The problem is not with R; the problem is with Windows, as well as the x86 architecture. You'll never really be able to access more than 3GB of physical memory (for a single process). Accessing more than 4GB requires a 64 bit processor.
-roger
Alternatively, if you move to Linux you could compile a kernel with support for large amounts memory (>4GB) which doesn't require a 64 bit processor.
Joel
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