[BioC] reposTool package: permission problems on liblisting.Rda file

[Conrad Halling]

Short version:

Under Mac OS X and Linux, there is a permissions problem with the 
library/liblisting.Rda file created by the reposTools package. There 
doesn't seem to be a similar problem under Windows. For Mac OS X and 
Linux, the system administrator must set write permissions on this file 
so all users can modify it.

Long version:

My apologies if this has already been discussed; I searched the 
BioConductor archives and found some reports of this bug but no replies. 
I also read the PDFs in the library/reposTools/doc folder and found no 
mention of this problem.

OS: Mac OS X 10.3.8
R: 2.0.1
reposTools: 1.5.2

On a multi-user Macintosh, I installed R and then all of the 
BioConductor packages as the system administrator using the sudo 
command. When I use the library() command to load the reposTools 
package, the file 
/Library/Frameworks/R.framework/Resources/library/liblisting.Rda is 
updated normally. But when another user loads the reposTools package, 
the following warning appears:

 > library( package = reposTools )
Loading required package: tools
Error in file(file, "wb") : unable to open connection
In addition: Warning message:
cannot open file 
`/Library/Frameworks/R.framework/Resources/library/liblisting.Rda'
Error in library(package = reposTools) : .First.lib failed for 'reposTools'

When I list the file, I see that I'm the owner, but other users of that 
Macintosh don't have permission to write to the file.

-rw-r--r--  1 challing  admin  17857 15 Mar 16:09 liblisting.Rda

The fix is to have the administrator set the permissions to 666 on the 
file so everyone has write permission:

 > cd /Library/Frameworks/R.framework/Resources/library
 > sudo chmod 666 liblisting.Rda
 > ls -l liblisting.Rda
-rw-rw-rw-  1 challing  admin  17857 15 Mar 16:09 liblisting.Rda


OS: Fedora Core 3, updated 15-Mar-2005
R: 2.0.1
reposTools: 1.5.2

On a multi-user Linux box, I experience the same problem. I installed R 
and then all of the BioConductor packages as the root user. When I log 
in as an ordinary user, I get the following error when I attempt to load 
the reposTools package:

 > library( package = reposTools )
Loading required package: tools
Warning messge:
Incorrect permissions to edit package database, 
/usr/lib/R/library/liblisting.Rda in: save.locLib(locLibList, curLib)
 >

When I list the file, I see that root is the owner of the file, and no 
other user has permission to change the file.

-rw-r--r-  1 root root 76825 Mar 15 16:03 liblisting.Rda

The fix is to have the Linux administrator set the permissions to 666 on 
the file so everyone has write permission:

 > su
Password:
# cd /usr/lib/R/library
# chmod 666 liblisting.Rda
# ls -l liblisting.Rda
-rw-rw-rw  1 root root 76825 Mar 15 16:03 liblisting.Rda
# exit
 >

OS: Windows XP Professional SP2
R: 2.0.1
reposTools: 1.5.2

Under Windows, all users appear to have permission to alter the 
liblisting.Rda file, which on my machine is C:\Program 
Files\R\rw2001\library\liblisting.Rda. Since most users of R appear to 
be Windows users, this is probably why most users don't experience this 
problem.

-- 
Conrad Halling
chhalling at alumni.ls.berkeley.edu
chhalling at verizon.net