[R-SIG-Mac] Error updating packages

[Ista Zahn]

On 29 Feb 2008 Michael <wuolong at gmail.com> wrote:
>
> 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
>

Yes, I have symlinks like this in my library directories. I also have  
no idea how they got there .

> 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 {} \;
>

I removed the symlinks, but haven't had a chance to see if it fixed my  
problem because I already updated all my out-of-date packages  
manually. Thanks for the tip!


> 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