How to repair Ubuntu after messing up permissions on critical directories?

Question

So I ran a stupid command as root (DO NOT RUN THIS)

# chown -R root:root /{usr,lib,var,etc,bin,sbin,tools}

So... oops. I happened to have a root shell open (from when I caused this), so I was able to get sudo working by doing

# chown root:root /usr/bin/sudo
# chmod 4755 /usr/bin/sudo

Yay, sudo works again. I wanted to install a package (ncdu), so I ran sudo apt-get install ncdu.

$ sudo apt-get install ncdu
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following NEW packages will be installed:
  ncdu
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/43.4 kB of archives.
After this operation, 106 kB of additional disk space will be used.
Selecting previously unselected package ncdu.
(Reading database ... 233654 files and directories currently installed.)
Preparing to unpack .../ncdu_1.15.1-1_amd64.deb ...
Unpacking ncdu (1.15.1-1) ...
Setting up ncdu (1.15.1-1) ...
Processing triggers for man-db (2.9.4-2) ...
/usr/bin/mandb: can't chmod /var/cache/man/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/es/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/es/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/es/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/zh_TW/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/zh_TW/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/zh_TW/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/fi/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/fi/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/fi/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/de/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/de/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/de/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/uk/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/uk/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/uk/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/sr/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/sr/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/sr/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/sl/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/sl/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/sl/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/nb/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/nb/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/nb/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/pt/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/pt/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/pt/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/ru/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/ru/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/ru/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/ko/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/ko/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/ko/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/it/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/it/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/it/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/fr/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/fr/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/fr/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/et/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/et/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/et/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/ca/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/ca/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/ca/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/tr/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/tr/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/tr/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/nl/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/nl/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/nl/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/fr.UTF-8/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/fr.UTF-8/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/fr.UTF-8/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/hu/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/hu/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/hu/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/fr.ISO8859-1/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/fr.ISO8859-1/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/fr.ISO8859-1/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/sv/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/sv/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/sv/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/id/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/id/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/id/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/el/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/el/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/el/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/pt_BR/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/pt_BR/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/pt_BR/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/ro/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/ro/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/ro/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/zh_CN/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/zh_CN/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/zh_CN/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/cs/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/cs/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/cs/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/gl/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/gl/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/gl/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/da/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/da/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/da/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/pl/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/pl/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/pl/1053532: Permission denied
/usr/bin/mandb: can't chmod /var/cache/man/ja/CACHEDIR.TAG: Operation not permitted
/usr/bin/mandb: can't remove /var/cache/man/ja/CACHEDIR.TAG: Permission denied
/usr/bin/mandb: fopen /var/cache/man/ja/1053532: Permission denied

Clearly I didn't do enough to fix my system. I'd prefer not to reinstall the OS if possible, but I have a root shell (it's a physical laptop in front of me), so I'm wondering how to fix apt so I can install packages again. I'm using Kubuntu 21.10.

This would be like mixing two different colors of sand together and trying to separate them back out. Technically you can, but it's not worth the time or effort. Reinstall the OS and don't make the same mistake in the future. — Nmath, Dec 21 '21 at 20:24
I can't login anymore, so I'm giving up and reinstalling. I've saved a few files to a flash drive. — cocomac, Dec 21 '21 at 21:26

score 1 · Accepted Answer · edited Jan 09 '22 at 23:53

1

As mentioned in the comments, you will still run into issues so it would be easiest to reinstall.

However, for this particular problem, you can return the ownership to man:man by running the following commands:

chown -R man:man /var/cache/man/
chown -R man:man /var/cache/man/*

edited Jan 09 '22 at 23:53

Thomas Ward

74,764

answered Dec 21 '21 at 20:37

mchid

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How to repair Ubuntu after messing up permissions on critical directories?

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