Arch Linux

Automath

Member

Registered: 2016-05-16

Posts: 115

Problem while updating the system (inconsistent database, file exists)

Hello I'm updating arch-linux after a month of not doing so.

A quick pacman -Syu returned me a bunch of errors; first of all

error: local database is inconsistent: name mismatch on package python-shiboken2
error: local database is inconsistent: version mismatch on package python-shiboken2
resolving dependencies...
error: local database is inconsistent: name mismatch on package python-gitdb
error: local database is inconsistent: version mismatch on package python-gitdb
error: local database is inconsistent: name mismatch on package python-smmap
error: local database is inconsistent: version mismatch on package python-smmap

by second something about a few unknown signatures; so I did

 sudo pacman -S archlinux-keyring

and it dissapeared, but then I had a lot of complains about:

checking for file conflicts...
error: failed to commit transaction (conflicting files)
hwdata: /usr/share/hwdata/pci.ids exists in filesystem (owned by hwids)
hwdata: /usr/share/hwdata/pnp.ids exists in filesystem (owned by hwids)
hwdata: /usr/share/hwdata/usb.ids exists in filesystem (owned by hwids)
git: /usr/bin/git exists in filesystem
git: /usr/bin/git-cvsserver exists in filesystem
git: /usr/bin/git-receive-pack exists in filesystem
git: /usr/bin/git-shell exists in filesystem

(replace all the '...' for a sucession of same error from the same package (probably all the files from it)

opencascade: /etc/profile.d/opencascade.sh exists in filesystem
...
python-shiboken2: /usr/lib/libshiboken2.cpython-310-x86_64-linux-gnu.so exists in filesystem
...
python-fonttools: /usr/bin/fonttools exists in filesystem
python-fonttools: /usr/bin/pyftmerge exists in filesystem
python-fonttools: /usr/bin/pyftsubset exists in filesystem
python-fonttools: /usr/bin/ttx exists in filesystem

...
python-pillow: /usr/include/python3.10/Bcn.h exists in filesystem
...
python-matplotlib: /usr/lib/python3.10/site-packages/__pycache__/pylab.cpython-310.opt-1.pyc exists in filesystem
...
python-pivy: /usr/lib/python3.10/site-packages/Pivy-0.6.6-py3.10.egg-info exists in filesystem
...
libixion: /usr/bin/ixion-formula-tokenizer exists in filesystem
...
libmm-glib: /usr/include/ModemManager/ModemManager-compat.h exists in filesystem
...
libmwaw: /usr/bin/mwaw2csv exists in filesystem
...
libgit2: /usr/include/git2.h exists in filesystem
...
Errors occurred, no packages were upgraded.

I'm not sure what to do, for now i'll see which packages depends on those but seeing matplotlib, pillow, glib and git in middle the situation is not very promising.

Checking over /var/log/pacman:

[2022-02-19T19:30:44-0300] [PACMAN] Running 'pacman -S archlinux-keyring'
[2022-02-19T19:31:18-0300] [ALPM] transaction started
[2022-02-19T19:31:18-0300] [ALPM] upgraded archlinux-keyring (20211028-1 -> 20220125-1)
[2022-02-19T19:31:18-0300] [ALPM-SCRIPTLET] ==> Añadiendo las claves de archlinux.gpg...
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ==> Desactivando las claves revocadas en el depósito...
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET]   -> Se han desactivado 5 claves.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ==> Actualizando la base de datos de claves de confianza...
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 786C63F330D7CB92: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 1EB2638FF56C0C53: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: key 1EB2638FF56C0C53: no user ID for key signature packet of class 10
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: marginals needed: 3  completes needed: 1  trust model: pgp
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: nivel: 0  validez:   1  firmada:   5  confianza: 0-, 0q, 0n, 0m, 0f, 1u
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: nivel: 1  validez:   5  firmada:  94  confianza: 0-, 0q, 0n, 5m, 0f, 0u
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: nivel: 2  validez:  87  firmada:  33  confianza: 87-, 0q, 0n, 0m, 0f, 0u
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: siguiente comprobación de base de datos de confianza el: 2022-05-06
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ==> Actualizando la base de datos de claves de confianza...
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] gpg: siguiente comprobación de base de datos de confianza el: 2022-05-06
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libimagequant.so.0 no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libpyside2.cpython-310-x86_64-linux-gnu.so.5.15 no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libpyside2.cpython-310-x86_64-linux-gnu.so.5.15.2 no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libshiboken2.cpython-310-x86_64-linux-gnu.so.5.15.2 no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libimagequant.so no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libshiboken2.cpython-310-x86_64-linux-gnu.so.5.15 no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libpyside2.cpython-310-x86_64-linux-gnu.so no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] ldconfig: /usr/lib/libshiboken2.cpython-310-x86_64-linux-gnu.so no es un fichero ELF - tiene los bytes mágicos equivocados en el comienzo.
[2022-02-19T19:31:20-0300] [ALPM-SCRIPTLET] 
[2022-02-19T19:31:21-0300] [ALPM] transaction completed
[2022-02-19T19:31:21-0300] [ALPM] running '30-systemd-update.hook'...

Something wwent wrong with updating the keyring?

Last edited by Automath (2022-02-19 23:10:06)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,729

Re: Problem while updating the system (inconsistent database, file exists)

You have serious filesystem issues. Is your drive dying?

You're going to want to use fsck and check with SMART before doing anything else.

Last edited by Scimmia (2022-02-19 23:18:56)

Automath

Member

Registered: 2016-05-16

Posts: 115

Re: Problem while updating the system (inconsistent database, file exists)

You have serious filesystem issues. Is your drive dying?

pls not again!!!! There was a time when archlinux worked for me, but lately everything is going wrong, no clue about the cause. Anyway this isn't a clean install at last, I cloned this installation from a dying drive four months ago but everything seemed ok untill now, this is the first time this hapens and that I have a serious error in this setup. I didn't expected this.

Last edited by Automath (2022-02-19 23:33:37)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,729

Re: Problem while updating the system (inconsistent database, file exists)

Ah, this could be left over issues from the previous drive, then.

For the errors, start with https://wiki.archlinux.org/title/Pacman … )%22_error

If you still see those ldconfig errors, make sure to reinstall those packages. I would probably just reinstall all packages.

Automath

Member

Registered: 2016-05-16

Posts: 115

Re: Problem while updating the system (inconsistent database, file exists)

I would probably just reinstall all packages.

Just in case, how do I reinstall all packages? And anyway how do I reinnstall any package. Sorry for the question as I should know how but I never had the strict need till now.

jasonwryan

Anarchist

From: .nz

Registered: 2009-05-09

Posts: 30,426

Website

Re: Problem while updating the system (inconsistent database, file exists)

Read the wiki. Eg., https://wiki.archlinux.org/title/Pacman … l_packages

---

Arch + dwm   •   Mercurial repos  •   Surfraw

Registered Linux User #482438

Automath

Member

Registered: 2016-05-16

Posts: 115

Re: Problem while updating the system (inconsistent database, file exists)

Read the wiki. Eg., https://wiki.archlinux.org/title/Pacman … l_packages

For sake of simplicy the first link given has a detailed guide also.