On Thu, 13 Nov 2008, Alexy Khrabrov wrote:
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...
See the rw-FAQ Q2.8. If you use a separate library tree for non-core
packages (highly recommended), then all you have to do when you update R
is to run update.packages(checkBuilt=TRUE, ask=FALSE) . Simple!
(If you have a personal library, that is versioned so you need to do
cp -r ~/Library/R/2.7/library ~/Library/R/2.8/library
first, or move it if you are wiping out 2.7.x.)
Steven is giving 2.8.0 credit for a much earlier concept,
sub-architectures. The difference in 2.8.0 is that 64-bit
sub-architectures were added to i386 and ppc in the CRAN distribution.
He also has an unfortunate tendency to write '64-bit' when he means
'ppc64' and not 'x86_64'. I've been thrown several times when the issue
was specific to ppc64.
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: [EMAIL PROTECTED] [mailto:r-sig-mac-
[EMAIL PROTECTED] On Behalf Of Steven McKinney
Sent: Thursday, November 13, 2008 5:49 PM
To: Alexy Khrabrov; [email protected]
Subject: Re: [R-SIG-Mac] upgradeable R layout
Greetings Alexy,
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:r-sig-mac-
[EMAIL PROTECTED] On Behalf Of Alexy Khrabrov
Sent: Thursday, November 13, 2008 4:29 PM
To: [email protected]
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
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Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: [EMAIL PROTECTED]
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
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Canada
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--
Brian D. Ripley, [EMAIL PROTECTED]
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)
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