Disable/suppress tcltk popup for CRAN mirror selection in R

Dirk provides ways to avoid the menus altogether, but to answer your question as posed, I think you want

options(menu.graphics=FALSE)

I tracked this option down by finding the class of objects returned from help (it's help_files_with_topic), scanning utils:::print.help_files_with_topic and finding the line

menu(txt, title = gettext("Choose one"), graphics = getOption("menu.graphics"))

Just set a mirror in the startup files. I have this in my ~/.Rprofile and I never see that prompt:

## Default repolocal({r <- getOption("repos");       r["CRAN"] <- "http://cran.us.r-project.org";        options(repos=r)})

See help(Startup) for more things you can customize here, and also see this excellent SO question on customizing ~/.Rprofile.

Edit: As for your additional question just added in the comments, that is different. In this case you could specify the mapply explicitly by using the namespace and :: operator. For example, base::mapply(foo, bar) would unambiguously pick one from the standard library, and similarly help(mapply, package="base") asks for the help for a given function from a given package.

Also have a look at the interactivity package in CRAN if you wish to completley disable interactive funky stuff.