Hey @quintinm,
I think you ran into an issue with using R conda environments and having R/R-Studio installed at the same time. Assuming you have R Studio and DADA2 already installed normally (outside of QIIME 2), we have a kind of gross work-around.
Does adding an .Rprofile file in your home directory like described in this issue fix the problem? You'll need to add/remove (or comment out) that line depending on if you are using QIIME 2 or R Studio, but it's the best workaround we have at the moment.
If you don't have R outside of QIIME 2, then there must be something else going wrong, did you use the correct install command for OS X? If you install the linux version by mistake, things can look like they are working until something very odd like this happens.
Let me know if any of that helps!