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@alumni.ls.berkeley.edu chhalling@verizon.net