> If I use the Avrdude version that's bundled with Arduino IDE > (https://github.com/facchinm/avrdude) it works fine, but if I build my own > Avrdude version from this repo I get the same error as Victor get.
Have you tried to build with libhidapi? The autoconf script just grabs what is available, but it is not always a sane choice. There is hidapi, hidapi-libusb, and hidapi-hidraw, and libusb-1.0 support as a fallback. I suspect that plain HID access via hidapi requires the least permissions.
