In sum, there's a stray preference-like file or two (probably just one) that i can't find.
Here's the whole story:
I recently attempted to update my R install from 2.10 to 2.11. As i have done before, i installed from source. I know that all of the dependencies are correctly installed and made available to R, because my prior install worked fine. When i upgraded to 2.11, i am unable to install packages (no exception thrown, it just doesn't appear to complete the install and is unresponsive so i have to quit + restart R.
Given i install from source, there are any number of points in the process that i could have messed up.
What i need to do now is "start over" which requires that i clear out my my prior install. I am having trouble doing that. There is still at least one preference file or something like that i can't find and one of these is causing the problem, so i need to find it and terminate it with extreme prejudice before i do a fresh install. Although i set a number of flags during the install, i have never opted out of the default install locations during the config step.
There has to be one or more preference files still in my file structure (and that's also accessible to the new install of R) because after i follow all of the steps below, then do a fresh install, when i start R for the first time, some of my preferences have persisted (e.g., quartz settings, GUI background color, editor selection, etc.). Again, the problem is that i just cannot locate those files. Finally, the problem can't be that during my last install from source, i inadvertently caused a preference file to be sent to an off-spec location--because again, a fresh R install (whether from source or from the OS X binaries) is finding those files
Here's what i've done prior to attempting a clean install of R:
Removed files from these locations:
~/.RData
~/.RHistory
/Applications/R64.app
/Applications/R.app
/Library/Frameworks/R.framework
(i also removed all symlinks from these)
Cleared all RAM and disk caches, in particular the directory where i know R caches:
~/Library/Caches/R* (in fact i've cleared this entire directory)
Checked for all 'hidden' files in the OS X directories where login/startup files are often placed:
/etc/
~/
In addition, i've checked R-help, and i've also read through the relevant portions of 'R Installation and Administration'--no luck.
I've also searched searched my file structure using the various bash utilities, which nearly always solves problems of this sort quite easily, but in this case obviously searching by name or even pattern is more problematic.
