this post was submitted on 26 Jan 2024

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[Solved] Had a power outage while updating my fedora system, and now dnf has file conflicts. Is it recoverable? (lemmy.eco.br)

submitted 9 months ago* (last edited 9 months ago) by nossaquesapao@lemmy.eco.br to c/linux@lemmy.ml

25 comments fedilink hide all child comments

The system booted normally after the energy was cut, but if I try to run a dnf update again, I get this error:

Last metadata expiration check: 0:51:09 ago on Fri 26 Jan 2024 05:02:36 PM -03.
Dependencies resolved.

 Problem: The operation would result in removing the following protected packages: systemd, systemd-udev
================================================================================
 Package                         Arch     Version               Repo       Size
================================================================================
Upgrading:
 ImageMagick                     x86_64   1:7.1.1.26-2.fc39     updates    81 k
 ImageMagick-c++                 x86_64   1:7.1.1.26-2.fc39     updates   201 k
 at-spi2-atk                     i686     2.50.1-1.fc39         updates    92 k
 at-spi2-core                    i686     2.50.1-1.fc39         updates   378 k
 atk                             i686     2.50.1-1.fc39         updates    82 k
 bluez-libs                      i686     5.72-1.fc39           updates    88 k
 chkconfig                       x86_64   1.26-1.fc39           updates   176 k
 crun                            x86_64   1.13-1.fc39           updates   218 k
 darktable                       x86_64   4.6.0-1.fc39          updates   7.2 M
 device-mapper-persistent-data   x86_64   1.0.9-1.fc39          updates   1.0 M
 eog                             x86_64   45.2-1.fc39           updates   1.6 M
 epiphany-runtime                x86_64   1:45.2-1.fc39         updates   853 k
 fluidsynth-libs                 x86_64   2.3.4-2.fc39          updates   235 k
 folks                           x86_64   1:0.15.7-1.fc39       updates   588 k
 gnome-maps                      x86_64   45.3-1.fc39           updates   1.0 M
 gtk3                            i686     3.24.41-1.fc39        updates   5.8 M
 gtk3-devel                      x86_64   3.24.41-1.fc39        updates   4.3 M
 gvfs-afc                        x86_64   1.52.2-1.fc39         updates    57 k
 gvfs-afp                        x86_64   1.52.2-1.fc39         updates    67 k
 gvfs-archive                    x86_64   1.52.2-1.fc39         updates    23 k
 gvfs-fuse                       x86_64   1.52.2-1.fc39         updates    29 k
 gvfs-goa                        x86_64   1.52.2-1.fc39         updates    67 k
 gvfs-gphoto2                    x86_64   1.52.2-1.fc39         updates    61 k
 gvfs-mtp                        x86_64   1.52.2-1.fc39         updates    61 k
 iwlegacy-firmware               noarch   20240115-2.fc39       updates   146 k
 iwlwifi-dvm-firmware            noarch   20240115-2.fc39       updates   1.8 M
 iwlwifi-mvm-firmware            noarch   20240115-2.fc39       updates    50 M
 kde-settings                    noarch   39.1-1.fc39           updates    40 k
 krb5-libs                       i686     1.21.2-3.fc39         updates   809 k
 libblockdev-lvm-dbus            x86_64   3.1.0-1.fc39          updates    48 k
 libblockdev-plugins-all         x86_64   3.1.0-1.fc39          updates    10 k
 libdecor                        i686     0.2.2-1.fc39          updates    60 k
 libdrm                          i686     2.4.120-1.fc39        updates   172 k
 libertas-firmware               noarch   20240115-2.fc39       updates   1.3 M
 libmwaw                         x86_64   0.3.22-1.fc39         updates   2.6 M
 libpeas                         x86_64   2.0.1-1.fc39          updates   117 k
 librbd1                         x86_64   2:18.2.1-4.fc39       updates   3.5 M
 libva                           i686     2.20.0-2.fc39         updates   113 k
 libwpg                          x86_64   0.3.4-1.fc39          updates    74 k
 libwps                          x86_64   0.4.14-1.fc39         updates   879 k
 libxmlb                         x86_64   0.3.15-1.fc39         updates   115 k
 lutris                          x86_64   0.5.16-2.fc39         updates   1.9 M
 papirus-icon-theme              noarch   20231201-2.fc39       updates    39 M
 perl-common-sense               x86_64   3.7.5-15.fc39         updates    29 k
 publicsuffix-list-dafsa         noarch   20240107-1.fc39       updates    58 k
 python3-audit                   x86_64   3.1.2-6.fc39          updates    87 k
 python3-beautifulsoup4          noarch   4.12.3-1.fc39         updates   320 k
 python3-blockdev                x86_64   3.1.0-1.fc39          updates    37 k
 python3-fonttools               x86_64   4.43.1-1.fc39         updates   2.9 M
 python3-jinja2                  noarch   3.1.3-1.fc39          updates   507 k
 python3-pyatspi                 noarch   2.46.1-1.fc39         updates   112 k
 python3-pyrate-limiter          noarch   3.2.0-1.fc39          updates    65 k
 qadwaitadecorations-qt6         x86_64   0.1.3-5.fc39          updates    65 k
 qt5-srpm-macros                 noarch   5.15.12-1.fc39        updates   8.4 k
 readline                        i686     8.2-6.fc39            updates   218 k
 sos                             noarch   4.6.1-1.fc39          updates   1.2 M
 syncthing                       x86_64   1.27.2-1.fc39         updates   8.8 M
 systemd-boot-unsigned           x86_64   254.8-2.fc39          updates    98 k
 systemd-libs                    i686     254.8-2.fc39          updates   727 k
 vim-filesystem                  noarch   2:9.1.031-1.fc39      updates    17 k
 wine                            x86_64   9.0-1.fc39            updates    10 k
 wine-alsa                       i686     9.0-1.fc39            updates    86 k
 wine-core                       i686     9.0-1.fc39            updates    88 M
 wine-opencl                     i686     9.0-1.fc39            updates    72 k
 wine-pulseaudio                 i686     9.0-1.fc39            updates    62 k
 wine-twain                      i686     9.0-1.fc39            updates   136 k
 zenity                          x86_64   4.0.1-1.fc39          updates   3.2 M

Transaction Summary
================================================================================
Upgrade  67 Packages

Total size: 233 M
Is this ok [y/N]: y
Downloading Packages:
[SKIPPED] ImageMagick-7.1.1.26-2.fc39.x86_64.rpm: Already downloaded           
[SKIPPED] ImageMagick-c++-7.1.1.26-2.fc39.x86_64.rpm: Already downloaded       
[SKIPPED] at-spi2-atk-2.50.1-1.fc39.i686.rpm: Already downloaded               
[SKIPPED] at-spi2-core-2.50.1-1.fc39.i686.rpm: Already downloaded              
[SKIPPED] atk-2.50.1-1.fc39.i686.rpm: Already downloaded                       
[SKIPPED] bluez-libs-5.72-1.fc39.i686.rpm: Already downloaded                  
[SKIPPED] chkconfig-1.26-1.fc39.x86_64.rpm: Already downloaded                 
[SKIPPED] crun-1.13-1.fc39.x86_64.rpm: Already downloaded                      
[SKIPPED] darktable-4.6.0-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] device-mapper-persistent-data-1.0.9-1.fc39.x86_64.rpm: Already downloaded
[SKIPPED] eog-45.2-1.fc39.x86_64.rpm: Already downloaded                       
[SKIPPED] epiphany-runtime-45.2-1.fc39.x86_64.rpm: Already downloaded          
[SKIPPED] fluidsynth-libs-2.3.4-2.fc39.x86_64.rpm: Already downloaded          
[SKIPPED] folks-0.15.7-1.fc39.x86_64.rpm: Already downloaded                   
[SKIPPED] gnome-maps-45.3-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] gtk3-3.24.41-1.fc39.i686.rpm: Already downloaded                     
[SKIPPED] gtk3-devel-3.24.41-1.fc39.x86_64.rpm: Already downloaded             
[SKIPPED] gvfs-afc-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] gvfs-afp-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] gvfs-archive-1.52.2-1.fc39.x86_64.rpm: Already downloaded            
[SKIPPED] gvfs-fuse-1.52.2-1.fc39.x86_64.rpm: Already downloaded               
[SKIPPED] gvfs-goa-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] gvfs-gphoto2-1.52.2-1.fc39.x86_64.rpm: Already downloaded            
[SKIPPED] gvfs-mtp-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
[SKIPPED] iwlegacy-firmware-20240115-2.fc39.noarch.rpm: Already downloaded     
[SKIPPED] iwlwifi-dvm-firmware-20240115-2.fc39.noarch.rpm: Already downloaded  
[SKIPPED] iwlwifi-mvm-firmware-20240115-2.fc39.noarch.rpm: Already downloaded  
[SKIPPED] kde-settings-39.1-1.fc39.noarch.rpm: Already downloaded              
[SKIPPED] krb5-libs-1.21.2-3.fc39.i686.rpm: Already downloaded                 
[SKIPPED] libblockdev-lvm-dbus-3.1.0-1.fc39.x86_64.rpm: Already downloaded     
[SKIPPED] libblockdev-plugins-all-3.1.0-1.fc39.x86_64.rpm: Already downloaded  
[SKIPPED] libdecor-0.2.2-1.fc39.i686.rpm: Already downloaded                   
[SKIPPED] libdrm-2.4.120-1.fc39.i686.rpm: Already downloaded                   
[SKIPPED] libertas-firmware-20240115-2.fc39.noarch.rpm: Already downloaded     
[SKIPPED] libmwaw-0.3.22-1.fc39.x86_64.rpm: Already downloaded                 
[SKIPPED] libpeas-2.0.1-1.fc39.x86_64.rpm: Already downloaded                  
[SKIPPED] librbd1-18.2.1-4.fc39.x86_64.rpm: Already downloaded                 
[SKIPPED] libva-2.20.0-2.fc39.i686.rpm: Already downloaded                     
[SKIPPED] libwpg-0.3.4-1.fc39.x86_64.rpm: Already downloaded                   
[SKIPPED] libwps-0.4.14-1.fc39.x86_64.rpm: Already downloaded                  
[SKIPPED] libxmlb-0.3.15-1.fc39.x86_64.rpm: Already downloaded                 
[SKIPPED] lutris-0.5.16-2.fc39.x86_64.rpm: Already downloaded                  
[SKIPPED] papirus-icon-theme-20231201-2.fc39.noarch.rpm: Already downloaded    
[SKIPPED] perl-common-sense-3.7.5-15.fc39.x86_64.rpm: Already downloaded       
[SKIPPED] publicsuffix-list-dafsa-20240107-1.fc39.noarch.rpm: Already downloaded
[SKIPPED] python3-audit-3.1.2-6.fc39.x86_64.rpm: Already downloaded            
[SKIPPED] python3-beautifulsoup4-4.12.3-1.fc39.noarch.rpm: Already downloaded  
[SKIPPED] python3-blockdev-3.1.0-1.fc39.x86_64.rpm: Already downloaded         
[SKIPPED] python3-fonttools-4.43.1-1.fc39.x86_64.rpm: Already downloaded       
[SKIPPED] python3-jinja2-3.1.3-1.fc39.noarch.rpm: Already downloaded           
[SKIPPED] python3-pyatspi-2.46.1-1.fc39.noarch.rpm: Already downloaded         
[SKIPPED] python3-pyrate-limiter-3.2.0-1.fc39.noarch.rpm: Already downloaded   
[SKIPPED] qadwaitadecorations-qt6-0.1.3-5.fc39.x86_64.rpm: Already downloaded  
[SKIPPED] qt5-srpm-macros-5.15.12-1.fc39.noarch.rpm: Already downloaded        
[SKIPPED] readline-8.2-6.fc39.i686.rpm: Already downloaded                     
[SKIPPED] sos-4.6.1-1.fc39.noarch.rpm: Already downloaded                      
[SKIPPED] syncthing-1.27.2-1.fc39.x86_64.rpm: Already downloaded               
[SKIPPED] systemd-boot-unsigned-254.8-2.fc39.x86_64.rpm: Already downloaded    
[SKIPPED] systemd-libs-254.8-2.fc39.i686.rpm: Already downloaded               
[SKIPPED] vim-filesystem-9.1.031-1.fc39.noarch.rpm: Already downloaded         
[SKIPPED] wine-9.0-1.fc39.x86_64.rpm: Already downloaded                       
[SKIPPED] wine-alsa-9.0-1.fc39.i686.rpm: Already downloaded                    
[SKIPPED] wine-core-9.0-1.fc39.i686.rpm: Already downloaded                    
[SKIPPED] wine-opencl-9.0-1.fc39.i686.rpm: Already downloaded                  
[SKIPPED] wine-pulseaudio-9.0-1.fc39.i686.rpm: Already downloaded              
[SKIPPED] wine-twain-9.0-1.fc39.i686.rpm: Already downloaded                   
[SKIPPED] zenity-4.0.1-1.fc39.x86_64.rpm: Already downloaded                   
Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
  file /usr/share/doc/at-spi2-core/NEWS from install of at-spi2-core-2.50.1-1.fc39.i686 conflicts with file from package at-spi2-core-2.50.0-1.fc39.x86_64
  file /usr/share/doc/gtk3/NEWS from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/gtk-3.0/emoji/de.gresource from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/gtk-3.0/emoji/es.gresource from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/gtk-3.0/emoji/fr.gresource from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/gtk-3.0/emoji/zh.gresource from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/locale/he/LC_MESSAGES/gtk30.mo from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/man/man1/broadwayd.1.gz from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/man/man1/gtk-launch.1.gz from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/man/man1/gtk-query-immodules-3.0.1.gz from install of gtk3-3.24.41-1.fc39.i686 conflicts with file from package gtk3-3.24.39-1.fc39.x86_64
  file /usr/share/doc/wine-core/AUTHORS from install of wine-core-9.0-1.fc39.i686 conflicts with file from package wine-core-8.19-1.fc39.x86_64
  file /usr/share/doc/wine-core/LICENSE from install of wine-core-9.0-1.fc39.i686 conflicts with file from package wine-core-8.19-1.fc39.x86_64
  file /usr/share/doc/wine-core/VERSION from install of wine-core-9.0-1.fc39.i686 conflicts with file from package wine-core-8.19-1.fc39.x86_64
  file /usr/share/man/man5/k5identity.5.gz from install of krb5-libs-1.21.2-3.fc39.i686 conflicts with file from package krb5-libs-1.21.2-2.fc39.x86_64
  file /usr/share/man/man5/k5login.5.gz from install of krb5-libs-1.21.2-3.fc39.i686 conflicts with file from package krb5-libs-1.21.2-2.fc39.x86_64
  file /usr/share/man/man5/krb5.conf.5.gz from install of krb5-libs-1.21.2-3.fc39.i686 conflicts with file from package krb5-libs-1.21.2-2.fc39.x86_64

The error mentions using "dnf clean packages", but it only downloads the packages again, and the same error happens. I tried searching for a solution, and found people recommending running "dnf upgrade --allowerasing --best " and "dnf distro-sync", but both these commands result in an error saying that the operation would lead to systemd and systemd-udev being removed.

Did someone experience similar issues? How did you solve it?

EDIT: I ran "dnf reinstall" on the conflicting packages, and it seemed to work for most of them, except for at-spi2-core. However, I noticed that the conflict was between the i686 and the x86_64 package, so I removed wine along with all i686 packages and tried again. It worked, and I managed to complete the upgrade, but I would still get the following error when running "dnf update":

Last metadata expiration check: 1:20:21 ago on Fri 26 Jan 2024 05:02:36 PM -03.
Dependencies resolved.

 Problem: The operation would result in removing the following protected packages: systemd, systemd-udev
Nothing to do.
Complete!

So I did a dnf reinstall systemd systemd-udev and it finally solved the issue.

Thanks for the interest in helping. I will leave the post here in case someone else has a similar problem and google for it.

top 25 comments

sorted by: hot top controversial new old

[–] SnotFlickerman@lemmy.blahaj.zone 17 points 9 months ago (4 children)

This is honestly why anyone and everyone should invest in at least a small UPS that can keep your PC powered for at least five minutes so in this kind of scenario you can cancel the update, shut down safely, and resume when the power is back.

[–] iopq@lemmy.world 20 points 9 months ago (1 children)

Or use a system that has rollbacks so you can use the last known good configuration

[–] russjr08@bitforged.space 9 points 9 months ago (1 children)

Btrfs snapshots + Timeshift that is configured to run pre-update is great for this, though I cannot remember if Fedora's layout is compatible with Timeshift's expected configuration.

OP, If you really want to go 100% with this, something like NixOS (which is definitely an extreme investment) or an Atomic distro like Fedora Silverblue works very well for this.

[–] Lichtblitz@discuss.tchncs.de 2 points 9 months ago* (last edited 9 months ago)

As you mentioned, with Fedora the best alternatives are immutable spins. Updating means downloading a new base image, applying overlays and additional installations to it and on the next reboot you start from that image. You can configure it to keep as many previous versions as you need and boot into those directly on startup. Since you never change your current image once it's built, you can't break a known good system. You can only ever break your next version and in that case, just boot the previous.

I've created an Ansible playbook that configures a vanilla Kinoite the way I want it. No need to back up the system if I can recreate it with less than a megabyte of text files. Secrets are in my password vault, personal files are in my personal cloud and get synced to and from the laptop continuously. I would never go back to backing up system files as opposed to recreating it with a playbook. That seems so wasteful in hindsight.

[–] rizoid@lemmy.dbzer0.com 6 points 9 months ago (1 children)

This is why my main personal machine will always be a laptop.

[–] SnotFlickerman@lemmy.blahaj.zone 5 points 9 months ago

I have far too many networking appliances for that, myself.

[–] Infiltrated_ad8271@kbin.social 5 points 9 months ago

Ideally yes, but using btrfs with something like timeshift is enough.

[–] LostXOR@kbin.social 3 points 9 months ago (1 children)

Any recommendations for a fairly cheap one? It would definitely come in handy.

[–] SnotFlickerman@lemmy.blahaj.zone 2 points 9 months ago* (last edited 9 months ago)

Well for one, are we in the same country? US here. I'm not as savvy on pricings in the EU or anywhere else for that matter.

For two, it's helpful to assume what you need is based on your PCs max wattage input imho. That way, if it can run your machine drawing max power (wattage) for 5 minutes, it can run it for longer when its drawing less power than that.

[–] bushvin@lemmy.world 6 points 9 months ago

dnf upgrade And package-cleanup --cleandupes Should have fixed it.

[–] prettybunnys@sh.itjust.works 3 points 9 months ago (1 children)

First things first, run the command you want to run and provide us the error output.

[–] nossaquesapao@lemmy.eco.br 5 points 9 months ago (1 children)

I was running dnf update when the system was shut down, and I rebooted when the power was back. The system apparently booted normally, and I tried to complete the upgrade process, to avoid issued. Now, the "dnf update" command shows the error message I posted.

In the original post, the error was in portuguese. Now I changed system language to english and posted the entire output of dnf update in the original post, to make it more readable for the community.

[–] prettybunnys@sh.itjust.works 2 points 9 months ago* (last edited 9 months ago) (2 children)

I’m not seeing your error output but I do see your paraphrasing of the error output.

Idk if it’s my app not showing it or what.

It was the Memmy app everyone, shame

[–] SnotFlickerman@lemmy.blahaj.zone 3 points 9 months ago* (last edited 9 months ago) (1 children)

Error: Problem: cannot install both at-spi2-core-2.50.1-1.fc39.x86_64 from updates and at-spi2-core-2.50.0-1.fc39.x86_64 from fedora

conflicting requests (try to add '--allowerasing' to command line to replace conflicting packages or '--skip-broken' to skip uninstallable packages)

Not OP, but this looks like the error message.

[–] prettybunnys@sh.itjust.works 1 points 9 months ago* (last edited 9 months ago) (2 children)

Are you using markdown or something?

My app is only showing “Not OP, but this looks like the error message” and nothing else.

we’re out here troubleshooting all kinds of shit

[–] SnotFlickerman@lemmy.blahaj.zone 3 points 9 months ago* (last edited 9 months ago) (1 children)

I am, I will remove the codeblock markdown.

Edit: removed, let me know if you can see it now.

[–] prettybunnys@sh.itjust.works 4 points 9 months ago

Yes, and that is the nail in the coffin of the Memmy app for me.

Thanks!

[–] BigFatNips@sh.itjust.works 1 points 9 months ago (1 children)

Shows up fine on voyager (Android)

[–] prettybunnys@sh.itjust.works 2 points 9 months ago

Memmy App on iOS and it doesn’t seem to show code blocks. Lame

[–] nossaquesapao@lemmy.eco.br 0 points 9 months ago (1 children)

That's strange, but anyway, I managed to solve the problem and edited the post with the solution. Thank you for the support.

[–] PseudoSpock@lemmy.dbzer0.com 2 points 9 months ago (1 children)

I suggest a filesystem that supports taking snapshots in the future. It's a lifesaver for moments like these.

[–] nossaquesapao@lemmy.eco.br 2 points 9 months ago

I'm using btrfs, but I still need to read more about how it works. I will try to use this experience as a motivator, thank you.

[–] RiderExMachina@lemmy.ml 1 points 9 months ago (1 children)

Are you sure its removing those packages and not updating them?

[–] nossaquesapao@lemmy.eco.br 2 points 9 months ago

yes, the last 2 mentioned commands throw the error below and won't continue the operation:

Error: 
 Problem: The operation would result in removing the following protected packages: systemd, systemd-udev

[–] mvirts@lemmy.world 1 points 9 months ago

Yes