[R] Difficulty with saving .Rhistory

[Patrick Connolly]

Hello T (short for TC, no doubt),


It appears to me that you're trying to run as a user in the /root/
directory.  Move to a directory down from /home/ and I think you'll
find it works.  

If my guess is incorrect, perhaps if you provide a long list of the
working directory and we'll see what's going on with the permissions.


HTH


On Tue, 13-Sep-2011 at 09:55PM -0700, T wrote:

|> 
|> Current systems
|> 
|>     OS: RedHat SE Linux 5.7, fully patched
|>     R: R-2.13.1
|> 
|> 
|> I am a new R user.
|> 
|> 
|> The R installation needs to be very tight because I plan to use it after I am employed on Internet facing systems to analyse firewall and filesystem log data.  Everything to my knowledge regarding R installed correctly.  I saw no warnings until saving THE WORKSPACE.
|> 
|> 
|> NON-ROOT OUTPUT CURRENTLY YIELDS THE FOLLOWING ERROR
|> > q()
|> Save workspace image? [y/n/c]: y
|> Warning message:
|> problem in saving the history file '.Rhistory'
|> [Object at localhost R]$
|> 
|> 
|> 
|> The sitrep...
|> 
|> 
|> ------------------------------------------------------------------------------
|> INITIAL NON-ROOT OUTPUT WAS THE FOLLOWING
|> > q()
|> Save workspace image? [y/n/c]: y
|> Error in gzfile(file, "wb") : cannot open the connection
|> In addition: Warning message:
|> In gzfile(file, "wb") :
|>   cannot open compressed file '.RDataTmp', probable reason 'Permission denied'
|> >
|> > q()
|> Save workspace image? [y/n/c]: n
|> Warning message:
|> In file.remove(outfile) :
|>   cannot remove file '.RDataTmp', reason 'No such file or directory'
|> 
|> 
|> INITIAL ROOT WAS THE FOLLOWING:
|> >
|> > q()
|> Save workspace image? [y/n/c]: y
|> [root at localhost ~]#
|> 
|> 
|> Here is what I did, which I thought would fix everything:
|> 
|> [root at localhost ~]# groupadd -g 666 r_users
|> [root at localhost ~]# usermod --groups r_users Object
|> [root at localhost ~]# cat /etc/group | grep r_users
|> r_users:x:666:Object
|> 
|> [root at localhost ~]# chown -R root:r_users /var/R/R-2.13.1
|> [root at localhost ~]# 
|> [root at localhost ~]# find /var/R/R-2.13.1 -type d | xargs chmod g+rwx
|> 
|> 
|> 
|> 
|> Note that I have gREpped for the .RDataTmp file and any variation between "R[Dd]ata" and I see nothing being written but the warnings have stopped...so maybe I am not generating anything to save the workspace.
|> 
|> 
|> Now, when using a non-root account I have an issue with the .Rhistory file in that I have the following warnings.
|> 
|> ROOT NOW YIELDS THE FOLLOWING:
|> > q()
|> Save workspace image? [y/n/c]: y
|> [root at localhost ~]#
|> 
|> 
|> NON-ROOT OUTPUT NOW YIELDS ANOTHER ERROR
|> > q()
|> Save workspace image? [y/n/c]: y
|> Warning message:
|> problem in saving the history file '.Rhistory'
|> [Object at localhost R]$
|> 
|> 
|> [Object at localhost R]$ ls -al /var/R/
|> total 21604
|> drwxr-xr-x  3 root root        4096 Sep  9 19:02 .
|> drwxr-xr-x 28 root root        4096 Sep  9 18:57 ..
|> drwxrwxr-x 15 root r_users     4096 Sep  9 19:05 R-2.13.1
|> -rw-r--r--  1 root root    22063747 Sep  9 18:58 R-2.13.1.tar.gz
|> 
|> [Object at localhost R]$ ls -al /var/R/R-2.13.1
|> total 3772
|> drwxrwxr-x 15 root r_users    4096 Sep  9 19:05 .
|> drwxr-xr-x  3 root root       4096 Sep  9 19:02 ..
|> drwxrwxr-x  3 root r_users    4096 Sep  9 19:05 bin
|> -rw-r--r--  1 root r_users       0 Mar 17  2010 ChangeLog
|> -rw-r--r--  1 root r_users  356442 Sep  9 19:04 config.log
|> -rw-r--r--  1 root r_users    9277 Mar 29 17:02 config.site
|> -rwxr-xr-x  1 root r_users  110293 Sep  9 19:03 config.status
|> -rwxr-xr-x  1 root r_users 1350078 Jun 30 17:05 configure
|> -rw-r--r--  1 root r_users   83993 May 30 17:05 configure.ac
|> -rw-r--r--  1 root r_users   18011 Mar 17  2010 COPYING
|> drwxrwxr-x  4 root r_users    4096 Sep  9 19:06 doc
|> drwxrwxr-x  2 root r_users    4096 Sep  9 19:03 etc
|> drwxrwxr-x  3 root r_users    4096 Sep  9 19:03 include
|> -rw-r--r--  1 root r_users    1747 Mar 17  2010 INSTALL
|> drwxrwxr-x  3 root r_users    4096 Sep  9 22:29 lib
|> ...
|> 
|> ______________________________________________
|> 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.

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.