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We tried a CR2 image with ImageMagick 6.3.0 and it converted without complaint. ImageMagick forks the dcraw delegate program to convert CR2 images.
Use Google to find the dcraw program.
We cannot reproduce the problem you are having. Try converting the image directly with the dcraw program and see if that works for you.
Thanks for alerting us to the problem. The dcraw folks should have left -3 as a deprecated option. We'll investigate and add a patch to the latest release of ImageMagick.
You can grab the patch right now. Get ImageMagick 6.3.0-1 Beta in ftp://ftp.imagemagick.org/pub/ImageMagick/beta
. The release version should be available within a week or two.