Click the Output tab, then select the built-in speakers. Just tried them with the MacBook Pro, and after a few minutes of playback the right channel speaker started popping.
I checked my hardware, cables, and instruments, but the crackling sound also occurs with digital instruments where I haven't used any hardware outside of my computer. There is not a list of affected models, it is completely random as I've said, I've had it happen to my 2011 MacBook Air 13' (USB2) and 2013 MacBook Air 11' (USB3).
