R CMD build/check Documentation in Writing R Extensions 1.3
In WRE section 1.3, there is a note that says "R CMD check and R CMD build
run R processes with --vanilla in which none of the user’s startup files
are read." While this is true, is it somewhat confusing? When reading
quickly, it is possible to read that statement as "running R CMD check is
the same thing as running R --vanilla CMD check". It is easy to read WRE
and think that your .Rprofile file is being ignored by the parent R process
in a call to R CMD check when this is not the case.