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Downloading packages recently moved from fetching a fixed URL to fetching a list of mirrors, so you should upgrade to Sage 6.7 to let it work. Then, you should be able to use sage -i nauty.

Downloading packages recently moved from fetching a fixed URL to fetching a list of mirrors, mirrors and use the fastest, so you should upgrade to Sage 6.7 to let it work. Then, you should be able to use sage -i nauty.