I'm not sure I can include reproducible code on this, given there's 4,000 lines of code and that may be part of the problem, but let me try to explain my question the best I can:
I love using beepr to play an audible sound when a bunch of code is done processing. If my computer is taking a while to run it, I'll go look at a different screen or do something else in the room when its thinking.
I have a large .rmd file. Its 4187 lines long and beep() is on line 4185. I made sure it was nowhere else in the document using ctrl+f. When I "run all", the beep goes off when I'm about this far through the document:

And then it'll continue thinking for another few minutes before its done. This defeats the entire purpose of beepr().
So I guess my question is: is this a known problem? Is there anything particular to a .rmd document that does this? Any known fixes?