upgradeable R layout
-----Original Message----- From: Alexy Khrabrov [mailto:deliverable at gmail.com] Sent: Thursday, November 13, 2008 7:13 PM To: Steven McKinney Cc: r-sig-mac at stat.math.ethz.ch Subject: Re: [R-SIG-Mac] upgradeable R layout 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?
With R 2.8.0, as with any major release change, structure can change substantially, including with associated software such as the Bioconductor set of packages, so I have not found a useful way to just put everything back that was in a prior release.
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...
No, sometimes I'd rather be poking a stick in my eye, but other things can make it fun, like remembering how few packages were available with other commercial statistical software programs, or how hard it was to get technical support or answers about internal code from their tech support, or how much money I had to spend ;-) while I install the R packages. (Though once I donated to the R project via PayPal while nursing a new installation!) I've learned that some R / Bioconductor packages require many others, and thanks to improved dependency checking and installation I can install e.g. snapCGH in the Bioconductor suite and get dozens of other packages installed as a side effect. I can select several packages in the R.app and click the beautiful "Install Selected" button, and mostly it all works in one go, so I'm no longer typing in 60+ install.packages() at the command prompt. Smarter people than I may have more useful techniques for you here. Sorry. Best SteveM
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
| 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: 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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