[R-SIG-Mac] [R] Upgrading R means I lose my packages

Thu Aug 28 13:17:44 CEST 2008

On Aug 28, 2008, at 6:35 AM, James Milks wrote:

> So, what it boils down to is that I'm installing my packages at too  
> high of a level (I'm an administrator for my system) and should  
> save them in places other than the R framework folder.

Exactly, and your situation is similar to mine. To answer Rolf's  
question about R_LIBS not being seen when you click R.app from the  
Finder, the answer is that any application run through the GUI does  
not at all read your shell login files, like .bash_profile or  
whatever else you are using. It inherits the Finder's environment  
instead of the shell's environment. There are two solutions:

1) Set R_LIBS in a file like .bash_profile, which is then read  
whenever a terminal window opens, and then every time start R.app  
from the terminal window via the command:
"open -a R". Then this R process will be inheriting the shell's  
environment.
2) Create a file ~/.MacOSX/environment.plist containing this R_LIBS  
definition, as specified in http://developer.apple.com/qa/qa2001/ 
qa1067.html. This file is respected by all GUI apps as well. Requires  
a system restart. If you go with this option, I would try to keep  
this file as minimal as possible.

> Thanks too all for the tips and links.
>
> Jim Milks

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

> On Aug 28, 2008, at 5:08 AM, Prof Brian Ripley wrote:
>
>> The standard R mechanisms for installing packages into a different  
>> library
>> apply on Mac OS X just as anywhere else.  It was not said that R  
>> was being run from the R.app GUI, but I'll assume that is the case.
>>
>> The rw-FAQ provides detailed advice for Windows users: see
>>
>> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s- 
>> the-best-way-to-upgrade_003f
>> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-don_0027t- 
>> have-permission-to-write-to-the-R_002d2_002e7_002e2_005clibrary- 
>> directory
>>
>> The differences for Mac OS users are small -- some of the names  
>> and how to set the library path via R_LIBS.
>>
>> We arrange not to install packages within .Library on any of our  
>> systems -- and for most users they do not have permission to do so.
>>
>> On Wed, 27 Aug 2008, William Revelle wrote:
>>
>>> This is actually an R-sig-mac question so I am responding there.
>>>
>>>
>>> In general, if you want to install a new version without losing  
>>> the previous packages,  using the finder, go to Library/Receipts  
>>> and remove the R.app and R.Gui receipts.  Then install the new  
>>> version. That will keep the previous packages.  This is not  
>>> mysterious, this is R.
>>>
>>>
>>> Thanks to Simon et al. for the upgrade.
>>>
>>> Bill
>>>
>>>
>>>
>>> At 11:00 PM -0400 8/27/08, 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.
>>>>
>>>>> 	cheers,
>>>>>
>>>>> 		Rolf Turner
>>>> Haris Skiadas
>>>> Department of Mathematics and Computer Science
>>>> Hanover College
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/ 
>>>> posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>> -- 
>>> William Revelle		http://personality-project.org/revelle.html
>>> Professor http://personality-project.org/personality.html
>>> Department of Psychology             http:// 
>>> www.wcas.northwestern.edu/psych/
>>> Northwestern University	http://www.northwestern.edu/
>>> Attend  ISSID/ARP:2009               http://issid.org/issid.2009/
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>