[R-SIG-Mac] upgradeable R layout

[Steven McKinney]

 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 This website is out of date because of the changes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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