Whew - this is much belated , but just as an FYI this type of "System Dependency" issue with R is usually a better fit for the "R Admins" category There are generally more people there who can help out with this type of issue!
That said, hopefully you have worked around / found a solution by now!! Usually the best way to iterate on this type of thing is to try to create a minimally reproducible example in an "interactive" R session (rather than continuing to run the Rmd, which presumably takes a while / is complicated / etc.).
I believe this thread / comment may have a useful tidbit on this issue! If not, please open a new thread in R Admins so we can try to help get it resolved!
, but just as an FYI this type of "System Dependency" issue with R is usually a better fit for the "R Admins" category 
There are generally more people there who can help out with this type of issue!