I’ve recently converted to R Studio for R package development and I love it.  As someone who doesn’t really understand the details of git, it makes git incredibly easy to use (And git is DEFINITELY worth using!)  However, when you check a package in R for upload to CRAN, you need to use the –as-cran option, which R studio does not use by default.  Though you can set it to be your default.  The screen shots of how to do this are below.  Cheers.