Arch Linux

Gede

Member

Registered: 2009-09-03

Posts: 28

[Solved] Filesystem corrupts package install systematically

Hello. This is an odd problem. running

pacman -Qkk

shows some files are not as they were expected to be. Some are config files I changed, but others are more unexpected.

Reinstalling some packages resolves some cases, but I have seen once the same (or a similar) problem return a bit later by itself, even when not running that program. (Some times reinstalling a package led to even more file errors!)

All this seems to point to a filesystem problem. However

btrfs scrub

and

btrfs check --check-data-csum

(after booting from the latest arch ISO) showed no problem. I hesitate to run badblocks on an SSD, to determine if it is a storage problem. A memory problem could also be a possibility, but the problem appears strangely consistent across reboots and package re-installation. I re-install a package multiple times and the same files show the same problem, while problems with other files seem to come and go.

At the moment the problem seems to have reduced to the files below (output of pacman -Qkk).

warning: audit: /var/log/audit (Permissions mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Modification time mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.alias (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.alias.bin (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.builtin.alias.bin (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.builtin.bin (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep (Size mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep (MD5 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep (SHA256 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin (Size mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin (MD5 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin (SHA256 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.devname (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.softdep (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols (Size mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols (MD5 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols (SHA256 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin (Modification time mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin (Size mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin (MD5 checksum mismatch)
warning: linux: /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin (SHA256 checksum mismatch)
warning: shadow: /usr/bin/newgidmap (Permissions mismatch)
warning: shadow: /usr/bin/newuidmap (Permissions mismatch)
warning: systemd: /var/log/journal (GID mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Modification time mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Size mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (MD5 checksum mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (SHA256 checksum mismatch)

No matter how many times I re-install these packages, these same files always present these same problems. I am running out of plausible ideas as to what could be causing this.

Just to provide more information:

#ls -Lld /var/log/audit /usr/lib/jvm/default /usr/lib/jvm/default-runtime /usr/lib/modules/5.16.0-arch1-1/modules.alias /usr/lib/modules/5.16.0-arch1-1/modules.alias.bin /usr/lib/modules/5.16.0-arch1-1/modules.builtin.alias.bin /usr/lib/modules/5.16.0-arch1-1/modules.dep /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin /usr/lib/modules/5.16.0-arch1-1/modules.devname /usr/lib/modules/5.16.0-arch1-1/modules.softdep /usr/lib/modules/5.16.0-arch1-1/modules.symbols /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin /usr/bin/newgidmap /usr/bin/newuidmap /var/log/journal /usr/lib/vlc/plugins/plugins.dat
-rwxr-xr-x  1 root root              41088 set  7  2020 /usr/bin/newgidmap
-rwxr-xr-x  1 root root              36992 set  7  2020 /usr/bin/newuidmap
drwxr-xr-x  1 root root                 12 mai 16  2021 /usr/lib/jvm/default
drwxr-xr-x  1 root root                 12 mai 16  2021 /usr/lib/jvm/default-runtime
-rw-r--r--  1 root root            1452602 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.alias
-rw-r--r--  1 root root            1430573 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.alias.bin
-rw-r--r--  1 root root              20891 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.builtin.alias.bin
-rw-r--r--  1 root root             737350 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.dep
-rw-r--r--  1 root root             980763 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.dep.bin
-rw-r--r--  1 root root                455 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.devname
-rw-r--r--  1 root root               1577 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.softdep
-rw-r--r--  1 root root             612246 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.symbols
-rw-r--r--  1 root root             746313 jan 16 13:53 /usr/lib/modules/5.16.0-arch1-1/modules.symbols.bin
-rw-r--r--  1 root root             308328 jan 16 13:41 /usr/lib/vlc/plugins/plugins.dat
drwxr-xr-x  1 root root                  0 set  6  2018 /var/log/audit
drwxr-sr-x+ 1 root systemd-journal      76 mai 10  2015 /var/log/journal

Last edited by Gede (2022-01-16 17:12:43)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,729

Re: [Solved] Filesystem corrupts package install systematically

Those are normal and expected. They are changed post-install.

Edit: I didn't see the audit log dir in there before. IIRC, that one got changed in the package, and pacman would have warned you about it when you updated. That just needs the permissions change.

Last edited by Scimmia (2022-01-16 16:06:34)

Gede

Member

Registered: 2009-09-03

Posts: 28

Re: [Solved] Filesystem corrupts package install systematically

Those are normal and expected. They are changed post-install.

Oh. That was a twist I was not expecting.

Thank you very much for your help, then. I was starting to pull my hair out.