What a great question.
It's not clear whether R is a library from your question. I don't think it matters whether it is or isn't.
So we all know that the GPL v03 applies to "The Program". The GPL refers to "the Program" other ways as well, such as "a work" and "the work", depending on the context in which those alternatives are used.
The GPL V 03 doesn't say that Program needs to be bug-free, complete, prone to failure, fit for purpose or ..... be fully functional.
So my half-cut C# code that will never run can be licensed under the GPL as well. As a receiver of my C# code you've got a right to run it under the GPL v03. It just so happens you can't.
What about GPL v03, section 5, 3rd bullet point? Sure, you have to "license the entire work". But what is the entire work? Couldn't it be your "incomplete" GPL v 03 software which fails gracefully, if R is not present and ready for use?
You could structure your code base to look for plugins - or named plugins. Of the sort of "R", as referred to in your question.
So your GPL code would - unmodified - checks to see if the code ("R") is available and ready to use. (For instance, your GPL code checks to see whether "R" is installed and in a particular location on the disk, and runs some preliminary polling to make sure it's installed correctly and will operate properly).
That way, the receiver of your software can (1) download your GPL package, (2) pull R from elsewhere and install it so as to enable the functionality in your code that would otherwise not be available, because the R plugin is not present.
What about GPL v03, section 5, 3rd bullet point? (the reference to the "entire work" and "whole work"). The R code would not be "packaged" with your release. So it's not covered by the GPL v03. And no licensing conflict.
Let's say I'm wrong on what I say above....
The sentence at the end GPL v03, section 5, 3rd bullet point says:
"This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it."
Well, let's think about that from the receiver's perspective. As a receiver of your GPL v03 software, I'm licensed anyway. Just because you don't do the right thing, doesn't mean I'm not licensed to run your code with R.
Also, see the last paragraph of section 5, 3rd bullet point. You wouldn't be distributing R with your GPL v03 package. Therefore, it doesn't apply.
There'd be no problem telling your licensees how to install R. I wouldn't do that in your your distribution package, but I'm not sure it matters.
Lastly, a warning. Make sure the license for R doesn't prohibit it from being used with GPL v03.