Fixing "exists in filesystem" errors without reinstall

finnblue8 · 2024-01-18 22:04:39

Hi all:

I had some kind of error doing a full system upgrade on Tuesday and restored a Timeshift backup of my root partition from Monday.

Since then my entire system is full of "exists in filesystem" errors in pacman. I've been deleting these one by one, and that works, but I expect I'll continue to have this problem likely for every package installed on my machine that Timeshift touched. Not sure why my install is having problems with Timeshift either - I've restored these backups before with no issues. In that regard Timeshift actually made the original problem, busted pipewire audio after upgrading to 6.7, worse.

The wiki mentions

 pacman -S --overwrite glob package

as a solution. I don't understand this "glob" variable - what do I put here? Name of the file to be overwritten doesn't work for me, nor does the package name.

Thanks!

Last edited by finnblue8 (2024-01-18 22:07:15)

seth · 2024-01-18 22:49:59

https://en.wikipedia.org/wiki/Glob_(programming)

But not with

Since then my entire system is full of "exists in filesystem" errors in pacman

sudo LC_ALL=C pacman -Qkk 2>&1 | grep -v ', 0 altered files' > /tmp/imlost.txt
cat /tmp/imlost.txt | curl -F 'file=@-' 0x0.st

Most likely the package database got corrupted in which case you want to re-install all packages as --dbonly first (technically only those with broken mtrees) and then run a proper update.

finnblue8 · 2024-01-19 00:40:43

Thanks for your reply.

I did

 pacman -Qnq | pacman -S - --overwrite '*'

which appears to have fixed it by merely reinstalling the system - so not really what I was initially asking about, but it only took a few minutes. My system is up-to-date for now, so we'll see if things revert to having problems tomorrow.

Any idea why Timeshift would have borked things like this? This is a 2-year-old install that has operated pretty much without incident since the GRUB kerfuffle a year or so ago. I haven't needed to use a backup in ages.

I did try the restore from a Linux Mint USB to have a desktop environment, if Mint makes a difference - though I believe I recall using Mint with no problems before...

seth · 2024-01-19 08:59:17

That wasn't a very smart approach:
https://wiki.archlinux.org/title/Pacman … )%22_error

Warning: Generally avoid using the --overwrite switch. See System maintenance#Avoid certain pacman commands.

and you passed the general match to all packages…

We don't even know what happened and we won't since you steamrolled over the place.

Please always remember to mark resolved threads by editing your initial posts subject - so others will know that there's no task left, but maybe a solution to find.
Thanks.

Arch Linux

#1 2024-01-18 22:04:39

Fixing "exists in filesystem" errors without reinstall

#2 2024-01-18 22:49:59

Re: Fixing "exists in filesystem" errors without reinstall

#3 2024-01-19 00:40:43

Re: Fixing "exists in filesystem" errors without reinstall

#4 2024-01-19 08:59:17

Re: Fixing "exists in filesystem" errors without reinstall

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