I think that the Rsamtools::FaFile function should check whether it got a proper file to read. If it unwittingly is given a directory name, nothing happens, but the whole R session crashes when you subsequently pass the object to an open() call . To reproduce, simply try this:

library(Rsamtools)

open(FaFile("."))

This is the latest Rsamtools, v. 1.22.0

Philip