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There is a software bug that affects LUFA-based programmers in newest releases of AVRDUDE.
Either use AVRDUDE versions prior to 6.x.x or apply this patch to the AVRDUDE sources and compile.
The same problems appears in newest releases of Arduino IDE – they use AVRDUDE versions 6.0.1 or newer.
The last suitable Arduino IDE version that uses pre-6.x.x AVRDUDE version is Arduino IDE 1.5.7.
There is a software bug that affects LUFA-based programmers in newest releases of AVRDUDE.
Either use AVRDUDE versions prior to 6.x.x or apply this patch to the AVRDUDE sources and compile.
The same problems appears in newest releases of Arduino IDE – they use AVRDUDE versions 6.0.1 or newer.
The last suitable Arduino IDE version that uses pre-6.x.x AVRDUDE version is Arduino IDE 1.5.7.
The official bug report is here: https://savannah.nongnu.org/bugs/index.php?40831
More about the issue can be found here: http://www.avrfreaks.net/forum/lufa-based-avrisp-mkii-doesnt-work-avrdude-601
How I can resolve this issue?
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