Sometimes you just need a graphical messagebox....know what I mean? If only because it pops up in front of all the other open windows and alerts you to the fact that your R script is waiting for you to do something, or is finished doing something else.
The R package "tcltk" is the easiest way I have found to do this. On Mac OSX you need to first install the Universal Tcl/Tk for X11(available here). I haven't tried it on Windows, but I don't think this extra step is necessary. Now just install the R package "tcltk" in the normal way, for example
Now you should have access to functions like this.....
tk_messageBox(type="ok",message="I am a tkMessageBox!")
There are different types of messagebox (yesno, okcancel, etc). See ?tk_messageBox.