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I'm currently trying to set up a mirror for several apt-repositories that use Packages.bz2 files instead of regular gzip.

Unfortunately, apt-mirror on Ubuntu always tries to fetch Packages.gz files and fails.

Are there any options I can set? (running Ubuntu 12.04)

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It has been reported as a bug, and a patch has been released. You will have to wait for a new version/patched binary to be released, or you can compile it from patched source. Here is the bug report and patch.

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