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R vs. Microsoft R-Open updates?

Yes, Apple Installer will upgrade the app wherever it is. Since MS doesn't change the ID it pretends to be CRAN R.app so as far as OS X goes they are indistinguishable. Only MS can fix that problem by not re-using our ID for their binaries... I suspect that the same may be true for the framework (i.e. they may be using R Foundation ID there as well), but I didn't check.

Cheers,
Simon