Sorry for the late reply, today I will prepare the reproduction.
I am noticing that the error is coming up NOT because select() function is called, but because another (unknown) function is in common with org.Hs.egPFAM and causes an error in such package.
When we identify the function (it is not select()) a quick fix could be modify only the call to that function as PACKAGE::function().
It is not needed to change all function calling in Rstan.
Said that, it is good habit to not import any library in R packages, but call every function with it’s explicit form. This is necessary for present and future compatibility with other software and user environments. More package are being produced and more and more functions with generic names will collide with those if not explicitly called. It is a tedious work, but will pay in the long run.