[R-SIG-Mac] Error updating packages

[Michael]

On 29 Feb 2008, Ista Zahn wrote:

> Hi,
> When I try to update packages I get an error saying
> 
> Error: cannot remove prior installation of package ‘boot’
> 
> This happens both when I use the GUI and when I issue  
> update.packages() from the command prompt. Does anyone know what the  
> problem might be? I'm running R 2.6.2 on OS X 10.5.2.

I have been troubled by this problem for some time as well. (although boot
is a system library so your situation might be different). I can run 'R CMD
REMOVE' to remove a package but not from 'update.packages ()' inside R.

After some probing around, I found somehow there were extra symlinks under
the troublesome library directories, e.g.,

/Library/R/library/gee/gee -> /Library/R/library/gee

which can not be deleted by 'remove.packages()' whereas the command line has
no trouble.

I cleaned it up using

find /Library/R/library -type l -exec rm {} \;

Now everything seems fine (R 2.6.2) and there is no more such symlinks.  Not
sure how it got there in the first place.  (I ususally use 'install.packages
()'.)

Michael