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I am using Fedora 9. I removed the user using userdel -r command. The user is removed, but the home directory still remains. When I tried to remove the home directory (rm -rf /home/user/), I get the following message:

rm: cannot remove '/home/user/.gvfs': Permission denied

This happens on random occasions. Which scenario does this occur? Why is this occurring?

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Most likely it's related to this bug.

/home/$USER/.gvfs is used as a mount point for the GVFS of $USER. Try to unmount it prior to delete it:

umount /home/$USER/.gvfs
rm –r /home/$USER/.gvfs
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