Follow-up Comment #2, bug #49376 (project avrdude):

Indeed, as far as I know from Arduino-related forums (when investigating a
similar issue - cdc comms are also buggy in El Capitan -  I bumped into
complains that their environment/projects stopped working after upgrade to El
Capitan) - it turns out that starting 10.11 Apple somehow changed the way OSX
works with usb (enumerates usb?). Besides, they removed tty devices. 
Do you mean to say that avrdude needs tty to work properly? 
Anyway, I though there were some users of avrdude running El Capitan - wanted
to learn if they face such problem and their solutions... 

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