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I have set up avr studio 6 as an Arduino IDE with the help of the tutorial at: http://www.engblaze.com/tutorial-using-atmel-studio-6-with-arduino-projects/#final

I added an external tool as described in the tutorial and used the following argument:

-CC:\Program Files (x86)\arduino-1.0.1\hardware/tools/avr/etc/avrdude.conf -v -v -patmega328p -carduino -P\\.\COM4 -b57600 -D -Uflash:w:"$(ProjectDir)Debug\$(ItemFileName).hex":i

When I try to flash the Arduino Uno board this results in the following error:

avrdude.exe: invalid file format '\Users\UserName\Documents\ElectronicsProjects\bt-controller\software\gamecontroller\snes-controller\Debug\snes-contro.' in update specifier
avrdude.exe: error parsing update operation 'flash:w:C:\Users\UserName\Documents\ElectronicsProjects\bt-controller\software\gamecontroller\snes-controller\Debug\snes-contro.'

I tried renaming one of the folders, since the very first time one of the names contained a space. However the problem continues to exist. Is there any setting that I should change in the argument?

user1243742
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    Looks like i figured it out by moving the arduino-1.0.1 folder out of the Program Files and straight on the c: drive. Now the avrdude programs the board in a flash. – user1243742 Nov 25 '12 at 22:43

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I made the same, and after triggering "Tools\Send to Arduino UNO", it returned exactly the same error message. I have just fixed it by installing the Arduino IDE in \C: , in a folder without spaces in the filename (actually I also had forgotten the right COM port number...).

The correct string seems to be: -CC:\Arduino\hardware/tools/avr/etc/avrdude.conf -v -p atmega328p -c arduino -P COM6 -b 115200 -D -U flash:w:"$(ProjectDir)Debug\$(ItemFileName).hex":i

The baud rate (-b 11500) may be different, and the file path must be the right one. More, the program only sees he right file name (in my version) if I click on the Project name on the far left window prior to flash... otherwise it looks for a file main.hex, not finding it ...