Follow-up Comment #5, bug #29913 (project avrdude):
Perhaps we should file another bug report for not mentioning the
prerequisites regarding kernel/libusb in the AVRDUDE documentation?
Even if there is no clean solution this would help some people when they hit
this problem. It took my about two days of working power to find an
explanation; it was very important for me to figure it out because I am using
an AVRISP mkII with AVRDUDE in a production test system. Of course changing
just the file size could have solved/obfuscated the problem but I had to be
sure that the in-circuit tester works reliable.
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