Hey y'all, if you're doing a bunch of SDM/ENM stuff in R and are finding that many of your operations are running really slowly, you should check your R version. R version 3.3.0 has some sort of bug going on that causes it to handle many raster operations VERY slowly, including extracting data from a raster using points.
It's a very odd bug, because it causes the operation to get slower and slower the more points you add (which makes sense), but then suddenly gets considerably faster when you're using over 250 points. So extracting data using 250 points might take three minutes, while 251 points takes three seconds. Crazy, but at least the fix is easy!