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.