[BioC] Installing Rv2.0.0 on MacOS 10.3.x

[Rahul Kakkar]

My goal was to get Rv2.0.0 running on my MacOS 10.3.x machine with 
affy, annaffy, genefilter and chip libraries running (with widgets).  
The following is the protocol that worked (many thanks to R. 
Gentleman).

Installed a fresh copy of Rv2.0.0 (uninstalled previous versions by 
removing the R application from "Applications" folder, R folder from 
the Library folder in my Home folder, and the R.Framework folder from 
the hard drive->library->fremeworks folder).

I did allow the R installed to update tcl/tk (under "Customize..." 
button during the installation).  Launched R and typed > capabilities() 
to see if tcltk and X11 were installed.

If these are not installed, tcl/tk can be obtained by following the 
instructions under the R FAQ for MacOS X 
(http://cran.r-project.org/bin/macosx/RAqua-FAQ.html).  X11 should be 
at http://www.apple.com/macosx/features/x11/download/.  I also 
installed the MacOS X developer tools (which were sitting in my 
Applications->Installers folder but should also be on the original 
MacOS 10.3.x install disks).  I also installed g77 (again, instructions 
are at the R FAQ for MacOS X 
(http://cran.r-project.org/bin/macosx/RAqua-FAQ.html)).  My 
understanding is that for R to compile packages from source and run 
widgets, all these components are needed.

Once that was done, I went to the Bioconductor developer page 
(http://www.bioconductor.org/repository/devel/package/html/index.html)  
and downloaded the source file for the developer version of reposTools. 
  I launched X11 and THEN launched R.  I used the Package Installer 
("Packages & Data" menu) to install reposTools.  I loaded reposTools 
">library(reposTools)" and then used ">install.packages2("affy", 
develOK=T)" to install affy.  I said yes to all dependent packages it 
tried to download.  I then used the same function to install 
genefilter.

This did not work for annaffy.  I had to download the source files for 
developer versions of annotate and annaffy and install them as I 
installed reposTools.  Again, I said yes to any dependencies.

I used the install.packages2 commad to get the packages corresponding 
to my chip, cdf and probe packages (in my case moe430a, moe430acdf and 
moe430aprobe).

After all that, all libraries loaded without issue and as long as I had 
X11 running, widgets worked fine.