Oh cool, this is actually a bug I reported here:
https://bugs.launchpad.net/calibre/+bug/1240797
Quote:
Originally Posted by kovidgoyal@launchpad.net
For some reason, your OS is raising permission denied (EPERM) errors
when calibre tries to delete a non-empty directory, instead of
ENOTEMPTY, which is causing the problem. Do you have your calibre
library on some kind of special filesystem?
In any case, I have changed the code to not rely on the OS sending the
proper error code, it will now manually check if the directory is empty.
That should fix your problem.
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It was fixed in calibre 1.7