I too am encountering this problem. When I have a large script, if I select all in the editor and then ctrl-r to run, if it encounters a stop() function it simply prints an error message and continues to execute the remainder of the script, as opposed to terminating execution at that line. The quit() function exits R altogether, which I don't want. Yes, I could manually select only the portion of script which I want to run, but for lengthy scripts which I run repeatedly (generally changing only the name of the file I want analyzed), this can be quite tedious. It appears that the only solution is to put most of the code in a separate file and call it using source(); this has the downside of reducing the clarity of the code -- it's a sort-of structural spaghetti code approach.
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