[R-SIG-Mac] upgradeable R layout

[Alexy Khrabrov]

Steven -- thanks a lot!  Now it's clearer what to do with the 64 bits,  
but still it doesn't answer the question of upgradeability -- meaning,  
you went ahead and installed a bunch of packages, then a new version  
of R comes along, and what do you do?

One way I can see handling it it with a local install, outside of the  
framework, and reinstalling with the command from the previous list --  
and you still have to do that.  Going over a list of 60+ packages in  
the installer is not really fun...

Cheers,
Alexy

On Nov 13, 2008, at 9:03 PM, Steven McKinney wrote:

>
>
> One last bit - I set up a shell script in
> /usr/bin
>
> called R64
>
> containing
>
> #!/bin/sh
> R --arch=ppc64
>
> to allow easy command line startup of
> 64 bit R and to allow ESS to find
> and start up 64 bit R sessions in Emacs.
>
>
>> -----Original Message-----
>> From: r-sig-mac-bounces at stat.math.ethz.ch [mailto:r-sig-mac-
>> bounces at stat.math.ethz.ch] On Behalf Of Steven McKinney
>> Sent: Thursday, November 13, 2008 5:49 PM
>> To: Alexy Khrabrov; r-sig-mac at stat.math.ethz.ch
>> Subject: Re: [R-SIG-Mac] upgradeable R layout
>>
>> Greetings Alexy,
>>
>>
>>> -----Original Message-----
>>> From: r-sig-mac-bounces at stat.math.ethz.ch [mailto:r-sig-mac-
>>> bounces at stat.math.ethz.ch] On Behalf Of Alexy Khrabrov
>>> Sent: Thursday, November 13, 2008 4:29 PM
>>> To: r-sig-mac at stat.math.ethz.ch
>>> Subject: [R-SIG-Mac] upgradeable R layout
>>>
>>> Greetings -- I'd like to keep my R on Mac in an upgradeable way. I
>>> noticed that currently all packages I installed from R.app are in
> the
>>> R.framework -- are they going to be clobbered when I replace R 2.7.2
>>> by 2.8.0?
>>
>> There are quite a few changes between R 2.7.2 and R 2.8.0
>>
>> I abandoned my R 2.7.2 and have no regrets so far (but you
>> don't have to - you can have different versions and Simon Urbanek
>> provides a small RSwitch gui app that lets you switch back and  
>> forth).
>>
>>>
>>> At the same time with the upgrade, I'd also like to switch to 64
> bit.
>>> One good page I found about it is
>>>
>>> http://www.matthewckeller.com/html/64_bit_r_on_mac.html
>>>
>>> It suggests that packages are installed into a separate directory by
>>> doing it from command line install.packages with a lib= parameter.
>>
>> This website is out of date because of the changes
>> in place for R 2.8.0
>>
>> For R 2.8.0 if you look into one of a package's library
>> directories, e.g.
>>
> /MacintoshHD/Library/Frameworks/R.framework/Versions/2.8/Resources/ 
> libra
>> ry/Matrix
>>
>> you will see a subdirectory
>> /libs
>> which will contain further subdirectories (once you've installed for
> the
>> arch involved), e.g.
>> /ppc
>> /pp64
>> which hold the architecture-specific files.  So you don't have to  
>> keep
> a
>> 64 bit version somewhere separate from your 32 bit version.  Nice.
>>
>> I installed R from Simon Urbanek's website - always up to date -
>> http://r.research.att.com/
>> using the method
>>
>> Leopard builds can be installed as follows - paste in Terminal (for R
>> 2.8.x):
>> curl -s
> http://r.research.att.com/R-2.8-branch-leopard-universal.tar.gz
>> | sudo tar fvxz - -C /
>>
>> after setting up the various compilers and other software discussed
>> in the "Tools for R Development" and "Other binaries and tools"
>> sections.
>>
>> Now you have R installed and it has all architectures ready.
>> (I've wrestled through 64 bit configure / make / install for
>> prior R versions, this is much better!  Thank you Simon Urbanek
>> and others!)
>>
>> I then installed the 32 bit R-Gui and renamed it to R32.app.
>> I installed the 64 bit R-Gui and renamed it to R64.app,
>> so I can fire up either 32 bit or 64 bit (or both!) and
>> use the excellent package manager and package installer.
>> The package installer installs the package using the
>> architecture of the R-Gui it is invoked from, so architecture
>> is handled automagically.
>>
>>>
>>> Now I'd like to install everything into a lib anyways, but
> preferably
>>> without having to specify lib= all the time -- is there a way to
> make
>>> my local location the default for install.packages?
>>
>> With the R-Gui apps in place, you can install packages easily, they
>> are installed in their standard place and I've had no problems with
>> this.
>>
>>>
>>> Also -- can the R.app be tweaked to do all this, if I want to use it
>>> with the 64 bit and local install for packages?
>>
>> Yes - one way is described above.
>>
>>>
>>> The idea is to make upgrading R smooth -- ideally, it would do
>>> update.packages(checkBuilt =
>>> TRUE) by itself as a part of the upgrade.
>>
>> The only hiccup I encountered was a TCL/TK issue (now resolved)
>> but otherwise getting 32 bit and 64 bit R up and running
>> has been very smooth.  (Now the issue is that ppc64 is going
>> extinct in the not too distant future - time to put in a
>> request for an Intel Mac!)
>>
>>>
>>> Are there other ways to simplify R upgrade on Mac and/or am I
> missing
>>> something?
>>
>> Once you get set up as I have, you won't be missing anything!
>>
>> Good luck
>>
>>>
>>> Cheers,
>>> Alexy
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>> Steven McKinney
>>
>> Statistician
>> Molecular Oncology and Breast Cancer Program
>> British Columbia Cancer Research Centre
>>
>> email: smckinney at bccrc.ca
>> tel: 604-675-8000 x7561
>>
>> BCCRC
>> Molecular Oncology
>> 675 West 10th Ave, Floor 4
>> Vancouver B.C.
>> V5Z 1L3
>>
>> Canada
>>
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