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As a workaround for Gatekeeper under Mac OS X, the IDE ships with a simple wrapper script to change the exec permissions of Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude_bin after install. #3468
However, this script will fail for non-admin users running the Arduino IDE ( students in a lab ) since it doesn't have admin access. #4270
When pushing code, the faculty members ( local admins ) also get a chmod warning: #4270
chmod: Unable to change file mode on /Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude_bin: Operation not permitted
/Applications/Arduino.app/Contents/Java/hardware/tools/avr/bin/avrdude_bin: line 6: ... : Permission denied
A more graceful degradation might be to check to see if the current user is the owner of the file being chmod'ed, or provide a command line fix wrapped in sudo. I don't know how wrapping the chmod call in the avrdude script with a sudo call would bubble up the authentication challenge in the IDE UI.