Flashing from .elf files - has it been "fixed"?

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Some people are having a problem flashing the contiki AT90USB1287 .elf file with AVR Studio/JTAGICE mkII. Google found this from June 2008
http://www.nabble.com/Remove-.bss-size-from-RAM-segment-of-AVR-ELF--td17672388.html
which says Studio erroneously flashes too much data to progmem, basically everything in the .elf file including debugging information, and that this might be fixed in a new version.

All is working for me with AVR Studio 4.14, but I note that the .elf flash is indeed excessive, writing an extra copy of the bootloader as well as debugging information.

I am wondering if AVR Studio 4.15 fixed the problem and possibly introduced a bug?

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The latest AVR Studio release is 4.16. You could download the latest version and see if it's fixed.

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Just to note that the originally issued 4.16 (that is 4.16.628) had a flash programming bug that would prevent code being programmed for a bootloader correctly. This was fixed by SP1 that brings it up to 4.16.638 so if you haven't got .638 make sure to apply SP1

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Studio 4.15 still has this problem. From what I can remember from my tests, 4.14 and 4.15 behaved the same way as far as this problem is concerned.

Studio 4.16 has it fixed but also introduced a bootloader programming bug.

You should be safest with Studio 4.16 SP1.