3930K:~/Rtest$ R --slave --args Data01 < scriptB.R
I got the error message:
sean at I7-3930K:~/Rtest$ R --slave --args Data01 < scriptB.RAttempting to
load the environment ?package:R.utils?Loading required package:
R.methodsS3R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See
?R.methodsS3 for help.Loading required package: utilsR.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 directoryExecution halted
What did I do wrong? I think I have the right to read and write to the
directories.
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
sean at I7-3930K:~/Rtest$ ls -ltotal 56drwx------ 3 sean sean 4096
2012-02-25 20:39 Data01drwx------ 2 sean sean 4096 2012-02-25 20:28
Data02drwx------ 2 sean sean 4096 2012-02-26 07:41 Data03drwx------ 2
sean sean 4096 2012-02-25 21:18 Data04drwx------ 2 sean sean 4096
2012-02-25 20:27 Data05-rw-r--r-- 1 sean sean  437 2012-02-26 15:28
scriptA.R.......

From: michael.weylandt at gmail.com
Date: Sun, 26 Feb 2012 12:48:57 -0500
Subject: Re: [R] Help needed! Error in setwd(newdir) : cannot change

working directory

To: ying_chen at live.com
CC: r-help at r-project.org

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]]

Hi, 
 
I am sorry about the format it showed up. I do not know what happened as now it looks worse even on my own machine. I do not know what to do, I just add "\n" to the end of each line and hope it will come out OK this time. The packages A, B, C are not the real package names.  Basically I have  scriptA.R 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. My point is that when I put the scriptA.R in data directory such as Data01, it works. Here are my scriptB.R script: 
 
######################scriptA.R######################################### 
 
# load the necessary libraries 
library("A");  # A fake package name 
library("B");  # B fake package name 
library("C");  # C fake package name 
........    #data processing 
........    #data processing 
........    #data processing 
# unload the libraries 
detach("package:A");   
detach("package:B"); 
detach("package:C"); 
q(); 
####################################################################### 

But, when I tried to modify scriptA.R to scriptB.R to run it from the directory just above Data directories, I got the error message. 

###########################scriptB.R#######################################

# 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");  # A fake package name 
library("B");  # B fake package name 
library("C");  # C fake package name 

# 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); 

################################################################## 

I run the scriptB.R by 

sean at I7-3930K:~/Rtest$ R --slave --args Data01 < scriptB.R 

I got the error message: 

sean at I7-3930K:~/Rtest$ R --slave --args Data01 < scriptB.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