[R] Upgrading R means I lose my packages

[Phil Spector]

Could this be related to the administrative rights of the user?
If a user had administrative rights, packages would be installed 
into the /Library/Frameworks directory, and then updating (to, I
think a new major version) would remove them.  Without the 
administrative rights it would install the packages in your home
directory, where the R_LIBS environmental variable would always
point to the same place.

                                        - Phil Spector
 					 Statistical Computing Facility
 					 Department of Statistics
 					 UC Berkeley
 					 spector at stat.berkeley.edu


On Thu, 28 Aug 2008, Rolf Turner wrote:

>
> On 28/08/2008, at 3:00 PM, Charilaos Skiadas wrote:
>
>> On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:
>> 
>>> 
>>> On 28/08/2008, at 2:02 PM, James Milks wrote:
>>> 
>>>> The title says it all.  Does anyone know of a way to save your packages 
>>>> when you upgrade to a new version of R?  This may seem petty, but I'm 
>>>> accumulating enough packages that having to download and install each of 
>>>> them anew every time I install a new version of R is rather of a pain. 
>>>> Ideally, I would like the new version of R to recognize the packages I've 
>>>> installed on the previous version without needing to reinstall the 
>>>> packages.  Is that possible?
>>>> 
>>>> My system: Mac OS 10.5.4.
>>>> Current R version: 2.7.1
>>> 
>>> Mac OS moves in mysterious ways, but apparently your installation moves in 
>>> more mysterious
>>> ways than most.
>>> 
>>> I also (by necessity, not by choice) run Mac OS.  But I certainly don't 
>>> lose my
>>> packages when I update R.  The new version of R certainly ``recognizes'' 
>>> the packages
>>> that I have installed.  No action required.
>>> 
>>> There may be something funny about *where* you have your packages 
>>> installed, and
>>> what environment variables you have set.
>>> 
>>> To answer your question ``Is that possible?'' --- Yes.  Not just possible,
>>> but universal.  Except, it would seem, in your case.  What have you done
>>> to offend the gods? :-)
>>> 
>> 
>> Actually have had the same problem as James. By default, unless I'm 
>> mistaken, R will save installed packages within the "R.framework" framework 
>> (system-wide installation). This framework gets completely replaced when a 
>> new version is installed. In my system, the location of these packages is:
>> /Library/Frameworks/R.framework/Resources/library
>> 
>> So unless I am mistaken you have to take some action to prevent packages 
>> from being installed there. I do hope I am wrong.
>
>
> 	I'm not sure --- I find Mac OS very confusing.  But I have the 
> ***impression*** that
> 	(on my system) by default packages get installed into
>
> 		~/Library/R/2.7/library
>
> 	i.e. into a library inside the directory tree rooted in my login 
> directory.
>
> 	I don't use this --- I've created my own library ~/Rlib and have
> 	set up an environment variable to point to it.
>
> 	(This works properly only if you start R from the command line; for
> 	reasons I don't understand if you start R by clicking on the icon
> 	then R doesn't know about the R_LIBS environment variable.  But since
> 	all civilized people start R from the command line .....)
>
> 	I have no idea why youse guys' systems would eschew using 
> ~/Library/<whatever>.
>
> 		cheers,
>
> 			Rolf Turner
>
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