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After running 'sudo apt-get update && sudo apt-get upgrade' on my raspberry pi 3 running raspbian jessy, I get:

E: Failed to fetch http://mirrordirector.raspbian.org/raspbian/pool/main/g/ghostscript/libgs9-common_9.06~dfsg-2+deb8u5_all.deb  rename failed, Structure needs cleaning (/var/cache/apt/archives/partial/libgs9-common_9.06~dfsg-2+deb8u5_all.deb -> /var/cache/apt/archives/libgs9-common_9.06~dfsg-2+deb8u5_all.deb).

E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

A quick search on the net and here revealed that this probably is related to a corrupted filesystem on the SD card. As this is my fileserver and I would prefer not reconfiguring it: Could I just make a backup with dd and then restore on a new SD card or would this also copy the filesystem corruption?

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That would also copy the file system corruption (dd copies the contents of the block device, without caring about their structure).

To fix your problem, I would suggest running apt-get clean to clear your package cache, and fsck. If your file system has detected errors, rebooting the Pi should force a full fsck.

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  • Thank you. I get a warning when running fsck since it is mounted. Obviously I cannot unmount it as it is the root partition. So I guess I can try to fsck the sd card from my laptop as soon I have physical access to the box (Only access via ssh at the moment) or during reboot as you suggested. Will accept, when this is done and confirmed to work.
    – Bruni
    May 18, 2017 at 9:36

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