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 This website is out of date because of the changes in place for R 2.8.0 For R 2.8.0 if you look into one of a package's library directories, e.g.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 > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac 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. V5Z 1L3 Canada _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
