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Alright, so I have managed to pin down the problem and also found a workaround. I am getting this warning, because I am working in a shared folder of a virtual box linux. In order to enable the automatic sharing with the host machine, virtual box gives the ownership (and write permission) of these shared folders to a group called 'vboxsf', which in turn upsets sage. Since I cannot remove the write permission without messing with the functionality of the shared folders, I created a copy of the shared folders in my home directory and set up a cron job to sync the two periodically.