Hi @Peris,
You mentioned that you have an existing R installation. With this latest QIIME 2, we're now using R 3.4.1, but I'm wondering if we're just running into an old linking issue, where the R in our QIIME 2 conda environment finds packages compiled to your other installation.
Are you using the .Rpofile hack that we've recommended in the past? If not, here's a thread describing what to do. It isn't great but it kind of works.